**************************************************************************** File name: 7f36.pdb no. of DNA/RNA chains: 4 [E=73,F=76,G=76,H=72] no. of nucleotides: 297 no. of atoms: 11302 no. of waters: 0 no. of metals: 41 [Ca=41] **************************************************************************** List of 137 base pairs nt1 nt2 bp name Saenger LW DSSR 1 F.G1 F.C72 G-C WC 19-XIX cWW cW-W 2 F.C2 F.G71 C-G WC 19-XIX cWW cW-W 3 F.G3 F.C70 G-C WC 19-XIX cWW cW-W 4 F.G3 G.U16 G-U -- -- cSS cm-m 5 F.G4 F.C69 G-C WC 19-XIX cWW cW-W 6 F.G5 F.C68 G-C WC 19-XIX cWW cW-W 7 F.A6 F.U67 A-U WC 20-XX cWW cW-W 8 F.A7 F.U66 A-U WC 20-XX cWW cW-W 9 F.U8 F.A14 U-A rHoogsteen 24-XXIV tWH tW-M 10 F.A9 F.A23 A+A -- 02-II tHH tM+M 11 F.G10 F.C25 G-C WC 19-XIX cWW cW-W 12 F.G10 F.G45 G+G -- -- cHS cM+m 13 F.C11 F.G24 C-G WC 19-XIX cWW cW-W 14 F.U12 F.A23 U-A WC 20-XX cWW cW-W 15 F.C13 F.G22 C-G WC 19-XIX cWW cW-W 16 F.G15 F.C48 G+C rWC 22-XXII tWW tW+W 17 F.G18 F.U55 G+U -- -- tWS tW+m 18 F.G19 F.C56 G-C WC 19-XIX cWW cW-W 19 F.G22 F.G46 G-G -- 07-VII tHW tM-W 20 F.A26 F.G44 A-G Imino 08-VIII cWW cW-W 21 F.C27 F.G43 C-G WC 19-XIX cWW cW-W 22 F.G28 F.C42 G-C WC 19-XIX cWW cW-W 23 F.A29 F.U41 A-U WC 20-XX cWW cW-W 24 F.C30 F.G40 C-G WC 19-XIX cWW cW-W 25 F.C31 F.G39 C-G WC 19-XIX cWW cW-W 26 F.U32 F.A38 U-A WC 20-XX cWW cW-W 27 F.U33 F.C35 U-C -- -- cHH cM-M 28 F.G49 F.U65 G-U Wobble 28-XXVIII cWW cW-W 29 F.C50 F.G64 C-G WC 19-XIX cWW cW-W 30 F.G51 F.C63 G-C WC 19-XIX cWW cW-W 31 F.A52 F.U62 A-U WC 20-XX cWW cW-W 32 F.G53 F.C61 G-C WC 19-XIX cWW cW-W 33 F.U54 F.A58 U-A rHoogsteen 24-XXIV tWH tW-M 34 F.C70 G.U16 C+U -- -- tSW tm+W 35 F.G71 G.U17 G-U -- -- cSW cm-W 36 G.G1 G.C72 G-C WC 19-XIX cWW cW-W 37 G.C2 G.G71 C-G WC 19-XIX cWW cW-W 38 G.G3 G.C70 G-C WC 19-XIX cWW cW-W 39 G.G4 G.C69 G-C WC 19-XIX cWW cW-W 40 G.G5 G.C68 G-C WC 19-XIX cWW cW-W 41 G.A6 G.U67 A-U WC 20-XX cWW cW-W 42 G.A7 G.U66 A-U WC 20-XX cWW cW-W 43 G.U8 G.A14 U-A rHoogsteen 24-XXIV tWH tW-M 44 G.U8 G.A21 U+A -- -- tSW tm+W 45 G.A9 G.A23 A+A -- 02-II tHH tM+M 46 G.G10 G.C25 G-C WC 19-XIX cWW cW-W 47 G.G10 G.G45 G+G -- -- cHS cM+m 48 G.C11 G.G24 C-G WC 19-XIX cWW cW-W 49 G.U12 G.A23 U-A WC 20-XX cWW cW-W 50 G.C13 G.G22 C-G WC 19-XIX cWW cW-W 51 G.A14 G.A21 A-A -- -- cWS cW-m 52 G.G15 G.C48 G+C rWC 22-XXII tWW tW+W 53 G.G18 G.U55 G+U -- -- tWS tW+m 54 G.G19 G.C56 G-C WC 19-XIX cWW cW-W 55 G.G22 G.G46 G-G -- 07-VII tHW tM-W 56 G.A26 G.G44 A-G Imino 08-VIII cWW cW-W 57 G.C27 G.G43 C-G WC 19-XIX cWW cW-W 58 G.G28 G.C42 G-C WC 19-XIX cWW cW-W 59 G.A29 G.U41 A-U WC 20-XX cWW cW-W 60 G.C30 G.G40 C-G WC 19-XIX cWW cW-W 61 G.C31 G.G39 C-G WC 19-XIX cWW cW-W 62 G.U32 G.A38 U-A -- -- cWW cW-W 63 G.G49 G.U65 G-U Wobble 28-XXVIII cWW cW-W 64 G.C50 G.G64 C-G WC 19-XIX cWW cW-W 65 G.G51 G.C63 G-C WC 19-XIX cWW cW-W 66 G.A52 G.U62 A-U WC 20-XX cWW cW-W 67 G.G53 G.C61 G-C WC 19-XIX cWW cW-W 68 G.U54 G.A58 U-A rHoogsteen 24-XXIV tWH tW-M 69 H.G1 H.C72 G-C WC 19-XIX cWW cW-W 70 H.C2 H.G71 C-G WC 19-XIX cWW cW-W 71 H.G3 H.C70 G-C WC 19-XIX cWW cW-W 72 H.G4 H.C69 G-C WC 19-XIX cWW cW-W 73 H.G5 H.C68 G-C WC 19-XIX cWW cW-W 74 H.A6 H.U67 A-U WC 20-XX cWW cW-W 75 H.A7 H.U66 A-U WC 20-XX cWW cW-W 76 H.U8 H.A14 U-A rHoogsteen 24-XXIV tWH tW-M 77 H.U8 H.A21 U+A -- -- tSW tm+W 78 H.A9 H.A23 A+A -- 02-II tHH tM+M 79 H.G10 H.C25 G-C WC 19-XIX cWW cW-W 80 H.G10 H.G45 G+G -- 06-VI cHW cM+W 81 H.C11 H.G24 C-G WC 19-XIX cWW cW-W 82 H.U12 H.A23 U-A WC 20-XX cWW cW-W 83 H.C13 H.G22 C-G WC 19-XIX cWW cW-W 84 H.A14 H.A21 A-A -- -- cWS cW-m 85 H.G15 H.C48 G+C rWC 22-XXII tWW tW+W 86 H.G18 H.U55 G+U -- -- tWS tW+m 87 H.G19 H.C56 G-C WC 19-XIX cWW cW-W 88 H.G22 H.G46 G-G ~rHoogsteen 07-VII tHW tM-W 89 H.A26 H.G44 A-G Imino 08-VIII cWW cW-W 90 H.C27 H.G43 C-G WC 19-XIX cWW cW-W 91 H.G28 H.C42 G-C WC 19-XIX cWW cW-W 92 H.A29 H.U41 A-U WC 20-XX cWW cW-W 93 H.C30 H.G40 C-G WC 19-XIX cWW cW-W 94 H.C31 H.G39 C-G WC 19-XIX cWW cW-W 95 H.U32 H.A38 U-A -- -- cW. cW-. 96 H.U33 H.A37 U-A -- -- cWW cW-W 97 H.G49 H.U65 G-U Wobble 28-XXVIII cWW cW-W 98 H.C50 H.G64 C-G WC 19-XIX cWW cW-W 99 H.G51 H.C63 G-C WC 19-XIX cWW cW-W 100 H.A52 H.U62 A-U WC 20-XX cWW cW-W 101 H.G53 H.C61 G-C WC 19-XIX cWW cW-W 102 H.U54 H.A58 U-A rHoogsteen 24-XXIV tWH tW-M 103 E.G1 E.C72 G-C WC 19-XIX cWW cW-W 104 E.C2 E.G71 C-G WC 19-XIX cWW cW-W 105 E.G3 E.C70 G-C WC 19-XIX cWW cW-W 106 E.G4 E.C69 G-C WC 19-XIX cWW cW-W 107 E.G5 E.C68 G-C WC 19-XIX cWW cW-W 108 E.A6 E.U67 A-U WC 20-XX cWW cW-W 109 E.A7 E.U66 A-U WC 20-XX cWW cW-W 110 E.U8 E.A14 U-A rHoogsteen 24-XXIV tWH tW-M 111 E.U8 E.A21 U+A -- -- tSW tm+W 112 E.A9 E.A23 A+A -- 02-II tHH tM+M 113 E.G10 E.C25 G-C WC 19-XIX cWW cW-W 114 E.G10 E.G45 G+G -- -- cHS cM+m 115 E.C11 E.G24 C-G WC 19-XIX cWW cW-W 116 E.U12 E.A23 U-A WC 20-XX cWW cW-W 117 E.C13 E.G22 C-G WC 19-XIX cWW cW-W 118 E.A14 E.A21 A-A -- -- cW. cW-. 119 E.G15 E.C48 G+C rWC 22-XXII tWW tW+W 120 E.G18 E.U55 G+U -- -- tWS tW+m 121 E.G19 E.C56 G-C WC 19-XIX cWW cW-W 122 E.G22 E.G46 G-G -- 07-VII tHW tM-W 123 E.A26 E.G44 A-G Imino 08-VIII cWW cW-W 124 E.C27 E.G43 C-G WC 19-XIX cWW cW-W 125 E.G28 E.C42 G-C WC 19-XIX cWW cW-W 126 E.A29 E.U41 A-U WC 20-XX cWW cW-W 127 E.C30 E.G40 C-G WC 19-XIX cWW cW-W 128 E.C31 E.G39 C-G WC 19-XIX cWW cW-W 129 E.U32 E.A37 U-A ~Wobble -- cWW cW-W 130 E.U32 E.A38 U-A -- -- .WW .W-W 131 E.A37 E.A38 A+A Platform -- cSH cm+M 132 E.G49 E.U65 G-U Wobble 28-XXVIII cWW cW-W 133 E.C50 E.G64 C-G WC 19-XIX cWW cW-W 134 E.G51 E.C63 G-C WC 19-XIX cWW cW-W 135 E.A52 E.U62 A-U WC 20-XX cWW cW-W 136 E.G53 E.C61 G-C WC 19-XIX cWW cW-W 137 E.U54 E.A58 U-A rHoogsteen 24-XXIV tWH tW-M **************************************************************************** List of 18 multiplets 1 nts=3 CGU F.C2,F.G71,G.U17 2 nts=3 GCU F.G3,F.C70,G.U16 3 nts=3 AUA F.A9,F.U12,F.A23 4 nts=3 GCG F.G10,F.C25,F.G45 5 nts=3 CGG F.C13,F.G22,F.G46 6 nts=3 UAA G.U8,G.A14,G.A21 7 nts=3 AUA G.A9,G.U12,G.A23 8 nts=3 GCG G.G10,G.C25,G.G45 9 nts=3 CGG G.C13,G.G22,G.G46 10 nts=3 UAA H.U8,H.A14,H.A21 11 nts=3 AUA H.A9,H.U12,H.A23 12 nts=3 GCG H.G10,H.C25,H.G45 13 nts=3 CGG H.C13,H.G22,H.G46 14 nts=3 UAA E.U8,E.A14,E.A21 15 nts=3 AUA E.A9,E.U12,E.A23 16 nts=3 GCG E.G10,E.C25,E.G45 17 nts=3 CGG E.C13,E.G22,E.G46 18 nts=3 UAA E.U32,E.A37,E.A38 **************************************************************************** List of 8 helices Note: A helix is defined by base-stacking interactions, regardless of pair type and backbone connectivity, and may contain more than one stem. helix#number[stems-contained] bps=number-of-base-pairs in the helix bp-type: '|' for a canonical WC/wobble pair, '.' otherwise helix-form: classification of a dinucleotide step comprising the bp above the given designation and the bp that follows it. Types include 'A', 'B' or 'Z' for the common A-, B- and Z-form helices, '.' for an unclassified step, and 'x' for a step without a continuous backbone. -------------------------------------------------------------------- helix#1[2] bps=15 strand-1 5'-GCGGGAAGCGAGUUC-3' bp-type ||||||||||||..| strand-2 3'-CGCCCUUUGCUCAGG-5' helix-form AAAAAAxAAA.xx. 1 F.G1 F.C72 G-C WC 19-XIX cWW cW-W 2 F.C2 F.G71 C-G WC 19-XIX cWW cW-W 3 F.G3 F.C70 G-C WC 19-XIX cWW cW-W 4 F.G4 F.C69 G-C WC 19-XIX cWW cW-W 5 F.G5 F.C68 G-C WC 19-XIX cWW cW-W 6 F.A6 F.U67 A-U WC 20-XX cWW cW-W 7 F.A7 F.U66 A-U WC 20-XX cWW cW-W 8 F.G49 F.U65 G-U Wobble 28-XXVIII cWW cW-W 9 F.C50 F.G64 C-G WC 19-XIX cWW cW-W 10 F.G51 F.C63 G-C WC 19-XIX cWW cW-W 11 F.A52 F.U62 A-U WC 20-XX cWW cW-W 12 F.G53 F.C61 G-C WC 19-XIX cWW cW-W 13 F.U54 F.A58 U-A rHoogsteen 24-XXIV tWH tW-M 14 F.U55 F.G18 U+G -- -- tSW tm+W 15 F.C56 F.G19 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[2] bps=13 strand-1 5'-AGGUCGGGCUCAG-3' bp-type ||||||.||||.. strand-2 3'-UCCAGCACGAGUC-5' helix-form AAAA..xAA.xx 1 F.A38 F.U32 A-U WC 20-XX cWW cW-W 2 F.G39 F.C31 G-C WC 19-XIX cWW cW-W 3 F.G40 F.C30 G-C WC 19-XIX cWW cW-W 4 F.U41 F.A29 U-A WC 20-XX cWW cW-W 5 F.C42 F.G28 C-G WC 19-XIX cWW cW-W 6 F.G43 F.C27 G-C WC 19-XIX cWW cW-W 7 F.G44 F.A26 G-A Imino 08-VIII cWW cW-W 8 F.G10 F.C25 G-C WC 19-XIX cWW cW-W 9 F.C11 F.G24 C-G WC 19-XIX cWW cW-W 10 F.U12 F.A23 U-A WC 20-XX cWW cW-W 11 F.C13 F.G22 C-G WC 19-XIX cWW cW-W 12 F.A14 F.U8 A-U rHoogsteen 24-XXIV tHW tM-W 13 F.G15 F.C48 G+C rWC 22-XXII tWW tW+W -------------------------------------------------------------------------- helix#3[2] bps=15 strand-1 5'-GCGGGAAGCGAGUUC-3' bp-type ||||||||||||..| strand-2 3'-CGCCCUUUGCUCAGG-5' helix-form AAAAAAx.AAAxx. 1 G.G1 G.C72 G-C WC 19-XIX cWW cW-W 2 G.C2 G.G71 C-G WC 19-XIX cWW cW-W 3 G.G3 G.C70 G-C WC 19-XIX cWW cW-W 4 G.G4 G.C69 G-C WC 19-XIX cWW cW-W 5 G.G5 G.C68 G-C WC 19-XIX cWW cW-W 6 G.A6 G.U67 A-U WC 20-XX cWW cW-W 7 G.A7 G.U66 A-U WC 20-XX cWW cW-W 8 G.G49 G.U65 G-U Wobble 28-XXVIII cWW cW-W 9 G.C50 G.G64 C-G WC 19-XIX cWW cW-W 10 G.G51 G.C63 G-C WC 19-XIX cWW cW-W 11 G.A52 G.U62 A-U WC 20-XX cWW cW-W 12 G.G53 G.C61 G-C WC 19-XIX cWW cW-W 13 G.U54 G.A58 U-A rHoogsteen 24-XXIV tWH tW-M 14 G.U55 G.G18 U+G -- -- tSW tm+W 15 G.C56 G.G19 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#4[2] bps=13 strand-1 5'-AGGUCGGGCUCAG-3' bp-type .|||||.||||.. strand-2 3'-UCCAGCACGAGUC-5' helix-form .AAAA.xAA.xx 1 G.A38 G.U32 A-U -- -- cWW cW-W 2 G.G39 G.C31 G-C WC 19-XIX cWW cW-W 3 G.G40 G.C30 G-C WC 19-XIX cWW cW-W 4 G.U41 G.A29 U-A WC 20-XX cWW cW-W 5 G.C42 G.G28 C-G WC 19-XIX cWW cW-W 6 G.G43 G.C27 G-C WC 19-XIX cWW cW-W 7 G.G44 G.A26 G-A Imino 08-VIII cWW cW-W 8 G.G10 G.C25 G-C WC 19-XIX cWW cW-W 9 G.C11 G.G24 C-G WC 19-XIX cWW cW-W 10 G.U12 G.A23 U-A WC 20-XX cWW cW-W 11 G.C13 G.G22 C-G WC 19-XIX cWW cW-W 12 G.A14 G.U8 A-U rHoogsteen 24-XXIV tHW tM-W 13 G.G15 G.C48 G+C rWC 22-XXII tWW tW+W -------------------------------------------------------------------------- helix#5[2] bps=15 strand-1 5'-GCGGGAAGCGAGUUC-3' bp-type ||||||||||||..| strand-2 3'-CGCCCUUUGCUCAGG-5' helix-form AAAAAAx.AAAxx. 1 H.G1 H.C72 G-C WC 19-XIX cWW cW-W 2 H.C2 H.G71 C-G WC 19-XIX cWW cW-W 3 H.G3 H.C70 G-C WC 19-XIX cWW cW-W 4 H.G4 H.C69 G-C WC 19-XIX cWW cW-W 5 H.G5 H.C68 G-C WC 19-XIX cWW cW-W 6 H.A6 H.U67 A-U WC 20-XX cWW cW-W 7 H.A7 H.U66 A-U WC 20-XX cWW cW-W 8 H.G49 H.U65 G-U Wobble 28-XXVIII cWW cW-W 9 H.C50 H.G64 C-G WC 19-XIX cWW cW-W 10 H.G51 H.C63 G-C WC 19-XIX cWW cW-W 11 H.A52 H.U62 A-U WC 20-XX cWW cW-W 12 H.G53 H.C61 G-C WC 19-XIX cWW cW-W 13 H.U54 H.A58 U-A rHoogsteen 24-XXIV tWH tW-M 14 H.U55 H.G18 U+G -- -- tSW tm+W 15 H.C56 H.G19 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#6[2] bps=14 strand-1 5'-AAGGUCGGGCUCAG-3' bp-type ..|||||.||||.. strand-2 3'-UUCCAGCACGAGUC-5' helix-form ..AAAA.xAA.xx 1 H.A37 H.U33 A-U -- -- cWW cW-W 2 H.A38 H.U32 A-U -- -- c.W c.-W 3 H.G39 H.C31 G-C WC 19-XIX cWW cW-W 4 H.G40 H.C30 G-C WC 19-XIX cWW cW-W 5 H.U41 H.A29 U-A WC 20-XX cWW cW-W 6 H.C42 H.G28 C-G WC 19-XIX cWW cW-W 7 H.G43 H.C27 G-C WC 19-XIX cWW cW-W 8 H.G44 H.A26 G-A Imino 08-VIII cWW cW-W 9 H.G10 H.C25 G-C WC 19-XIX cWW cW-W 10 H.C11 H.G24 C-G WC 19-XIX cWW cW-W 11 H.U12 H.A23 U-A WC 20-XX cWW cW-W 12 H.C13 H.G22 C-G WC 19-XIX cWW cW-W 13 H.A14 H.U8 A-U rHoogsteen 24-XXIV tHW tM-W 14 H.G15 H.C48 G+C rWC 22-XXII tWW tW+W -------------------------------------------------------------------------- helix#7[2] bps=15 strand-1 5'-GCGGGAAGCGAGUUC-3' bp-type ||||||||||||..| strand-2 3'-CGCCCUUUGCUCAGG-5' helix-form AAAAAAx.AAAxx. 1 E.G1 E.C72 G-C WC 19-XIX cWW cW-W 2 E.C2 E.G71 C-G WC 19-XIX cWW cW-W 3 E.G3 E.C70 G-C WC 19-XIX cWW cW-W 4 E.G4 E.C69 G-C WC 19-XIX cWW cW-W 5 E.G5 E.C68 G-C WC 19-XIX cWW cW-W 6 E.A6 E.U67 A-U WC 20-XX cWW cW-W 7 E.A7 E.U66 A-U WC 20-XX cWW cW-W 8 E.G49 E.U65 G-U Wobble 28-XXVIII cWW cW-W 9 E.C50 E.G64 C-G WC 19-XIX cWW cW-W 10 E.G51 E.C63 G-C WC 19-XIX cWW cW-W 11 E.A52 E.U62 A-U WC 20-XX cWW cW-W 12 E.G53 E.C61 G-C WC 19-XIX cWW cW-W 13 E.U54 E.A58 U-A rHoogsteen 24-XXIV tWH tW-M 14 E.U55 E.G18 U+G -- -- tSW tm+W 15 E.C56 E.G19 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#8[2] bps=13 strand-1 5'-AGGUCGGGCUCAG-3' bp-type ||||||.||||.. strand-2 3'-UCCAGCACGAGUC-5' helix-form xAAAAAxAA.xx 1 E.A37 E.U32 A-U WC 20-XX cWW cW-W 2 E.G39 E.C31 G-C WC 19-XIX cWW cW-W 3 E.G40 E.C30 G-C WC 19-XIX cWW cW-W 4 E.U41 E.A29 U-A WC 20-XX cWW cW-W 5 E.C42 E.G28 C-G WC 19-XIX cWW cW-W 6 E.G43 E.C27 G-C WC 19-XIX cWW cW-W 7 E.G44 E.A26 G-A Imino 08-VIII cWW cW-W 8 E.G10 E.C25 G-C WC 19-XIX cWW cW-W 9 E.C11 E.G24 C-G WC 19-XIX cWW cW-W 10 E.U12 E.A23 U-A WC 20-XX cWW cW-W 11 E.C13 E.G22 C-G WC 19-XIX cWW cW-W 12 E.A14 E.U8 A-U rHoogsteen 24-XXIV tHW tM-W 13 E.G15 E.C48 G+C rWC 22-XXII tWW tW+W **************************************************************************** List of 16 stems Note: A stem is defined as a helix consisting strictly of canonical WC/wobble pairs with a continuous backbone. stem#number[#helix-number containing this stem] Other terms are defined as in the above Helix section. -------------------------------------------------------------------- stem#1[#1] bps=7 strand-1 5'-GCGGGAA-3' bp-type ||||||| strand-2 3'-CGCCCUU-5' helix-form AAAAAA 1 F.G1 F.C72 G-C WC 19-XIX cWW cW-W 2 F.C2 F.G71 C-G WC 19-XIX cWW cW-W 3 F.G3 F.C70 G-C WC 19-XIX cWW cW-W 4 F.G4 F.C69 G-C WC 19-XIX cWW cW-W 5 F.G5 F.C68 G-C WC 19-XIX cWW cW-W 6 F.A6 F.U67 A-U WC 20-XX cWW cW-W 7 F.A7 F.U66 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=4 strand-1 5'-GCUC-3' bp-type |||| strand-2 3'-CGAG-5' helix-form AA. 1 F.G10 F.C25 G-C WC 19-XIX cWW cW-W 2 F.C11 F.G24 C-G WC 19-XIX cWW cW-W 3 F.U12 F.A23 U-A WC 20-XX cWW cW-W 4 F.C13 F.G22 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#3[#2] bps=6 strand-1 5'-CGACCU-3' bp-type |||||| strand-2 3'-GCUGGA-5' helix-form .AAAA 1 F.C27 F.G43 C-G WC 19-XIX cWW cW-W 2 F.G28 F.C42 G-C WC 19-XIX cWW cW-W 3 F.A29 F.U41 A-U WC 20-XX cWW cW-W 4 F.C30 F.G40 C-G WC 19-XIX cWW cW-W 5 F.C31 F.G39 C-G WC 19-XIX cWW cW-W 6 F.U32 F.A38 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#4[#1] bps=5 strand-1 5'-GCGAG-3' bp-type ||||| strand-2 3'-UGCUC-5' helix-form AAA. 1 F.G49 F.U65 G-U Wobble 28-XXVIII cWW cW-W 2 F.C50 F.G64 C-G WC 19-XIX cWW cW-W 3 F.G51 F.C63 G-C WC 19-XIX cWW cW-W 4 F.A52 F.U62 A-U WC 20-XX cWW cW-W 5 F.G53 F.C61 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#5[#3] bps=7 strand-1 5'-GCGGGAA-3' bp-type ||||||| strand-2 3'-CGCCCUU-5' helix-form AAAAAA 1 G.G1 G.C72 G-C WC 19-XIX cWW cW-W 2 G.C2 G.G71 C-G WC 19-XIX cWW cW-W 3 G.G3 G.C70 G-C WC 19-XIX cWW cW-W 4 G.G4 G.C69 G-C WC 19-XIX cWW cW-W 5 G.G5 G.C68 G-C WC 19-XIX cWW cW-W 6 G.A6 G.U67 A-U WC 20-XX cWW cW-W 7 G.A7 G.U66 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#6[#4] bps=4 strand-1 5'-GCUC-3' bp-type |||| strand-2 3'-CGAG-5' helix-form AA. 1 G.G10 G.C25 G-C WC 19-XIX cWW cW-W 2 G.C11 G.G24 C-G WC 19-XIX cWW cW-W 3 G.U12 G.A23 U-A WC 20-XX cWW cW-W 4 G.C13 G.G22 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#7[#4] bps=5 strand-1 5'-CGACC-3' bp-type ||||| strand-2 3'-GCUGG-5' helix-form AAAA 1 G.C27 G.G43 C-G WC 19-XIX cWW cW-W 2 G.G28 G.C42 G-C WC 19-XIX cWW cW-W 3 G.A29 G.U41 A-U WC 20-XX cWW cW-W 4 G.C30 G.G40 C-G WC 19-XIX cWW cW-W 5 G.C31 G.G39 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#8[#3] bps=5 strand-1 5'-GCGAG-3' bp-type ||||| strand-2 3'-UGCUC-5' helix-form .AAA 1 G.G49 G.U65 G-U Wobble 28-XXVIII cWW cW-W 2 G.C50 G.G64 C-G WC 19-XIX cWW cW-W 3 G.G51 G.C63 G-C WC 19-XIX cWW cW-W 4 G.A52 G.U62 A-U WC 20-XX cWW cW-W 5 G.G53 G.C61 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#9[#5] bps=7 strand-1 5'-GCGGGAA-3' bp-type ||||||| strand-2 3'-CGCCCUU-5' helix-form AAAAAA 1 H.G1 H.C72 G-C WC 19-XIX cWW cW-W 2 H.C2 H.G71 C-G WC 19-XIX cWW cW-W 3 H.G3 H.C70 G-C WC 19-XIX cWW cW-W 4 H.G4 H.C69 G-C WC 19-XIX cWW cW-W 5 H.G5 H.C68 G-C WC 19-XIX cWW cW-W 6 H.A6 H.U67 A-U WC 20-XX cWW cW-W 7 H.A7 H.U66 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#10[#6] bps=4 strand-1 5'-GCUC-3' bp-type |||| strand-2 3'-CGAG-5' helix-form AA. 1 H.G10 H.C25 G-C WC 19-XIX cWW cW-W 2 H.C11 H.G24 C-G WC 19-XIX cWW cW-W 3 H.U12 H.A23 U-A WC 20-XX cWW cW-W 4 H.C13 H.G22 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#11[#6] bps=5 strand-1 5'-CGACC-3' bp-type ||||| strand-2 3'-GCUGG-5' helix-form AAAA 1 H.C27 H.G43 C-G WC 19-XIX cWW cW-W 2 H.G28 H.C42 G-C WC 19-XIX cWW cW-W 3 H.A29 H.U41 A-U WC 20-XX cWW cW-W 4 H.C30 H.G40 C-G WC 19-XIX cWW cW-W 5 H.C31 H.G39 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#12[#5] bps=5 strand-1 5'-GCGAG-3' bp-type ||||| strand-2 3'-UGCUC-5' helix-form .AAA 1 H.G49 H.U65 G-U Wobble 28-XXVIII cWW cW-W 2 H.C50 H.G64 C-G WC 19-XIX cWW cW-W 3 H.G51 H.C63 G-C WC 19-XIX cWW cW-W 4 H.A52 H.U62 A-U WC 20-XX cWW cW-W 5 H.G53 H.C61 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#13[#7] bps=7 strand-1 5'-GCGGGAA-3' bp-type ||||||| strand-2 3'-CGCCCUU-5' helix-form AAAAAA 1 E.G1 E.C72 G-C WC 19-XIX cWW cW-W 2 E.C2 E.G71 C-G WC 19-XIX cWW cW-W 3 E.G3 E.C70 G-C WC 19-XIX cWW cW-W 4 E.G4 E.C69 G-C WC 19-XIX cWW cW-W 5 E.G5 E.C68 G-C WC 19-XIX cWW cW-W 6 E.A6 E.U67 A-U WC 20-XX cWW cW-W 7 E.A7 E.U66 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#14[#8] bps=4 strand-1 5'-GCUC-3' bp-type |||| strand-2 3'-CGAG-5' helix-form AA. 1 E.G10 E.C25 G-C WC 19-XIX cWW cW-W 2 E.C11 E.G24 C-G WC 19-XIX cWW cW-W 3 E.U12 E.A23 U-A WC 20-XX cWW cW-W 4 E.C13 E.G22 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#15[#8] bps=5 strand-1 5'-CGACC-3' bp-type ||||| strand-2 3'-GCUGG-5' helix-form AAAA 1 E.C27 E.G43 C-G WC 19-XIX cWW cW-W 2 E.G28 E.C42 G-C WC 19-XIX cWW cW-W 3 E.A29 E.U41 A-U WC 20-XX cWW cW-W 4 E.C30 E.G40 C-G WC 19-XIX cWW cW-W 5 E.C31 E.G39 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#16[#7] bps=5 strand-1 5'-GCGAG-3' bp-type ||||| strand-2 3'-UGCUC-5' helix-form .AAA 1 E.G49 E.U65 G-U Wobble 28-XXVIII cWW cW-W 2 E.C50 E.G64 C-G WC 19-XIX cWW cW-W 3 E.G51 E.C63 G-C WC 19-XIX cWW cW-W 4 E.A52 E.U62 A-U WC 20-XX cWW cW-W 5 E.G53 E.C61 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 4 isolated WC/wobble pairs Note: Isolated WC/wobble pairs are assigned negative indices to differentiate them from the stem numbers, which are positive. -------------------------------------------------------------------- [#1] -1 F.G19 F.C56 G-C WC 19-XIX cWW cW-W [#3] -2 G.G19 G.C56 G-C WC 19-XIX cWW cW-W [#5] -3 H.G19 H.C56 G-C WC 19-XIX cWW cW-W [#7] -4 E.G19 E.C56 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 8 coaxial stacks 1 Helix#1 contains 2 stems: [#1,#4] 2 Helix#2 contains 2 stems: [#3,#2] 3 Helix#3 contains 2 stems: [#5,#8] 4 Helix#4 contains 2 stems: [#7,#6] 5 Helix#5 contains 2 stems: [#9,#12] 6 Helix#6 contains 2 stems: [#11,#10] 7 Helix#7 contains 2 stems: [#13,#16] 8 Helix#8 contains 2 stems: [#15,#14] **************************************************************************** List of 43 base stacks Note: A stack is an ordered list of nucleotides assembled together via base-stacking interactions, regardless of backbone connectivity. Stacking interactions within a stem are *not* included. 1 nts=2 HA B.HIS130,F.A76 2 nts=2 UC F.U8,F.C13 3 nts=2 AA F.A37,F.A38 4 nts=2 GU F.G49,F.U66 5 nts=2 HA C.HIS130,G.A76 6 nts=2 UC G.U8,G.C13 7 nts=2 CU G.C31,G.U32 8 nts=2 GU G.G49,G.U66 9 nts=2 UC H.U8,H.C13 10 nts=2 AG H.A38,H.G39 11 nts=2 GU H.G49,H.U66 12 nts=2 UC E.U8,E.C13 13 nts=2 AG E.A38,E.G39 14 nts=2 GU E.G49,E.U66 15 nts=3 GUC F.G1,F.U73,F.C74 16 nts=3 GAC F.G10,F.A26,F.C27 17 nts=3 GGG F.G43,F.G44,F.G45 18 nts=3 GUU F.G53,F.U54,F.U55 19 nts=3 GAC G.G10,G.A26,G.C27 20 nts=3 AAG G.A37,G.A38,G.G39 21 nts=3 GUU G.G53,G.U54,G.U55 22 nts=3 CUC G.C72,G.U73,G.C74 23 nts=3 GAC H.G10,H.A26,H.C27 24 nts=3 CUU H.C31,H.U32,H.U33 25 nts=3 GUU H.G53,H.U54,H.U55 26 nts=3 CUC H.C72,H.U73,H.C74 27 nts=3 CAC E.C25,E.A26,E.C27 28 nts=3 GUU E.G53,E.U54,E.U55 29 nts=3 CUC E.C72,E.U73,E.C74 30 nts=4 AGAC F.A9,F.G46,F.A21,F.C48 31 nts=4 UCCG F.U32,F.C36,F.C35,F.G34 32 nts=4 UGCC G.U33,G.G34,G.C35,G.C36 33 nts=5 GGGAC F.G19,F.G57,F.G18,F.A58,F.C61 34 nts=5 GAGGU F.G22,F.A14,F.G15,F.G59,F.U60 35 nts=5 GGGAC G.G19,G.G57,G.G18,G.A58,G.C61 36 nts=5 GAGGU G.G22,G.A14,G.G15,G.G59,G.U60 37 nts=5 GGGAC H.G19,H.G57,H.G18,H.A58,H.C61 38 nts=5 GAGGU H.G22,H.A14,H.G15,H.G59,H.U60 39 nts=5 GGGAC E.G19,E.G57,E.G18,E.A58,E.C61 40 nts=5 GAGGU E.G22,E.A14,E.G15,E.G59,E.U60 41 nts=7 GGGAGAC G.G43,G.G44,G.G45,G.A9,G.G46,G.A21,G.C48 42 nts=7 GGGAGAC H.G43,H.G44,H.G45,H.A9,H.G46,H.A21,H.C48 43 nts=7 GGGAGAC E.G43,E.G44,E.G45,E.A9,E.G46,E.A21,E.C48 **************************************************************************** Nucleotides not involved in stacking interactions nts=25 UUUUUUUUUCUUUAUCUUUUUAUCA F.U16,F.U17,F.U20,F.U33,F.U47,G.U16,G.U17,G.U20,G.U47,G.C68,H.U16,H.U17,H.U20,H.A37,H.U47,H.C75,E.U16,E.U17,E.U20,E.U32,E.U33,E.A37,E.U47,E.C68,E.A76 **************************************************************************** List of 9 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 sugar O4'@F.C36 F.C35 3.07 2 sugar O4'@F.G59 F.C48 2.84 3 phosphate OP2@F.G57 F.U55 2.93 4 sugar O4'@G.G59 G.C48 2.92 5 phosphate OP2@G.G57 G.U55 3.12 6 sugar O4'@H.G59 H.C48 3.23 7 phosphate OP2@H.G57 H.U55 2.88 8 sugar O4'@E.G59 E.C48 3.26 9 phosphate OP2@E.G57 E.U55 2.76 **************************************************************************** Note: For the various types of loops listed below, numbers within the first set of brackets are the number of loop nts. Numbers in the second set of brackets are the identities of the stems (positive) or isolated WC/wobble pairs (negative) to which they are linked. **************************************************************************** List of 10 hairpin loops 1 hairpin loop: nts=10; [8]; linked by [#2] summary: [1] 8 [F.13 F.22] 4 nts=10 CAGUUGGUAG F.C13,F.A14,F.G15,F.U16,F.U17,F.G18,F.G19,F.U20,F.A21,F.G22 nts=8 AGUUGGUA F.A14,F.G15,F.U16,F.U17,F.G18,F.G19,F.U20,F.A21 2 hairpin loop: nts=7; [5]; linked by [#3] summary: [1] 5 [F.32 F.38] 6 nts=7 UUGCCAA F.U32,F.U33,F.G34,F.C35,F.C36,F.A37,F.A38 nts=5 UGCCA F.U33,F.G34,F.C35,F.C36,F.A37 3 hairpin loop: nts=9; [7]; linked by [#4] summary: [1] 7 [F.53 F.61] 5 nts=9 GUUCGAGUC F.G53,F.U54,F.U55,F.C56,F.G57,F.A58,F.G59,F.U60,F.C61 nts=7 UUCGAGU F.U54,F.U55,F.C56,F.G57,F.A58,F.G59,F.U60 4 hairpin loop: nts=10; [8]; linked by [#6] summary: [1] 8 [G.13 G.22] 4 nts=10 CAGUUGGUAG G.C13,G.A14,G.G15,G.U16,G.U17,G.G18,G.G19,G.U20,G.A21,G.G22 nts=8 AGUUGGUA G.A14,G.G15,G.U16,G.U17,G.G18,G.G19,G.U20,G.A21 5 hairpin loop: nts=9; [7]; linked by [#7] summary: [1] 7 [G.31 G.39] 5 nts=9 CUUGCCAAG G.C31,G.U32,G.U33,G.G34,G.C35,G.C36,G.A37,G.A38,G.G39 nts=7 UUGCCAA G.U32,G.U33,G.G34,G.C35,G.C36,G.A37,G.A38 6 hairpin loop: nts=9; [7]; linked by [#8] summary: [1] 7 [G.53 G.61] 5 nts=9 GUUCGAGUC G.G53,G.U54,G.U55,G.C56,G.G57,G.A58,G.G59,G.U60,G.C61 nts=7 UUCGAGU G.U54,G.U55,G.C56,G.G57,G.A58,G.G59,G.U60 7 hairpin loop: nts=10; [8]; linked by [#10] summary: [1] 8 [H.13 H.22] 4 nts=10 CAGUUGGUAG H.C13,H.A14,H.G15,H.U16,H.U17,H.G18,H.G19,H.U20,H.A21,H.G22 nts=8 AGUUGGUA H.A14,H.G15,H.U16,H.U17,H.G18,H.G19,H.U20,H.A21 8 hairpin loop: nts=9; [7]; linked by [#12] summary: [1] 7 [H.53 H.61] 5 nts=9 GUUCGAGUC H.G53,H.U54,H.U55,H.C56,H.G57,H.A58,H.G59,H.U60,H.C61 nts=7 UUCGAGU H.U54,H.U55,H.C56,H.G57,H.A58,H.G59,H.U60 9 hairpin loop: nts=10; [8]; linked by [#14] summary: [1] 8 [E.13 E.22] 4 nts=10 CAGUUGGUAG E.C13,E.A14,E.G15,E.U16,E.U17,E.G18,E.G19,E.U20,E.A21,E.G22 nts=8 AGUUGGUA E.A14,E.G15,E.U16,E.U17,E.G18,E.G19,E.U20,E.A21 10 hairpin loop: nts=9; [7]; linked by [#16] summary: [1] 7 [E.53 E.61] 5 nts=9 GUUCGAGUC E.G53,E.U54,E.U55,E.C56,E.G57,E.A58,E.G59,E.U60,E.C61 nts=7 UUCGAGU E.U54,E.U55,E.C56,E.G57,E.A58,E.G59,E.U60 **************************************************************************** List of 4 junctions 1 4-way junction: nts=16; [2,1,5,0]; linked by [#1,#2,#3,#4] summary: [4] 2 1 5 0 [F.7 F.66 F.10 F.25 F.27 F.43 F.49 F.65] 7 4 6 5 nts=16 AUAGCACGGGGUCGUU F.A7,F.U8,F.A9,F.G10,F.C25,F.A26,F.C27,F.G43,F.G44,F.G45,F.G46,F.U47,F.C48,F.G49,F.U65,F.U66 nts=2 UA F.U8,F.A9 nts=1 A F.A26 nts=5 GGGUC F.G44,F.G45,F.G46,F.U47,F.C48 nts=0 2 4-way junction: nts=16; [2,1,5,0]; linked by [#5,#6,#7,#8] summary: [4] 2 1 5 0 [G.7 G.66 G.10 G.25 G.27 G.43 G.49 G.65] 7 4 5 5 nts=16 AUAGCACGGGGUCGUU G.A7,G.U8,G.A9,G.G10,G.C25,G.A26,G.C27,G.G43,G.G44,G.G45,G.G46,G.U47,G.C48,G.G49,G.U65,G.U66 nts=2 UA G.U8,G.A9 nts=1 A G.A26 nts=5 GGGUC G.G44,G.G45,G.G46,G.U47,G.C48 nts=0 3 4-way junction: nts=16; [2,1,5,0]; linked by [#9,#10,#11,#12] summary: [4] 2 1 5 0 [H.7 H.66 H.10 H.25 H.27 H.43 H.49 H.65] 7 4 5 5 nts=16 AUAGCACGGGGUCGUU H.A7,H.U8,H.A9,H.G10,H.C25,H.A26,H.C27,H.G43,H.G44,H.G45,H.G46,H.U47,H.C48,H.G49,H.U65,H.U66 nts=2 UA H.U8,H.A9 nts=1 A H.A26 nts=5 GGGUC H.G44,H.G45,H.G46,H.U47,H.C48 nts=0 4 4-way junction: nts=16; [2,1,5,0]; linked by [#13,#14,#15,#16] summary: [4] 2 1 5 0 [E.7 E.66 E.10 E.25 E.27 E.43 E.49 E.65] 7 4 5 5 nts=16 AUAGCACGGGGUCGUU E.A7,E.U8,E.A9,E.G10,E.C25,E.A26,E.C27,E.G43,E.G44,E.G45,E.G46,E.U47,E.C48,E.G49,E.U65,E.U66 nts=2 UA E.U8,E.A9 nts=1 A E.A26 nts=5 GGGUC E.G44,E.G45,E.G46,E.U47,E.C48 nts=0 **************************************************************************** List of 6 non-loop single-stranded segments 1 nts=4 UCCA F.U73,F.C74,F.C75,F.A76 2 nts=4 UCCA G.U73,G.C74,G.C75,G.A76 3 nts=4* UUAA H.U32,H.U33,H.A37,H.A38 4 nts=3 UCC H.U73,H.C74,H.C75 5 nts=4* UUAA E.U32,E.U33,E.A37,E.A38 6 nts=4 UCCA E.U73,E.C74,E.C75,E.A76 **************************************************************************** List of 4 kissing loop interactions 1 isolated-pair #-4 between hairpin loops #9 and #10 2 isolated-pair #-3 between hairpin loops #7 and #8 3 isolated-pair #-2 between hairpin loops #4 and #6 4 isolated-pair #-1 between hairpin loops #1 and #3 **************************************************************************** List of 1 A-minor motif (types I, II, or X) 1 type=X A|U-A E.A38|E.U32,E.A37 ~Wobble -E.U32 H-bonds[1]: "N6(amino)-O2(carbonyl)[3.37]" +E.A37 H-bonds[2]: "O4'-O2'(hydroxyl)[3.40],N7*N3[2.71]" **************************************************************************** List of 33 splayed-apart dinucleotides 1 F.A7 F.U8 angle=122 distance=16.7 ratio=0.87 2 F.G15 F.U16 angle=125 distance=14.5 ratio=0.89 3 F.U17 F.G18 angle=97 distance=15.1 ratio=0.75 4 F.G19 F.U20 angle=90 distance=14.7 ratio=0.70 5 F.U20 F.A21 angle=151 distance=19.2 ratio=0.97 6 F.G46 F.U47 angle=119 distance=18.2 ratio=0.86 7 F.U47 F.C48 angle=143 distance=18.2 ratio=0.95 8 F.C48 F.G49 angle=157 distance=18.1 ratio=0.98 9 F.U60 F.C61 angle=85 distance=13.3 ratio=0.68 10 F.C75 F.A76 angle=116 distance=17.0 ratio=0.85 11 G.A7 G.U8 angle=123 distance=16.8 ratio=0.88 12 G.G15 G.U16 angle=118 distance=14.6 ratio=0.86 13 G.U17 G.G18 angle=140 distance=18.2 ratio=0.94 14 G.U20 G.A21 angle=98 distance=16.5 ratio=0.75 15 G.U32 G.U33 angle=86 distance=14.4 ratio=0.68 16 G.G46 G.U47 angle=134 distance=19.5 ratio=0.92 17 G.U47 G.C48 angle=163 distance=18.8 ratio=0.99 18 G.C48 G.G49 angle=158 distance=18.3 ratio=0.98 19 G.C75 G.A76 angle=126 distance=17.3 ratio=0.89 20 H.A7 H.U8 angle=116 distance=16.2 ratio=0.85 21 H.G15 H.U16 angle=158 distance=19.5 ratio=0.98 22 H.U17 H.G18 angle=123 distance=17.8 ratio=0.88 23 H.G19 H.U20 angle=132 distance=16.9 ratio=0.91 24 H.U20 H.A21 angle=128 distance=17.4 ratio=0.90 25 H.C48 H.G49 angle=157 distance=18.3 ratio=0.98 26 H.U60 H.C61 angle=89 distance=13.8 ratio=0.70 27 E.A7 E.U8 angle=117 distance=16.4 ratio=0.85 28 E.G15 E.U16 angle=120 distance=17.1 ratio=0.87 29 E.U17 E.G18 angle=96 distance=14.6 ratio=0.75 30 E.G19 E.U20 angle=119 distance=16.8 ratio=0.86 31 E.U20 E.A21 angle=129 distance=17.3 ratio=0.90 32 E.C48 E.G49 angle=154 distance=18.0 ratio=0.97 33 E.C75 E.A76 angle=146 distance=18.1 ratio=0.96 ---------------------------------------------------------------- Summary of 26 splayed-apart units 1 nts=2 AU F.A7,F.U8 2 nts=2 GU F.G15,F.U16 3 nts=2 UG F.U17,F.G18 4 nts=3 GUA F.G19,F.U20,F.A21 5 nts=4 GUCG F.G46,F.U47,F.C48,F.G49 6 nts=2 UC F.U60,F.C61 7 nts=2 CA F.C75,F.A76 8 nts=2 AU G.A7,G.U8 9 nts=2 GU G.G15,G.U16 10 nts=2 UG G.U17,G.G18 11 nts=2 UA G.U20,G.A21 12 nts=2 UU G.U32,G.U33 13 nts=4 GUCG G.G46,G.U47,G.C48,G.G49 14 nts=2 CA G.C75,G.A76 15 nts=2 AU H.A7,H.U8 16 nts=2 GU H.G15,H.U16 17 nts=2 UG H.U17,H.G18 18 nts=3 GUA H.G19,H.U20,H.A21 19 nts=2 CG H.C48,H.G49 20 nts=2 UC H.U60,H.C61 21 nts=2 AU E.A7,E.U8 22 nts=2 GU E.G15,E.U16 23 nts=2 UG E.U17,E.G18 24 nts=3 GUA E.G19,E.U20,E.A21 25 nts=2 CG E.C48,E.G49 26 nts=2 CA E.C75,E.A76 **************************************************************************** This structure contains 1-order pseudoknot o You may want to run DSSR again with the '--nested' option which removes pseudoknots to get a fully nested secondary structure representation. **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >7f36 nts=297 [whole] GCGGGAAUAGCUCAGUUGGUAGAGCACGACCUUGCCAAGGUCGGGGUCGCGAGUUCGAGUCUCGUUUCCCGCUCCA&GCGGGAAUAGCUCAGUUGGUAGAGCACGACCUUGCCAAGGUCGGGGUCGCGAGUUCGAGUCUCGUUUCCCGCUCCA&GCGGGAAUAGCUCAGUUGGUAGAGCACGACCUU&AAGGUCGGGGUCGCGAGUUCGAGUCUCGUUUCCCGCUCC&GCGGGAAUAGCUCAGUUGGUAGAGCACGACCUU&AAGGUCGGGGUCGCGAGUUCGAGUCUCGUUUCCCGCUCCA (((((((..((((.....[..)))).((((((.....)))))).....(((((..]....))))))))))))....&(((((((..((((.....[..)))).(((((.......))))).....(((((..]....))))))))))))....&(((((((..((((.....[..)))).(((((..&..))))).....(((((..]....))))))))))))...&(((((((..((((.....[..)))).(((((..&..))))).....(((((..]....)))))))))))).... >7f36-F #1 nts=76 0.18(3.44) [chain] RNA GCGGGAAUAGCUCAGUUGGUAGAGCACGACCUUGCCAAGGUCGGGGUCGCGAGUUCGAGUCUCGUUUCCCGCUCCA (((((((..((((.....[..)))).((((((.....)))))).....(((((..]....)))))))))))).... >7f36-G #2 nts=76 0.17(3.34) [chain] RNA GCGGGAAUAGCUCAGUUGGUAGAGCACGACCUUGCCAAGGUCGGGGUCGCGAGUUCGAGUCUCGUUUCCCGCUCCA (((((((..((((.....[..)))).(((((.......))))).....(((((..]....)))))))))))).... >7f36-H #3 nts=72 0.06(3.19) [chain] RNA* GCGGGAAUAGCUCAGUUGGUAGAGCACGACCUU&AAGGUCGGGGUCGCGAGUUCGAGUCUCGUUUCCCGCUCC (((((((..((((.....[..)))).(((((..&..))))).....(((((..]....))))))))))))... >7f36-E #4 nts=73 0.07(3.24) [chain] RNA* GCGGGAAUAGCUCAGUUGGUAGAGCACGACCUU&AAGGUCGGGGUCGCGAGUUCGAGUCUCGUUUCCCGCUCCA (((((((..((((.....[..)))).(((((..&..))))).....(((((..]....)))))))))))).... **************************************************************************** Summary of structural features of 297 nucleotides Note: the first five columns are: (1) serial number, (2) one-letter shorthand name, (3) dbn, (4) id string, (5) rmsd (~zero) of base ring atoms fitted against those in a standard base reference frame. The sixth (last) column contains a comma-separated list of features whose meanings are mostly self-explanatory, except for: turn: angle C1'(i-1)--C1'(i)--C1'(i+1) < 90 degrees break: no backbone linkage between O3'(i-1) and P(i) 1 G ( F.G1 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,phosphate 2 C ( F.C2 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 3 G ( F.G3 0.010 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 4 G ( F.G4 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 5 G ( F.G5 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 6 A ( F.A6 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 7 A ( F.A7 0.014 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate,splayed-apart 8 U . F.U8 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,phosphate,splayed-apart 9 A . F.A9 0.011 anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,phosphate 10 G ( F.G10 0.007 turn,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,phosphate 11 C ( F.C11 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 12 U ( F.U12 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,phosphate 13 C ( F.C13 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,kissing-loop 14 A . F.A14 0.014 anti,~C3'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,kissing-loop,phosphate 15 G . F.G15 0.007 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,kissing-loop,splayed-apart 16 U . F.U16 0.007 ~C2'-endo,non-stack,non-pair-contact,hairpin-loop,kissing-loop,phosphate,splayed-apart 17 U . F.U17 0.012 anti,~C3'-endo,non-stack,non-pair-contact,hairpin-loop,kissing-loop,splayed-apart 18 G . F.G18 0.006 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,kissing-loop,splayed-apart 19 G [ F.G19 0.018 pseudoknotted,anti,~C2'-endo,BII,isolated-canonical,non-pair-contact,helix-end,hairpin-loop,kissing-loop,phosphate,splayed-apart 20 U . F.U20 0.009 anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,kissing-loop,phosphate,splayed-apart 21 A . F.A21 0.023 anti,~C2'-endo,non-pair-contact,hairpin-loop,kissing-loop,splayed-apart 22 G ) F.G22 0.012 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,kissing-loop 23 A ) F.A23 0.007 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 24 G ) F.G24 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 25 C ) F.C25 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop 26 A . F.A26 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 27 C ( F.C27 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 28 G ( F.G28 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 29 A ( F.A29 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 30 C ( F.C30 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 31 C ( F.C31 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 32 U ( F.U32 0.016 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,hairpin-loop,phosphate 33 U . F.U33 0.003 anti,~C3'-endo,non-stack,non-canonical,hairpin-loop 34 G . F.G34 0.006 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 35 C . F.C35 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,hairpin-loop,cap-acceptor 36 C . F.C36 0.007 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-donor 37 A . F.A37 0.009 ~C3'-endo,non-pair-contact,hairpin-loop,phosphate 38 A ) F.A38 0.032 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,hairpin-loop 39 G ) F.G39 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 40 G ) F.G40 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 41 U ) F.U41 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 42 C ) F.C42 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 43 G ) F.G43 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 44 G . F.G44 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 45 G . F.G45 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,junction-loop 46 G . F.G46 0.013 anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,phosphate,splayed-apart 47 U . F.U47 0.012 turn,anti,non-stack,junction-loop,phosphate,splayed-apart 48 C . F.C48 0.007 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,cap-acceptor,phosphate,splayed-apart 49 G ( F.G49 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate,splayed-apart 50 C ( F.C50 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 51 G ( F.G51 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 52 A ( F.A52 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 53 G ( F.G53 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,kissing-loop 54 U . F.U54 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,kissing-loop 55 U . F.U55 0.007 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,kissing-loop,cap-acceptor 56 C ] F.C56 0.010 pseudoknotted,turn,u-turn,anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end,hairpin-loop,kissing-loop 57 G . F.G57 0.011 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,kissing-loop,cap-donor,phosphate 58 A . F.A58 0.014 u-turn,anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,hairpin-loop,kissing-loop,phosphate 59 G . F.G59 0.005 turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,kissing-loop,cap-donor,phosphate 60 U . F.U60 0.015 anti,~C2'-endo,non-pair-contact,hairpin-loop,kissing-loop,phosphate,splayed-apart 61 C ) F.C61 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,kissing-loop,splayed-apart 62 U ) F.U62 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 63 C ) F.C63 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 64 G ) F.G64 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 65 U ) F.U65 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 66 U ) F.U66 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 67 U ) F.U67 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 68 C ) F.C68 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 69 C ) F.C69 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 70 C ) F.C70 0.017 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,phosphate 71 G ) F.G71 0.006 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 72 C ) F.C72 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 73 U . F.U73 0.014 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 74 C . F.C74 0.009 anti,~C2'-endo,non-pair-contact,ss-non-loop 75 C . F.C75 0.015 anti,~C2'-endo,BII,non-pair-contact,ss-non-loop,phosphate,splayed-apart 76 A . F.A76 0.012 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 77 G ( G.G1 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,phosphate 78 C ( G.C2 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 79 G ( G.G3 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 80 G ( G.G4 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 81 G ( G.G5 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 82 A ( G.A6 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 83 A ( G.A7 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate,splayed-apart 84 U . G.U8 0.008 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,junction-loop,phosphate,splayed-apart 85 A . G.A9 0.006 ~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,phosphate 86 G ( G.G10 0.008 turn,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop 87 C ( G.C11 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 88 U ( G.U12 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 89 C ( G.C13 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,kissing-loop 90 A . G.A14 0.008 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,kissing-loop,phosphate 91 G . G.G15 0.012 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,kissing-loop,splayed-apart 92 U . G.U16 0.009 anti,~C2'-endo,non-stack,non-canonical,non-pair-contact,multiplet,hairpin-loop,kissing-loop,phosphate,splayed-apart 93 U . G.U17 0.007 syn,non-stack,non-canonical,non-pair-contact,multiplet,hairpin-loop,kissing-loop,phosphate,splayed-apart 94 G . G.G18 0.014 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,kissing-loop,splayed-apart 95 G [ G.G19 0.008 pseudoknotted,~C2'-endo,isolated-canonical,non-pair-contact,helix-end,hairpin-loop,kissing-loop,phosphate 96 U . G.U20 0.006 anti,BII,non-stack,non-pair-contact,hairpin-loop,kissing-loop,splayed-apart 97 A . G.A21 0.009 anti,~C2'-endo,BII,non-canonical,non-pair-contact,multiplet,hairpin-loop,kissing-loop,splayed-apart 98 G ) G.G22 0.011 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,kissing-loop 99 A ) G.A23 0.008 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 100 G ) G.G24 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 101 C ) G.C25 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop 102 A . G.A26 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 103 C ( G.C27 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 104 G ( G.G28 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 105 A ( G.A29 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 106 C ( G.C30 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 107 C ( G.C31 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 108 U . G.U32 0.003 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,splayed-apart 109 U . G.U33 0.009 turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,splayed-apart 110 G . G.G34 0.008 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 111 C . G.C35 0.006 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 112 C . G.C36 0.006 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 113 A . G.A37 0.008 anti,~C3'-endo,non-pair-contact,hairpin-loop 114 A . G.A38 0.005 ~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop 115 G ) G.G39 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 116 G ) G.G40 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 117 U ) G.U41 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 118 C ) G.C42 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 119 G ) G.G43 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 120 G . G.G44 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 121 G . G.G45 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,junction-loop 122 G . G.G46 0.012 anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,phosphate,splayed-apart 123 U . G.U47 0.006 turn,anti,non-stack,non-pair-contact,junction-loop,splayed-apart 124 C . G.C48 0.004 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,cap-acceptor,phosphate,splayed-apart 125 G ( G.G49 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate,splayed-apart 126 C ( G.C50 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 127 G ( G.G51 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 128 A ( G.A52 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 129 G ( G.G53 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,kissing-loop 130 U . G.U54 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,kissing-loop 131 U . G.U55 0.006 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,kissing-loop,cap-acceptor 132 C ] G.C56 0.005 pseudoknotted,turn,u-turn,anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end,hairpin-loop,kissing-loop 133 G . G.G57 0.007 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,kissing-loop,cap-donor,phosphate 134 A . G.A58 0.009 u-turn,anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,hairpin-loop,kissing-loop,phosphate 135 G . G.G59 0.006 turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,kissing-loop,cap-donor,phosphate 136 U . G.U60 0.009 anti,~C2'-endo,non-pair-contact,hairpin-loop,kissing-loop,phosphate 137 C ) G.C61 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,kissing-loop 138 U ) G.U62 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 139 C ) G.C63 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 140 G ) G.G64 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 141 U ) G.U65 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 142 U ) G.U66 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 143 U ) G.U67 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 144 C ) G.C68 0.007 anti,~C3'-endo,BI,non-stack,canonical,helix,stem,coaxial-stack 145 C ) G.C69 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 146 C ) G.C70 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 147 G ) G.G71 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 148 C ) G.C72 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 149 U . G.U73 0.010 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 150 C . G.C74 0.006 anti,~C2'-endo,non-pair-contact,ss-non-loop 151 C . G.C75 0.007 anti,~C2'-endo,ss-non-loop,splayed-apart 152 A . G.A76 0.008 anti,~C3'-endo,ss-non-loop,splayed-apart 153 G ( H.G1 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,phosphate 154 C ( H.C2 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 155 G ( H.G3 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 156 G ( H.G4 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 157 G ( H.G5 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 158 A ( H.A6 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 159 A ( H.A7 0.012 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate,splayed-apart 160 U . H.U8 0.004 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,junction-loop,phosphate,splayed-apart 161 A . H.A9 0.006 ~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,phosphate 162 G ( H.G10 0.007 turn,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop 163 C ( H.C11 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 164 U ( H.U12 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 165 C ( H.C13 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,kissing-loop 166 A . H.A14 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,kissing-loop,phosphate 167 G . H.G15 0.005 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,kissing-loop,splayed-apart 168 U . H.U16 0.003 anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,kissing-loop,phosphate,splayed-apart 169 U . H.U17 0.009 anti,non-stack,non-pair-contact,hairpin-loop,kissing-loop,splayed-apart 170 G . H.G18 0.011 anti,~C2'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,kissing-loop,splayed-apart 171 G [ H.G19 0.010 pseudoknotted,anti,~C2'-endo,isolated-canonical,non-pair-contact,helix-end,hairpin-loop,kissing-loop,splayed-apart 172 U . H.U20 0.006 anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,kissing-loop,splayed-apart 173 A . H.A21 0.006 ~C2'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,kissing-loop,phosphate,splayed-apart 174 G ) H.G22 0.011 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,kissing-loop 175 A ) H.A23 0.005 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 176 G ) H.G24 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 177 C ) H.C25 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop 178 A . H.A26 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 179 C ( H.C27 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 180 G ( H.G28 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 181 A ( H.A29 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 182 C ( H.C30 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 183 C ( H.C31 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack 184 U . H.U32 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop 185 U . H.U33 0.007 break,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop 186 A . H.A37 0.014 ~C3'-endo,non-stack,non-canonical,helix-end,ss-non-loop 187 A . H.A38 0.011 ~C3'-endo,non-canonical,non-pair-contact,helix,ss-non-loop 188 G ) H.G39 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 189 G ) H.G40 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 190 U ) H.U41 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 191 C ) H.C42 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 192 G ) H.G43 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 193 G . H.G44 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 194 G . H.G45 0.014 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,junction-loop 195 G . H.G46 0.015 anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop 196 U . H.U47 0.010 turn,anti,non-stack,non-pair-contact,junction-loop 197 C . H.C48 0.005 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,cap-acceptor,phosphate,splayed-apart 198 G ( H.G49 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate,splayed-apart 199 C ( H.C50 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 200 G ( H.G51 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 201 A ( H.A52 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 202 G ( H.G53 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,kissing-loop 203 U . H.U54 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,kissing-loop 204 U . H.U55 0.010 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,kissing-loop,cap-acceptor 205 C ] H.C56 0.006 pseudoknotted,turn,u-turn,anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end,hairpin-loop,kissing-loop 206 G . H.G57 0.004 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,kissing-loop,cap-donor,phosphate 207 A . H.A58 0.013 u-turn,anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,hairpin-loop,kissing-loop,phosphate 208 G . H.G59 0.009 turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,kissing-loop,cap-donor,phosphate 209 U . H.U60 0.007 anti,~C2'-endo,non-pair-contact,hairpin-loop,kissing-loop,phosphate,splayed-apart 210 C ) H.C61 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,kissing-loop,splayed-apart 211 U ) H.U62 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 212 C ) H.C63 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 213 G ) H.G64 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 214 U ) H.U65 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 215 U ) H.U66 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 216 U ) H.U67 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 217 C ) H.C68 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 218 C ) H.C69 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 219 C ) H.C70 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 220 G ) H.G71 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 221 C ) H.C72 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,phosphate 222 U . H.U73 0.009 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 223 C . H.C74 0.020 anti,~C2'-endo,non-pair-contact,ss-non-loop 224 C . H.C75 0.010 anti,~C2'-endo,non-stack,ss-non-loop,phosphate 225 G ( E.G1 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,phosphate 226 C ( E.C2 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 227 G ( E.G3 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 228 G ( E.G4 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 229 G ( E.G5 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 230 A ( E.A6 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 231 A ( E.A7 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate,splayed-apart 232 U . E.U8 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,junction-loop,phosphate,splayed-apart 233 A . E.A9 0.006 anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,phosphate 234 G ( E.G10 0.005 turn,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,phosphate 235 C ( E.C11 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 236 U ( E.U12 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,phosphate 237 C ( E.C13 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,kissing-loop 238 A . E.A14 0.006 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,kissing-loop,phosphate 239 G . E.G15 0.006 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,kissing-loop,splayed-apart 240 U . E.U16 0.006 anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,kissing-loop,phosphate,splayed-apart 241 U . E.U17 0.005 turn,anti,non-stack,non-pair-contact,hairpin-loop,kissing-loop,splayed-apart 242 G . E.G18 0.003 anti,~C2'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,kissing-loop,phosphate,splayed-apart 243 G [ E.G19 0.013 pseudoknotted,~C2'-endo,isolated-canonical,non-pair-contact,helix-end,hairpin-loop,kissing-loop,splayed-apart 244 U . E.U20 0.003 anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,kissing-loop,phosphate,splayed-apart 245 A . E.A21 0.006 ~C2'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,kissing-loop,phosphate,splayed-apart 246 G ) E.G22 0.008 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,kissing-loop 247 A ) E.A23 0.006 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 248 G ) E.G24 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 249 C ) E.C25 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop 250 A . E.A26 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 251 C ( E.C27 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 252 G ( E.G28 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 253 A ( E.A29 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 254 C ( E.C30 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 255 C ( E.C31 0.012 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack 256 U . E.U32 0.008 anti,~C3'-endo,non-stack,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,A-minor 257 U . E.U33 0.005 break,anti,~C3'-endo,non-stack,ss-non-loop 258 A . E.A37 0.014 ~C3'-endo,non-stack,non-canonical,helix-end,multiplet,ss-non-loop,A-minor 259 A . E.A38 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,ss-non-loop,A-minor 260 G ) E.G39 0.021 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 261 G ) E.G40 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 262 U ) E.U41 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 263 C ) E.C42 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 264 G ) E.G43 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 265 G . E.G44 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 266 G . E.G45 0.008 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,junction-loop 267 G . E.G46 0.009 anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop 268 U . E.U47 0.006 turn,anti,non-stack,non-pair-contact,junction-loop 269 C . E.C48 0.006 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,cap-acceptor,phosphate,splayed-apart 270 G ( E.G49 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate,splayed-apart 271 C ( E.C50 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 272 G ( E.G51 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 273 A ( E.A52 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 274 G ( E.G53 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,kissing-loop 275 U . E.U54 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,kissing-loop 276 U . E.U55 0.007 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,kissing-loop,cap-acceptor 277 C ] E.C56 0.009 pseudoknotted,turn,u-turn,anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end,hairpin-loop,kissing-loop 278 G . E.G57 0.010 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,kissing-loop,cap-donor,phosphate 279 A . E.A58 0.005 u-turn,anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,hairpin-loop,kissing-loop,phosphate 280 G . E.G59 0.012 turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,kissing-loop,cap-donor,phosphate 281 U . E.U60 0.004 anti,~C2'-endo,non-pair-contact,hairpin-loop,kissing-loop,phosphate 282 C ) E.C61 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,kissing-loop 283 U ) E.U62 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 284 C ) E.C63 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 285 G ) E.G64 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 286 U ) E.U65 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 287 U ) E.U66 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 288 U ) E.U67 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 289 C ) E.C68 0.007 anti,~C3'-endo,BI,non-stack,canonical,helix,stem,coaxial-stack 290 C ) E.C69 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 291 C ) E.C70 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 292 G ) E.G71 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 293 C ) E.C72 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,phosphate 294 U . E.U73 0.009 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 295 C . E.C74 0.016 anti,~C2'-endo,non-pair-contact,ss-non-loop 296 C . E.C75 0.010 anti,~C2'-endo,ss-non-loop,phosphate,splayed-apart 297 A . E.A76 0.013 anti,~C3'-endo,non-stack,ss-non-loop,phosphate,splayed-apart **************************************************************************** List of 18 additional files 1 dssr-pairs.pdb -- an ensemble of base pairs 2 dssr-multiplets.pdb -- an ensemble of multiplets 3 dssr-stems.pdb -- an ensemble of stems 4 dssr-helices.pdb -- an ensemble of helices (coaxial stacking) 5 dssr-hairpins.pdb -- an ensemble of hairpin loops 6 dssr-junctions.pdb -- an ensemble of junctions (multi-branch) 7 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 8 dssr-2ndstrs.ct -- secondary structure in connectivity table format 9 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 10 dssr-torsions.txt -- backbone torsion angles and suite names 11 dssr-splays.pdb -- an ensemble of splayed-apart units 12 dssr-Aminors.pdb -- an ensemble of A minor motifs (types I and II) 13 dssr-stacks.pdb -- an ensemble of base stacks 14 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions 15 dssr-rotmat.txt -- position vector and rotation matrix 16 dssr-viewV.pdb -- vertical view of the principal moment of inertia 17 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 18 dssr-viewT.pdb -- top view of the principal moment of inertia