**************************************************************************** File name: 4wfm.pdb no. of DNA/RNA chains: 2 [A=103,B=103] no. of nucleotides: 206 no. of atoms: 4600 no. of waters: 4 no. of metals: 24 [Mg=1,Co=23] **************************************************************************** List of 2 types of 4 modified nucleotides nt count list 1 CCC-c 2 A.CCC105,B.CCC105 2 GTP-g 2 A.GTP3,B.GTP3 **************************************************************************** List of 104 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.GTP3 A.CCC105 g-c WC 19-XIX cWW cW-W 2 A.G4 A.U104 G-U Wobble 28-XXVIII cWW cW-W 3 A.C5 A.G103 C-G WC 19-XIX cWW cW-W 4 A.C6 A.G102 C-G WC 19-XIX cWW cW-W 5 A.G7 A.C101 G-C WC 19-XIX cWW cW-W 6 A.U8 A.A100 U-A WC 20-XX cWW cW-W 7 A.G9 A.C99 G-C WC 19-XIX cWW cW-W 8 A.C10 A.G98 C-G WC 19-XIX cWW cW-W 9 A.U11 A.A63 U-A rHoogsteen 24-XXIV tWH tW-M 10 A.A12 A.G62 A-G -- -- tHS tM-m 11 A.A12 A.A64 A+A -- 01-I tWW tW+W 12 A.A13 A.C61 A-C -- -- .HW .M-W 13 A.G14 A.C60 G-C WC 19-XIX cWW cW-W 14 A.C15 A.G59 C-G WC 19-XIX cWW cW-W 15 A.G16 A.U34 G-U Wobble 28-XXVIII cWW cW-W 16 A.G17 A.C33 G-C WC 19-XIX cWW cW-W 17 A.G18 A.C32 G-C WC 19-XIX cWW cW-W 18 A.G19 A.C31 G-C WC 19-XIX cWW cW-W 19 A.A20 A.G30 A-G Imino 08-VIII cWW cW-W 20 A.G21 A.U29 G-U -- -- cW. cW-. 21 A.G22 A.G28 G-G -- -- t.H t.-M 22 A.A24 A.U50 A-U WC 20-XX cWW cW-W 23 A.G25 A.C49 G-C WC 19-XIX cWW cW-W 24 A.G25 A.A53 G+A Linker -- tSS tm+m 25 A.C26 A.G48 C-G WC 19-XIX cWW cW-W 26 A.G27 A.C47 G-C WC 19-XIX cWW cW-W 27 A.G27 A.G54 G-G -- -- cSS cm-m 28 A.G28 A.A43 G+A Linker -- tS. tm+. 29 A.G28 A.C46 G-C WC 19-XIX cWW cW-W 30 A.U29 A.A44 U+A Hoogsteen 23-XXIII cWH cW+M 31 A.G35 A.A37 G-A Sheared 11-XI tSH tm-M 32 A.C38 A.G58 C-G WC 19-XIX cWW cW-W 33 A.C39 A.G57 C-G WC 19-XIX cWW cW-W 34 A.U40 A.A56 U-A WC 20-XX cWW cW-W 35 A.G41 A.C55 G-C WC 19-XIX cWW cW-W 36 A.C42 A.G54 C-G WC 19-XIX cWW cW-W 37 A.C47 A.G54 C+G -- -- tWS tW+m 38 A.A64 A.U97 A-U rHoogsteen 24-XXIV tHW tM-W 39 A.C67 A.G96 C-G WC 19-XIX cWW cW-W 40 A.C68 A.G95 C-G WC 19-XIX cWW cW-W 41 A.U69 A.A94 U-A WC 20-XX cWW cW-W 42 A.U70 A.A93 U-A WC 20-XX cWW cW-W 43 A.C71 A.G92 C-G WC 19-XIX cWW cW-W 44 A.U72 A.A91 U-A WC 20-XX cWW cW-W 45 A.C73 A.C90 C-C -- -- cWW cW-W 46 A.G74 A.A89 G-A Sheared 11-XI tSH tm-M 47 A.A75 A.G88 A-G Sheared 11-XI tHS tM-m 48 A.G76 A.C87 G-C WC 19-XIX cWW cW-W 49 A.G77 A.U86 G-U Wobble 28-XXVIII cWW cW-W 50 A.U78 A.A85 U-A WC 20-XX cWW cW-W 51 A.G79 A.C84 G+C ~Hoogsteen -- cWH cW+M 52 A.G80 A.A83 G-A Sheared 11-XI tSH tm-M 53 B.GTP3 B.CCC105 g-c WC 19-XIX cWW cW-W 54 B.G4 B.U104 G-U Wobble 28-XXVIII cWW cW-W 55 B.C5 B.G103 C-G WC 19-XIX cWW cW-W 56 B.C6 B.G102 C-G WC 19-XIX cWW cW-W 57 B.G7 B.C101 G-C WC 19-XIX cWW cW-W 58 B.U8 B.A100 U-A WC 20-XX cWW cW-W 59 B.G9 B.C99 G-C WC 19-XIX cWW cW-W 60 B.C10 B.G98 C-G WC 19-XIX cWW cW-W 61 B.U11 B.A63 U-A rHoogsteen 24-XXIV tWH tW-M 62 B.A12 B.G62 A-G -- -- tHS tM-m 63 B.A12 B.A64 A+A -- 01-I tWW tW+W 64 B.A13 B.C61 A-C -- -- .HW .M-W 65 B.G14 B.C60 G-C WC 19-XIX cWW cW-W 66 B.C15 B.G59 C-G WC 19-XIX cWW cW-W 67 B.G16 B.U34 G-U Wobble 28-XXVIII cWW cW-W 68 B.G17 B.C33 G-C WC 19-XIX cWW cW-W 69 B.G18 B.C32 G-C WC 19-XIX cWW cW-W 70 B.G19 B.C31 G-C WC 19-XIX cWW cW-W 71 B.A20 B.G30 A-G Imino 08-VIII cWW cW-W 72 B.G21 B.G28 G-G -- -- tWH tW-M 73 B.G21 B.U29 G-U -- -- tWH tW-M 74 B.G22 B.G27 G-G -- -- tWH tW-M 75 B.A24 B.U50 A-U WC 20-XX cWW cW-W 76 B.G25 B.C49 G-C WC 19-XIX cWW cW-W 77 B.G25 B.A53 G+A Linker -- tSS tm+m 78 B.C26 B.G48 C-G WC 19-XIX cWW cW-W 79 B.G27 B.C47 G-C WC 19-XIX cWW cW-W 80 B.G27 B.G54 G-G -- -- cSS cm-m 81 B.G28 B.A43 G+A Linker -- tSS tm+m 82 B.G28 B.C46 G-C WC 19-XIX cWW cW-W 83 B.U29 B.A44 U-A WC 20-XX cWW cW-W 84 B.G35 B.A37 G-A Sheared 11-XI tSH tm-M 85 B.C38 B.G58 C-G WC 19-XIX cWW cW-W 86 B.C39 B.G57 C-G WC 19-XIX cWW cW-W 87 B.U40 B.A56 U-A WC 20-XX cWW cW-W 88 B.G41 B.C55 G-C WC 19-XIX cWW cW-W 89 B.C42 B.G54 C-G WC 19-XIX cWW cW-W 90 B.A64 B.U97 A-U rHoogsteen 24-XXIV tHW tM-W 91 B.C67 B.G96 C-G WC 19-XIX cWW cW-W 92 B.C68 B.G95 C-G WC 19-XIX cWW cW-W 93 B.U69 B.A94 U-A WC 20-XX cWW cW-W 94 B.U70 B.A93 U-A WC 20-XX cWW cW-W 95 B.C71 B.G92 C-G WC 19-XIX cWW cW-W 96 B.U72 B.A91 U-A WC 20-XX cWW cW-W 97 B.C73 B.C90 C-C -- -- cWW cW-W 98 B.G74 B.A89 G-A Sheared 11-XI tSH tm-M 99 B.A75 B.G88 A-G Sheared 11-XI tHS tM-m 100 B.G76 B.C87 G-C WC 19-XIX cWW cW-W 101 B.G77 B.U86 G-U Wobble 28-XXVIII cWW cW-W 102 B.U78 B.A85 U-A WC 20-XX cWW cW-W 103 B.G79 B.C84 G-C WC 19-XIX cWW cW-W 104 B.G80 B.A83 G-A Sheared 11-XI tSH tm-M **************************************************************************** List of 8 multiplets 1 nts=3 GCA A.G25,A.C49,A.A53 2 nts=3 GCA B.G25,B.C49,B.A53 3 nts=3 GAC B.G28,B.A43,B.C46 4 nts=4 AGAU A.A12,A.G62,A.A64,A.U97 5 nts=4 GGAC A.G22,A.G28,A.A43,A.C46 6 nts=4 GCCG A.G27,A.C42,A.C47,A.G54 7 nts=4 AGAU B.A12,B.G62,B.A64,B.U97 8 nts=5 GGCCG B.G22,B.G27,B.C42,B.C47,B.G54 **************************************************************************** List of 5 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[3] bps=18 strand-1 5'-gGCCGUGCUAAGCCCUGC-3' bp-type ||||||||...||||||| strand-2 3'-cUGGCACGAGCCGGGACG-5' helix-form ...AAAAx...AxAAAA 1 A.GTP3 A.CCC105 g-c WC 19-XIX cWW cW-W 2 A.G4 A.U104 G-U Wobble 28-XXVIII cWW cW-W 3 A.C5 A.G103 C-G WC 19-XIX cWW cW-W 4 A.C6 A.G102 C-G WC 19-XIX cWW cW-W 5 A.G7 A.C101 G-C WC 19-XIX cWW cW-W 6 A.U8 A.A100 U-A WC 20-XX cWW cW-W 7 A.G9 A.C99 G-C WC 19-XIX cWW cW-W 8 A.C10 A.G98 C-G WC 19-XIX cWW cW-W 9 A.U11 A.A63 U-A rHoogsteen 24-XXIV tWH tW-M 10 A.A12 A.G62 A-G -- -- tHS tM-m 11 A.A13 A.C61 A-C -- -- .HW .M-W 12 A.G14 A.C60 G-C WC 19-XIX cWW cW-W 13 A.C15 A.G59 C-G WC 19-XIX cWW cW-W 14 A.C38 A.G58 C-G WC 19-XIX cWW cW-W 15 A.C39 A.G57 C-G WC 19-XIX cWW cW-W 16 A.U40 A.A56 U-A WC 20-XX cWW cW-W 17 A.G41 A.C55 G-C WC 19-XIX cWW cW-W 18 A.C42 A.G54 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[4] bps=24 strand-1 5'-AGGGGAACCGCUAGCGGUGCCCUG-3' bp-type .||||..|||||||||||.||||. strand-2 3'-GUCCCGUGGCGAUCGCCAAGGGGA-5' helix-form x.AA.xx.A..x..AAxx.AA.x 1 A.A37 A.G35 A-G Sheared 11-XI tHS tM-m 2 A.G16 A.U34 G-U Wobble 28-XXVIII cWW cW-W 3 A.G17 A.C33 G-C WC 19-XIX cWW cW-W 4 A.G18 A.C32 G-C WC 19-XIX cWW cW-W 5 A.G19 A.C31 G-C WC 19-XIX cWW cW-W 6 A.A20 A.G30 A-G Imino 08-VIII cWW cW-W 7 A.A44 A.U29 A+U Hoogsteen 23-XXIII cHW cM+W 8 A.C46 A.G28 C-G WC 19-XIX cWW cW-W 9 A.C47 A.G27 C-G WC 19-XIX cWW cW-W 10 A.G48 A.C26 G-C WC 19-XIX cWW cW-W 11 A.C49 A.G25 C-G WC 19-XIX cWW cW-W 12 A.U50 A.A24 U-A WC 20-XX cWW cW-W 13 B.A24 B.U50 A-U WC 20-XX cWW cW-W 14 B.G25 B.C49 G-C WC 19-XIX cWW cW-W 15 B.C26 B.G48 C-G WC 19-XIX cWW cW-W 16 B.G27 B.C47 G-C WC 19-XIX cWW cW-W 17 B.G28 B.C46 G-C WC 19-XIX cWW cW-W 18 B.U29 B.A44 U-A WC 20-XX cWW cW-W 19 B.G30 B.A20 G-A Imino 08-VIII cWW cW-W 20 B.C31 B.G19 C-G WC 19-XIX cWW cW-W 21 B.C32 B.G18 C-G WC 19-XIX cWW cW-W 22 B.C33 B.G17 C-G WC 19-XIX cWW cW-W 23 B.U34 B.G16 U-G Wobble 28-XXVIII cWW cW-W 24 B.G35 B.A37 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#3[2] bps=15 strand-1 5'-ACCUUCUCGAGGUGG-3' bp-type .||||||...|||.. strand-2 3'-UGGAAGACAGCUACA-5' helix-form xAAAAA........ 1 A.A64 A.U97 A-U rHoogsteen 24-XXIV tHW tM-W 2 A.C67 A.G96 C-G WC 19-XIX cWW cW-W 3 A.C68 A.G95 C-G WC 19-XIX cWW cW-W 4 A.U69 A.A94 U-A WC 20-XX cWW cW-W 5 A.U70 A.A93 U-A WC 20-XX cWW cW-W 6 A.C71 A.G92 C-G WC 19-XIX cWW cW-W 7 A.U72 A.A91 U-A WC 20-XX cWW cW-W 8 A.C73 A.C90 C-C -- -- cWW cW-W 9 A.G74 A.A89 G-A Sheared 11-XI tSH tm-M 10 A.A75 A.G88 A-G Sheared 11-XI tHS tM-m 11 A.G76 A.C87 G-C WC 19-XIX cWW cW-W 12 A.G77 A.U86 G-U Wobble 28-XXVIII cWW cW-W 13 A.U78 A.A85 U-A WC 20-XX cWW cW-W 14 A.G79 A.C84 G+C ~Hoogsteen -- cWH cW+M 15 A.G80 A.A83 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#4[3] bps=18 strand-1 5'-gGCCGUGCUAAGCCCUGC-3' bp-type ||||||||...||||||| strand-2 3'-cUGGCACGAGCCGGGACG-5' helix-form ..A.AAAx...AxAAA. 1 B.GTP3 B.CCC105 g-c WC 19-XIX cWW cW-W 2 B.G4 B.U104 G-U Wobble 28-XXVIII cWW cW-W 3 B.C5 B.G103 C-G WC 19-XIX cWW cW-W 4 B.C6 B.G102 C-G WC 19-XIX cWW cW-W 5 B.G7 B.C101 G-C WC 19-XIX cWW cW-W 6 B.U8 B.A100 U-A WC 20-XX cWW cW-W 7 B.G9 B.C99 G-C WC 19-XIX cWW cW-W 8 B.C10 B.G98 C-G WC 19-XIX cWW cW-W 9 B.U11 B.A63 U-A rHoogsteen 24-XXIV tWH tW-M 10 B.A12 B.G62 A-G -- -- tHS tM-m 11 B.A13 B.C61 A-C -- -- .HW .M-W 12 B.G14 B.C60 G-C WC 19-XIX cWW cW-W 13 B.C15 B.G59 C-G WC 19-XIX cWW cW-W 14 B.C38 B.G58 C-G WC 19-XIX cWW cW-W 15 B.C39 B.G57 C-G WC 19-XIX cWW cW-W 16 B.U40 B.A56 U-A WC 20-XX cWW cW-W 17 B.G41 B.C55 G-C WC 19-XIX cWW cW-W 18 B.C42 B.G54 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#5[2] bps=15 strand-1 5'-ACCUUCUCGAGGUGG-3' bp-type .||||||...||||. strand-2 3'-UGGAAGACAGCUACA-5' helix-form xAAAAA......A. 1 B.A64 B.U97 A-U rHoogsteen 24-XXIV tHW tM-W 2 B.C67 B.G96 C-G WC 19-XIX cWW cW-W 3 B.C68 B.G95 C-G WC 19-XIX cWW cW-W 4 B.U69 B.A94 U-A WC 20-XX cWW cW-W 5 B.U70 B.A93 U-A WC 20-XX cWW cW-W 6 B.C71 B.G92 C-G WC 19-XIX cWW cW-W 7 B.U72 B.A91 U-A WC 20-XX cWW cW-W 8 B.C73 B.C90 C-C -- -- cWW cW-W 9 B.G74 B.A89 G-A Sheared 11-XI tSH tm-M 10 B.A75 B.G88 A-G Sheared 11-XI tHS tM-m 11 B.G76 B.C87 G-C WC 19-XIX cWW cW-W 12 B.G77 B.U86 G-U Wobble 28-XXVIII cWW cW-W 13 B.U78 B.A85 U-A WC 20-XX cWW cW-W 14 B.G79 B.C84 G-C WC 19-XIX cWW cW-W 15 B.G80 B.A83 G-A Sheared 11-XI tSH tm-M **************************************************************************** List of 14 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=8 strand-1 5'-gGCCGUGC-3' bp-type |||||||| strand-2 3'-cUGGCACG-5' helix-form ...AAAA 1 A.GTP3 A.CCC105 g-c WC 19-XIX cWW cW-W 2 A.G4 A.U104 G-U Wobble 28-XXVIII cWW cW-W 3 A.C5 A.G103 C-G WC 19-XIX cWW cW-W 4 A.C6 A.G102 C-G WC 19-XIX cWW cW-W 5 A.G7 A.C101 G-C WC 19-XIX cWW cW-W 6 A.U8 A.A100 U-A WC 20-XX cWW cW-W 7 A.G9 A.C99 G-C WC 19-XIX cWW cW-W 8 A.C10 A.G98 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=2 strand-1 5'-GC-3' bp-type || strand-2 3'-CG-5' helix-form A 1 A.G14 A.C60 G-C WC 19-XIX cWW cW-W 2 A.C15 A.G59 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#3[#2] bps=4 strand-1 5'-GGGG-3' bp-type |||| strand-2 3'-UCCC-5' helix-form .AA 1 A.G16 A.U34 G-U Wobble 28-XXVIII cWW cW-W 2 A.G17 A.C33 G-C WC 19-XIX cWW cW-W 3 A.G18 A.C32 G-C WC 19-XIX cWW cW-W 4 A.G19 A.C31 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#4[#2] bps=5 strand-1 5'-AGCGG-3' bp-type ||||| strand-2 3'-UCGCC-5' helix-form ..A. 1 A.A24 A.U50 A-U WC 20-XX cWW cW-W 2 A.G25 A.C49 G-C WC 19-XIX cWW cW-W 3 A.C26 A.G48 C-G WC 19-XIX cWW cW-W 4 A.G27 A.C47 G-C WC 19-XIX cWW cW-W 5 A.G28 A.C46 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#5[#1] bps=5 strand-1 5'-CCUGC-3' bp-type ||||| strand-2 3'-GGACG-5' helix-form AAAA 1 A.C38 A.G58 C-G WC 19-XIX cWW cW-W 2 A.C39 A.G57 C-G WC 19-XIX cWW cW-W 3 A.U40 A.A56 U-A WC 20-XX cWW cW-W 4 A.G41 A.C55 G-C WC 19-XIX cWW cW-W 5 A.C42 A.G54 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#6[#3] bps=6 strand-1 5'-CCUUCU-3' bp-type |||||| strand-2 3'-GGAAGA-5' helix-form AAAAA 1 A.C67 A.G96 C-G WC 19-XIX cWW cW-W 2 A.C68 A.G95 C-G WC 19-XIX cWW cW-W 3 A.U69 A.A94 U-A WC 20-XX cWW cW-W 4 A.U70 A.A93 U-A WC 20-XX cWW cW-W 5 A.C71 A.G92 C-G WC 19-XIX cWW cW-W 6 A.U72 A.A91 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#7[#3] bps=3 strand-1 5'-GGU-3' bp-type ||| strand-2 3'-CUA-5' helix-form .. 1 A.G76 A.C87 G-C WC 19-XIX cWW cW-W 2 A.G77 A.U86 G-U Wobble 28-XXVIII cWW cW-W 3 A.U78 A.A85 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#8[#4] bps=8 strand-1 5'-gGCCGUGC-3' bp-type |||||||| strand-2 3'-cUGGCACG-5' helix-form ..A.AAA 1 B.GTP3 B.CCC105 g-c WC 19-XIX cWW cW-W 2 B.G4 B.U104 G-U Wobble 28-XXVIII cWW cW-W 3 B.C5 B.G103 C-G WC 19-XIX cWW cW-W 4 B.C6 B.G102 C-G WC 19-XIX cWW cW-W 5 B.G7 B.C101 G-C WC 19-XIX cWW cW-W 6 B.U8 B.A100 U-A WC 20-XX cWW cW-W 7 B.G9 B.C99 G-C WC 19-XIX cWW cW-W 8 B.C10 B.G98 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#9[#4] bps=2 strand-1 5'-GC-3' bp-type || strand-2 3'-CG-5' helix-form A 1 B.G14 B.C60 G-C WC 19-XIX cWW cW-W 2 B.C15 B.G59 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#10[#2] bps=4 strand-1 5'-GGGG-3' bp-type |||| strand-2 3'-UCCC-5' helix-form .AA 1 B.G16 B.U34 G-U Wobble 28-XXVIII cWW cW-W 2 B.G17 B.C33 G-C WC 19-XIX cWW cW-W 3 B.G18 B.C32 G-C WC 19-XIX cWW cW-W 4 B.G19 B.C31 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#11[#2] bps=5 strand-1 5'-AGCGG-3' bp-type ||||| strand-2 3'-UCGCC-5' helix-form ..AA 1 B.A24 B.U50 A-U WC 20-XX cWW cW-W 2 B.G25 B.C49 G-C WC 19-XIX cWW cW-W 3 B.C26 B.G48 C-G WC 19-XIX cWW cW-W 4 B.G27 B.C47 G-C WC 19-XIX cWW cW-W 5 B.G28 B.C46 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#12[#4] bps=5 strand-1 5'-CCUGC-3' bp-type ||||| strand-2 3'-GGACG-5' helix-form AAA. 1 B.C38 B.G58 C-G WC 19-XIX cWW cW-W 2 B.C39 B.G57 C-G WC 19-XIX cWW cW-W 3 B.U40 B.A56 U-A WC 20-XX cWW cW-W 4 B.G41 B.C55 G-C WC 19-XIX cWW cW-W 5 B.C42 B.G54 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#13[#5] bps=6 strand-1 5'-CCUUCU-3' bp-type |||||| strand-2 3'-GGAAGA-5' helix-form AAAAA 1 B.C67 B.G96 C-G WC 19-XIX cWW cW-W 2 B.C68 B.G95 C-G WC 19-XIX cWW cW-W 3 B.U69 B.A94 U-A WC 20-XX cWW cW-W 4 B.U70 B.A93 U-A WC 20-XX cWW cW-W 5 B.C71 B.G92 C-G WC 19-XIX cWW cW-W 6 B.U72 B.A91 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#14[#5] bps=4 strand-1 5'-GGUG-3' bp-type |||| strand-2 3'-CUAC-5' helix-form ..A 1 B.G76 B.C87 G-C WC 19-XIX cWW cW-W 2 B.G77 B.U86 G-U Wobble 28-XXVIII cWW cW-W 3 B.U78 B.A85 U-A WC 20-XX cWW cW-W 4 B.G79 B.C84 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 1 isolated WC/wobble pair Note: Isolated WC/wobble pairs are assigned negative indices to differentiate them from the stem numbers, which are positive. -------------------------------------------------------------------- [#2] -1 B.U29 B.A44 U-A WC 20-XX cWW cW-W **************************************************************************** List of 5 coaxial stacks 1 Helix#1 contains 3 stems: [#1,#2,#5] 2 Helix#2 contains 4 stems: [#3,#4,#11,#10] 3 Helix#3 contains 2 stems: [#6,#7] 4 Helix#4 contains 3 stems: [#8,#9,#12] 5 Helix#5 contains 2 stems: [#13,#14] **************************************************************************** List of 36 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 GA A.G16,A.A37 2 nts=2 AA A.A24,B.A24 3 nts=2 CA A.C42,A.A43 4 nts=2 AC A.A44,A.C46 5 nts=2 UU A.U50,B.U50 6 nts=2 CA A.C51,A.A53 7 nts=2 GG A.G58,A.G59 8 nts=2 UC A.U65,A.C66 9 nts=2 GU A.G96,A.U97 10 nts=2 GA B.G16,B.A37 11 nts=2 CA B.C42,B.A43 12 nts=2 AC B.A44,B.C46 13 nts=2 CA B.C51,B.A53 14 nts=2 GG B.G58,B.G59 15 nts=2 UC B.U65,B.C66 16 nts=2 GG B.G79,B.G80 17 nts=2 GU B.G96,B.U97 18 nts=3 AAG A.A12,A.A13,A.G14 19 nts=3 UGU A.U34,A.G35,A.U36 20 nts=3 GGA A.G80,A.G79,A.A85 21 nts=3 UAA A.U81,A.A82,A.A83 22 nts=3 AAG B.A12,B.A13,B.G14 23 nts=3 UGU B.U34,B.G35,B.U36 24 nts=3 UAA B.U81,B.A82,B.A83 25 nts=4 GUGC A.G28,A.U29,A.G30,A.C31 26 nts=4 CAAG A.C67,A.A64,A.A63,A.G98 27 nts=4 GUGC B.G28,B.U29,B.G30,B.C31 28 nts=4 CAAG B.C67,B.A64,B.A63,B.G98 29 nts=5 CUGCC A.C10,A.U11,A.G62,A.C61,A.C60 30 nts=5 GAGGU A.G19,A.A20,A.G21,A.G22,A.U23 31 nts=5 UCGGC A.U72,A.C73,A.G74,A.G88,A.C87 32 nts=5 GAACA A.G76,A.A75,A.A89,A.C90,A.A91 33 nts=5 CUGCC B.C10,B.U11,B.G62,B.C61,B.C60 34 nts=5 GAGGU B.G19,B.A20,B.G21,B.G22,B.U23 35 nts=5 UCGGC B.U72,B.C73,B.G74,B.G88,B.C87 36 nts=5 GAACA B.G76,B.A75,B.A89,B.C90,B.A91 **************************************************************************** Nucleotides not involved in stacking interactions nts=4 UUUU A.U45,A.U52,B.U45,B.U52 **************************************************************************** List of 13 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 phosphate OP2@A.G25 A.U23 3.05 2 sugar O4'@A.U36 A.A37 3.03 3 sugar O4'@A.C26 A.A53 3.02 4 sugar O4'@A.A63 A.A64 3.04 5 phosphate OP2@A.A82 A.G80 2.98 6 phosphate OP2@B.G25 B.U23 2.96 7 sugar O4'@B.U36 B.A37 3.11 8 sugar O4'@B.U29 B.A43 3.09 9 sugar O4'@B.C46 B.A44 3.17 10 sugar O4'@B.C26 B.A53 2.92 11 sugar O4'@B.C51 B.A53 2.99 12 sugar O4'@B.A63 B.A64 3.08 13 phosphate OP2@B.A82 B.G80 2.99 **************************************************************************** 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 8 hairpin loops 1 hairpin loop: nts=13; [11]; linked by [#3] summary: [1] 11 [A.19 A.31] 4 nts=13 GAGGUAGCGGUGC A.G19,A.A20,A.G21,A.G22,A.U23,A.A24,A.G25,A.C26,A.G27,A.G28,A.U29,A.G30,A.C31 nts=11 AGGUAGCGGUG A.A20,A.G21,A.G22,A.U23,A.A24,A.G25,A.C26,A.G27,A.G28,A.U29,A.G30 2 hairpin loop: nts=19; [17]; linked by [#4] summary: [1] 17 [A.28 A.46] 5 nts=19 GUGCCCUGUACCUGCAAUC A.G28,A.U29,A.G30,A.C31,A.C32,A.C33,A.U34,A.G35,A.U36,A.A37,A.C38,A.C39,A.U40,A.G41,A.C42,A.A43,A.A44,A.U45,A.C46 nts=17 UGCCCUGUACCUGCAAU A.U29,A.G30,A.C31,A.C32,A.C33,A.U34,A.G35,A.U36,A.A37,A.C38,A.C39,A.U40,A.G41,A.C42,A.A43,A.A44,A.U45 3 hairpin loop: nts=13; [11]; linked by [#5] summary: [1] 11 [A.42 A.54] 5 nts=13 CAAUCCGCUCUAG A.C42,A.A43,A.A44,A.U45,A.C46,A.C47,A.G48,A.C49,A.U50,A.C51,A.U52,A.A53,A.G54 nts=11 AAUCCGCUCUA A.A43,A.A44,A.U45,A.C46,A.C47,A.G48,A.C49,A.U50,A.C51,A.U52,A.A53 4 hairpin loop: nts=8; [6]; linked by [#7] summary: [1] 6 [A.78 A.85] 3 nts=8 UGGUAACA A.U78,A.G79,A.G80,A.U81,A.A82,A.A83,A.C84,A.A85 nts=6 GGUAAC A.G79,A.G80,A.U81,A.A82,A.A83,A.C84 5 hairpin loop: nts=13; [11]; linked by [#10] summary: [1] 11 [B.19 B.31] 4 nts=13 GAGGUAGCGGUGC B.G19,B.A20,B.G21,B.G22,B.U23,B.A24,B.G25,B.C26,B.G27,B.G28,B.U29,B.G30,B.C31 nts=11 AGGUAGCGGUG B.A20,B.G21,B.G22,B.U23,B.A24,B.G25,B.C26,B.G27,B.G28,B.U29,B.G30 6 hairpin loop: nts=16; [14]; linked by [#-1] summary: [1] 14 [B.29 B.44] 1 nts=16 UGCCCUGUACCUGCAA B.U29,B.G30,B.C31,B.C32,B.C33,B.U34,B.G35,B.U36,B.A37,B.C38,B.C39,B.U40,B.G41,B.C42,B.A43,B.A44 nts=14 GCCCUGUACCUGCA B.G30,B.C31,B.C32,B.C33,B.U34,B.G35,B.U36,B.A37,B.C38,B.C39,B.U40,B.G41,B.C42,B.A43 7 hairpin loop: nts=13; [11]; linked by [#12] summary: [1] 11 [B.42 B.54] 5 nts=13 CAAUCCGCUCUAG B.C42,B.A43,B.A44,B.U45,B.C46,B.C47,B.G48,B.C49,B.U50,B.C51,B.U52,B.A53,B.G54 nts=11 AAUCCGCUCUA B.A43,B.A44,B.U45,B.C46,B.C47,B.G48,B.C49,B.U50,B.C51,B.U52,B.A53 8 hairpin loop: nts=6; [4]; linked by [#14] summary: [1] 4 [B.79 B.84] 4 nts=6 GGUAAC B.G79,B.G80,B.U81,B.A82,B.A83,B.C84 nts=4 GUAA B.G80,B.U81,B.A82,B.A83 **************************************************************************** List of 1 bulge 1 bulge: nts=5; [0,1]; linked by [#11,#-1] summary: [2] 0 1 [B.28 B.46 B.29 B.44] 5 1 nts=5 GUAUC B.G28,B.U29,B.A44,B.U45,B.C46 nts=0 nts=1 U B.U45 **************************************************************************** List of 2 internal loops 1 symmetric internal loop: nts=10; [3,3]; linked by [#6,#7] summary: [2] 3 3 [A.72 A.91 A.76 A.87] 6 3 nts=10 UCGAGCGACA A.U72,A.C73,A.G74,A.A75,A.G76,A.C87,A.G88,A.A89,A.C90,A.A91 nts=3 CGA A.C73,A.G74,A.A75 nts=3 GAC A.G88,A.A89,A.C90 2 symmetric internal loop: nts=10; [3,3]; linked by [#13,#14] summary: [2] 3 3 [B.72 B.91 B.76 B.87] 6 4 nts=10 UCGAGCGACA B.U72,B.C73,B.G74,B.A75,B.G76,B.C87,B.G88,B.A89,B.C90,B.A91 nts=3 CGA B.C73,B.G74,B.A75 nts=3 GAC B.G88,B.A89,B.C90 **************************************************************************** List of 6 junctions 1 3-way junction: nts=9; [0,3,0]; linked by [#2,#3,#5] summary: [3] 0 3 0 [A.15 A.59 A.16 A.34 A.38 A.58] 2 4 5 nts=9 CGUGUACGG A.C15,A.G16,A.U34,A.G35,A.U36,A.A37,A.C38,A.G58,A.G59 nts=0 nts=3 GUA A.G35,A.U36,A.A37 nts=0 2 3-way junction: nts=9; [0,3,0]; linked by [#9,#10,#12] summary: [3] 0 3 0 [B.15 B.59 B.16 B.34 B.38 B.58] 2 4 5 nts=9 CGUGUACGG B.C15,B.G16,B.U34,B.G35,B.U36,B.A37,B.C38,B.G58,B.G59 nts=0 nts=3 GUA B.G35,B.U36,B.A37 nts=0 3 3-way junction: nts=16; [3,6,1]; linked by [#1,#2,#6] summary: [3] 3 6 1 [A.10 A.98 A.14 A.60 A.67 A.96] 8 2 6 nts=16 CUAAGCCGAAUCCGUG A.C10,A.U11,A.A12,A.A13,A.G14,A.C60,A.C61,A.G62,A.A63,A.A64,A.U65,A.C66,A.C67,A.G96,A.U97,A.G98 nts=3 UAA A.U11,A.A12,A.A13 nts=6 CGAAUC A.C61,A.G62,A.A63,A.A64,A.U65,A.C66 nts=1 U A.U97 4 3-way junction: nts=16; [3,6,1]; linked by [#8,#9,#13] summary: [3] 3 6 1 [B.10 B.98 B.14 B.60 B.67 B.96] 8 2 6 nts=16 CUAAGCCGAAUCCGUG B.C10,B.U11,B.A12,B.A13,B.G14,B.C60,B.C61,B.G62,B.A63,B.A64,B.U65,B.C66,B.C67,B.G96,B.U97,B.G98 nts=3 UAA B.U11,B.A12,B.A13 nts=6 CGAAUC B.C61,B.G62,B.A63,B.A64,B.U65,B.C66 nts=1 U B.U97 5 4-way junction: nts=17; [4,3,1,1]; linked by [#10,#11,#12,#-1] summary: [4] 4 3 1 1 [B.19 B.31 B.24 B.50 B.54 B.42 B.44 B.29] 4 5 5 1 nts=17 GAGGUAUCUAGCAAUGC B.G19,B.A20,B.G21,B.G22,B.U23,B.A24,B.U50,B.C51,B.U52,B.A53,B.G54,B.C42,B.A43,B.A44,B.U29,B.G30,B.C31 nts=4 AGGU B.A20,B.G21,B.G22,B.U23 nts=3 CUA B.C51,B.U52,B.A53 nts=1 A B.A43 nts=1 G B.G30 6* 4-way junction: nts=20; [4,3,3,2]; linked by [#3,#4,#5,#4] summary: [4] 4 3 3 2 [A.19 A.31 A.24 A.50 A.54 A.42 A.46 A.28] 4 5 5 5 nts=20 GAGGUAUCUAGCAAUCGUGC A.G19,A.A20,A.G21,A.G22,A.U23,A.A24,A.U50,A.C51,A.U52,A.A53,A.G54,A.C42,A.A43,A.A44,A.U45,A.C46,A.G28,A.U29,A.G30,A.C31 nts=4 AGGU A.A20,A.G21,A.G22,A.U23 nts=3 CUA A.C51,A.U52,A.A53 nts=3 AAU A.A43,A.A44,A.U45 nts=2 UG A.U29,A.G30 **************************************************************************** List of 3 kissing loop interactions 1 isolated-pair #-1 between hairpin loops #5 and #7 2 stem #4 between hairpin loops #1 and #3 3 stem #11 between hairpin loops #5 and #7 **************************************************************************** List of 4 A-minor motifs (types I, II, or X) 1 type=I A|G-C A.A43|A.G28,A.C46 WC +A.G28 H-bonds[2]: "N1-O2'(hydroxyl)[2.68],N3-N2(amino)[3.16]" -A.C46 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.67],O2'(hydroxyl)-O2(carbonyl)[2.34]" 2 type=I A|G-C A.A53|A.G25,A.C49 WC +A.G25 H-bonds[2]: "N1-O2'(hydroxyl)[2.43],N3-N2(amino)[3.07]" -A.C49 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.79],O2'(hydroxyl)-O2(carbonyl)[2.68]" 3 type=I A|G-C B.A43|B.G28,B.C46 WC +B.G28 H-bonds[2]: "N1-O2'(hydroxyl)[2.72],N3-N2(amino)[3.08]" -B.C46 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.65],O2'(hydroxyl)-O2(carbonyl)[2.67]" 4 type=I A|G-C B.A53|B.G25,B.C49 WC +B.G25 H-bonds[2]: "N1-O2'(hydroxyl)[2.44],N3-N2(amino)[3.14]" -B.C49 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.80],O2'(hydroxyl)-O2(carbonyl)[2.83]" **************************************************************************** List of 4 ribose zippers 1 nts=4 CACC A.C42,A.A43,A.C46,A.C47 2 nts=4 GCAG A.G48,A.C49,A.A53,A.G54 3 nts=4 CACC B.C42,B.A43,B.C46,B.C47 4 nts=4 GCAG B.G48,B.C49,B.A53,B.G54 **************************************************************************** List of 16 splayed-apart dinucleotides 1 A.C15 A.G16 angle=169 distance=18.7 ratio=1.00 2 A.A37 A.C38 angle=139 distance=20.1 ratio=0.94 3 A.A44 A.U45 angle=100 distance=15.5 ratio=0.76 4 A.U45 A.C46 angle=114 distance=17.8 ratio=0.84 5 A.C51 A.U52 angle=119 distance=16.9 ratio=0.86 6 A.U52 A.A53 angle=115 distance=16.0 ratio=0.84 7 A.A53 A.G54 angle=129 distance=18.6 ratio=0.90 8 A.A64 A.U65 angle=94 distance=14.3 ratio=0.73 9 B.C15 B.G16 angle=167 distance=19.0 ratio=0.99 10 B.A37 B.C38 angle=141 distance=19.7 ratio=0.94 11 B.A44 B.U45 angle=110 distance=16.0 ratio=0.82 12 B.U45 B.C46 angle=109 distance=17.2 ratio=0.81 13 B.C51 B.U52 angle=120 distance=16.8 ratio=0.87 14 B.U52 B.A53 angle=98 distance=14.7 ratio=0.75 15 B.A53 B.G54 angle=127 distance=18.2 ratio=0.90 16 B.A64 B.U65 angle=98 distance=14.7 ratio=0.75 ---------------------------------------------------------------- Summary of 10 splayed-apart units 1 nts=2 CG A.C15,A.G16 2 nts=2 AC A.A37,A.C38 3 nts=3 AUC A.A44,A.U45,A.C46 4 nts=4 CUAG A.C51,A.U52,A.A53,A.G54 5 nts=2 AU A.A64,A.U65 6 nts=2 CG B.C15,B.G16 7 nts=2 AC B.A37,B.C38 8 nts=3 AUC B.A44,B.U45,B.C46 9 nts=4 CUAG B.C51,B.U52,B.A53,B.G54 10 nts=2 AU B.A64,B.U65 **************************************************************************** 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. **************************************************************************** List of 3 H-type pseudoknot loop segments 1 stem#3(hairpin#1) vs stem#4(hairpin#2) L1 groove=MAJOR nts=4 AGGU A.A20,A.G21,A.G22,A.U23 2 stem#3(hairpin#1) vs stem#4(hairpin#2) L2 groove=----- nts=2 UG A.U29,A.G30 3 stem#3(hairpin#1) vs stem#4(hairpin#2) L3 groove=MAJOR nts=11 GUACCUGCAAU A.G35,A.U36,A.A37,A.C38,A.C39,A.U40,A.G41,A.C42,A.A43,A.A44,A.U45 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >4wfm nts=206 [whole] gGCCGUGCUAAGCGGGGAGGUAGCGGUGCCCUGUACCUGCAAUCCGCUCUAGCAGGGCCGAAUCCCUUCUCGAGGUGGUAACAUCGACAGAAGGUGCACGGUc&gGCCGUGCUAAGCGGGGAGGUAGCGGUGCCCUGUACCUGCAAUCCGCUCUAGCAGGGCCGAAUCCCUUCUCGAGGUGGUAACAUCGACAGAAGGUGCACGGUc ((((((((...((((((....[[[[[..))))...(((((...]]]]]...)))))))......((((((...(((......)))...)))))).))))))))&((((((((...((((((....[[[[[[.))))...(((((.].]]]]]...)))))))......((((((...((((....))))...)))))).)))))))) >4wfm-A #1 nts=103 0.07(3.16) [chain] RNA gGCCGUGCUAAGCGGGGAGGUAGCGGUGCCCUGUACCUGCAAUCCGCUCUAGCAGGGCCGAAUCCCUUCUCGAGGUGGUAACAUCGACAGAAGGUGCACGGUc ((((((((...((((((....[[[[[..))))...(((((...]]]]]...)))))))......((((((...(((......)))...)))))).)))))))) >4wfm-B #2 nts=103 0.10(3.16) [chain] RNA gGCCGUGCUAAGCGGGGAGGUAGCGGUGCCCUGUACCUGCAAUCCGCUCUAGCAGGGCCGAAUCCCUUCUCGAGGUGGUAACAUCGACAGAAGGUGCACGGUc ((((((((...((((((....[[[[[[.))))...(((((.].]]]]]...)))))))......((((((...((((....))))...)))))).)))))))) **************************************************************************** Summary of structural features of 206 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 ( A.GTP3 0.073 modified,anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 2 G ( A.G4 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 3 C ( A.C5 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 4 C ( A.C6 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 5 G ( A.G7 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 6 U ( A.U8 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 7 G ( A.G9 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 8 C ( A.C10 0.001 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 9 U . A.U11 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,phosphate 10 A . A.A12 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,junction-loop,phosphate 11 A . A.A13 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 12 G ( A.G14 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 13 C ( A.C15 0.002 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate,splayed-apart 14 G ( A.G16 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 15 G ( A.G17 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 16 G ( A.G18 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 17 G ( A.G19 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop,phosphate 18 A . A.A20 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop,kissing-loop,phosphate 19 G . A.G21 0.001 anti,~C3'-endo,BI,non-canonical,non-pair-contact,hairpin-loop,junction-loop,kissing-loop 20 G . A.G22 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,junction-loop,kissing-loop 21 U . A.U23 0.003 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,junction-loop,kissing-loop,cap-acceptor 22 A [ A.A24 0.005 pseudoknotted,turn,u-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 23 G [ A.G25 0.002 pseudoknotted,u-turn,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop,A-minor,kissing-loop,cap-donor,phosphate 24 C [ A.C26 0.003 pseudoknotted,u-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop,cap-donor,phosphate 25 G [ A.G27 0.009 pseudoknotted,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop,kissing-loop 26 G [ A.G28 0.003 pseudoknotted,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,junction-loop,A-minor,kissing-loop,phosphate 27 U . A.U29 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop,kissing-loop,phosphate 28 G . A.G30 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop,kissing-loop 29 C ) A.C31 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 30 C ) A.C32 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,phosphate 31 C ) A.C33 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 32 U ) A.U34 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop 33 G . A.G35 0.003 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,junction-loop 34 U . A.U36 0.003 anti,~C2'-endo,BII,non-pair-contact,hairpin-loop,junction-loop,cap-donor,phosphate 35 A . A.A37 0.005 ~C2'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,junction-loop,cap-acceptor,splayed-apart 36 C ( A.C38 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,phosphate,splayed-apart 37 C ( A.C39 0.001 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 38 U ( A.U40 0.001 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 39 G ( A.G41 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 40 C ( A.C42 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,hairpin-loop,junction-loop,ribose-zipper,kissing-loop 41 A . A.A43 0.002 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,junction-loop,A-minor,ribose-zipper,kissing-loop 42 A . A.A44 0.003 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop,kissing-loop,splayed-apart 43 U . A.U45 0.004 turn,anti,~C2'-endo,non-stack,hairpin-loop,junction-loop,kissing-loop,splayed-apart 44 C ] A.C46 0.002 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,junction-loop,A-minor,ribose-zipper,kissing-loop,splayed-apart 45 C ] A.C47 0.003 pseudoknotted,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop,ribose-zipper,kissing-loop 46 G ] A.G48 0.003 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,ribose-zipper,kissing-loop 47 C ] A.C49 0.004 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop,A-minor,ribose-zipper,kissing-loop,phosphate 48 U ] A.U50 0.005 pseudoknotted,anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 49 C . A.C51 0.007 turn,syn,~C2'-endo,non-pair-contact,hairpin-loop,junction-loop,kissing-loop,splayed-apart 50 U . A.U52 0.004 turn,anti,~C2'-endo,non-stack,hairpin-loop,junction-loop,kissing-loop,splayed-apart 51 A . A.A53 0.005 anti,~C3'-endo,BII,non-canonical,non-pair-contact,multiplet,hairpin-loop,junction-loop,A-minor,ribose-zipper,kissing-loop,cap-acceptor,phosphate,splayed-apart 52 G ) A.G54 0.005 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,hairpin-loop,junction-loop,ribose-zipper,kissing-loop,phosphate,splayed-apart 53 C ) A.C55 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 54 A ) A.A56 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 55 G ) A.G57 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 56 G ) A.G58 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 57 G ) A.G59 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 58 C ) A.C60 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 59 C . A.C61 0.001 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,phosphate 60 G . A.G62 0.003 anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,junction-loop 61 A . A.A63 0.002 anti,~C2'-endo,non-canonical,non-pair-contact,helix,junction-loop,cap-donor,phosphate 62 A . A.A64 0.002 ~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,cap-acceptor,phosphate,splayed-apart 63 U . A.U65 0.003 turn,anti,~C3'-endo,non-pair-contact,junction-loop,splayed-apart 64 C . A.C66 0.006 syn,~C2'-endo,non-pair-contact,junction-loop,phosphate 65 C ( A.C67 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 66 C ( A.C68 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 67 U ( A.U69 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 68 U ( A.U70 0.001 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 69 C ( A.C71 0.001 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 70 U ( A.U72 0.001 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 71 C . A.C73 0.002 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 72 G . A.G74 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 73 A . A.A75 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 74 G ( A.G76 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 75 G ( A.G77 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 76 U ( A.U78 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 77 G . A.G79 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,phosphate 78 G . A.G80 0.003 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 79 U . A.U81 0.003 turn,u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop 80 A . A.A82 0.010 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-donor,phosphate 81 A . A.A83 0.002 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 82 C . A.C84 0.008 syn,~C3'-endo,non-canonical,non-pair-contact,helix,hairpin-loop 83 A ) A.A85 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 84 U ) A.U86 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 85 C ) A.C87 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 86 G . A.G88 0.007 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 87 A . A.A89 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 88 C . A.C90 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 89 A ) A.A91 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 90 G ) A.G92 0.001 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 91 A ) A.A93 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 92 A ) A.A94 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 93 G ) A.G95 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 94 G ) A.G96 0.001 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 95 U . A.U97 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop 96 G ) A.G98 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 97 C ) A.C99 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 98 A ) A.A100 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 99 C ) A.C101 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 100 G ) A.G102 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 101 G ) A.G103 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 102 U ) A.U104 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 103 c ) A.CCC105 0.026 modified,anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 104 g ( B.GTP3 0.072 modified,anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 105 G ( B.G4 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 106 C ( B.C5 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 107 C ( B.C6 0.001 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 108 G ( B.G7 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 109 U ( B.U8 0.001 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 110 G ( B.G9 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 111 C ( B.C10 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 112 U . B.U11 0.001 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,phosphate 113 A . B.A12 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,junction-loop,phosphate 114 A . B.A13 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 115 G ( B.G14 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 116 C ( B.C15 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate,splayed-apart 117 G ( B.G16 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 118 G ( B.G17 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 119 G ( B.G18 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 120 G ( B.G19 0.001 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop,phosphate 121 A . B.A20 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop,kissing-loop,phosphate 122 G . B.G21 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,hairpin-loop,junction-loop,kissing-loop 123 G . B.G22 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,junction-loop,kissing-loop 124 U . B.U23 0.002 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,junction-loop,kissing-loop,cap-acceptor 125 A [ B.A24 0.002 pseudoknotted,turn,u-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 126 G [ B.G25 0.002 pseudoknotted,u-turn,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop,A-minor,kissing-loop,cap-donor,phosphate 127 C [ B.C26 0.003 pseudoknotted,u-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop,cap-donor,phosphate 128 G [ B.G27 0.005 pseudoknotted,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop,kissing-loop 129 G [ B.G28 0.003 pseudoknotted,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,bulge,A-minor,kissing-loop,phosphate 130 U [ B.U29 0.005 pseudoknotted,anti,~C3'-endo,BI,isolated-canonical,non-canonical,non-pair-contact,helix,hairpin-loop,bulge,junction-loop,kissing-loop,cap-donor,phosphate 131 G . B.G30 0.001 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop,kissing-loop 132 C ) B.C31 0.001 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 133 C ) B.C32 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 134 C ) B.C33 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 135 U ) B.U34 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop 136 G . B.G35 0.003 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,junction-loop 137 U . B.U36 0.003 anti,~C2'-endo,BII,non-pair-contact,hairpin-loop,junction-loop,cap-donor,phosphate 138 A . B.A37 0.007 ~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,junction-loop,cap-acceptor,splayed-apart 139 C ( B.C38 0.001 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,phosphate,splayed-apart 140 C ( B.C39 0.001 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 141 U ( B.U40 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 142 G ( B.G41 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 143 C ( B.C42 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,hairpin-loop,junction-loop,ribose-zipper,kissing-loop 144 A . B.A43 0.004 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,junction-loop,A-minor,ribose-zipper,kissing-loop,cap-acceptor 145 A ] B.A44 0.004 pseudoknotted,turn,syn,~C2'-endo,isolated-canonical,non-pair-contact,helix,hairpin-loop,bulge,junction-loop,kissing-loop,cap-acceptor,splayed-apart 146 U . B.U45 0.001 turn,anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,bulge,kissing-loop,splayed-apart 147 C ] B.C46 0.002 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,bulge,A-minor,ribose-zipper,kissing-loop,cap-donor,splayed-apart 148 C ] B.C47 0.001 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop,ribose-zipper,kissing-loop 149 G ] B.G48 0.007 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,ribose-zipper,kissing-loop 150 C ] B.C49 0.003 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop,A-minor,ribose-zipper,kissing-loop,phosphate 151 U ] B.U50 0.003 pseudoknotted,anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 152 C . B.C51 0.004 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,junction-loop,kissing-loop,cap-donor,phosphate,splayed-apart 153 U . B.U52 0.004 turn,anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,junction-loop,kissing-loop,splayed-apart 154 A . B.A53 0.005 anti,~C3'-endo,BII,non-canonical,non-pair-contact,multiplet,hairpin-loop,junction-loop,A-minor,ribose-zipper,kissing-loop,cap-acceptor,splayed-apart 155 G ) B.G54 0.005 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,hairpin-loop,junction-loop,ribose-zipper,kissing-loop,phosphate,splayed-apart 156 C ) B.C55 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 157 A ) B.A56 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 158 G ) B.G57 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 159 G ) B.G58 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 160 G ) B.G59 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 161 C ) B.C60 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 162 C . B.C61 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,phosphate 163 G . B.G62 0.002 anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,junction-loop 164 A . B.A63 0.004 anti,~C2'-endo,non-canonical,non-pair-contact,helix,junction-loop,cap-donor,phosphate 165 A . B.A64 0.002 ~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,cap-acceptor,phosphate,splayed-apart 166 U . B.U65 0.003 turn,anti,~C3'-endo,non-pair-contact,junction-loop,splayed-apart 167 C . B.C66 0.005 syn,~C2'-endo,non-pair-contact,junction-loop,phosphate 168 C ( B.C67 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 169 C ( B.C68 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 170 U ( B.U69 0.001 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 171 U ( B.U70 0.001 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 172 C ( B.C71 0.001 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 173 U ( B.U72 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 174 C . B.C73 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 175 G . B.G74 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 176 A . B.A75 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 177 G ( B.G76 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 178 G ( B.G77 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 179 U ( B.U78 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 180 G ( B.G79 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 181 G . B.G80 0.002 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 182 U . B.U81 0.002 turn,u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 183 A . B.A82 0.002 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-donor,phosphate 184 A . B.A83 0.002 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 185 C ) B.C84 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 186 A ) B.A85 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 187 U ) B.U86 0.002 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 188 C ) B.C87 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 189 G . B.G88 0.006 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 190 A . B.A89 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 191 C . B.C90 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 192 A ) B.A91 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 193 G ) B.G92 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 194 A ) B.A93 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 195 A ) B.A94 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 196 G ) B.G95 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 197 G ) B.G96 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 198 U . B.U97 0.003 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop 199 G ) B.G98 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 200 C ) B.C99 0.002 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 201 A ) B.A100 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 202 C ) B.C101 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 203 G ) B.G102 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 204 G ) B.G103 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 205 U ) B.U104 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 206 c ) B.CCC105 0.025 modified,anti,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack **************************************************************************** List of 20 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-bulges.pdb -- an ensemble of bulges 7 dssr-iloops.pdb -- an ensemble of internal loops 8 dssr-junctions.pdb -- an ensemble of junctions (multi-branch) 9 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 10 dssr-2ndstrs.ct -- secondary structure in connectivity table format 11 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 12 dssr-torsions.txt -- backbone torsion angles and suite names 13 dssr-splays.pdb -- an ensemble of splayed-apart units 14 dssr-Aminors.pdb -- an ensemble of A minor motifs (types I and II) 15 dssr-stacks.pdb -- an ensemble of base stacks 16 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions 17 dssr-rotmat.txt -- position vector and rotation matrix 18 dssr-viewV.pdb -- vertical view of the principal moment of inertia 19 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 20 dssr-viewT.pdb -- top view of the principal moment of inertia