**************************************************************************** File name: 7vdv.pdb no. of DNA/RNA chains: 2 [I=135,J=137] no. of nucleotides: 273 no. of atoms: 40009 no. of waters: 0 no. of metals: 2 [Be=1,Mg=1] **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 ADP-a 1 A.ADP1703 **************************************************************************** List of 152 base pairs nt1 nt2 bp name Saenger LW DSSR 1 I.DG13 J.DC135 G-C WC 19-XIX cWW cW-W 2 I.DG14 J.DC134 G-C WC 19-XIX cWW cW-W 3 I.DG14 J.DC135 G-C -- -- cWW cW-W 4 I.DT15 J.DA133 T-A WC 20-XX cWW cW-W 5 I.DG16 J.DC132 G-C WC 19-XIX cWW cW-W 6 I.DC17 J.DG131 C-G WC 19-XIX cWW cW-W 7 I.DC18 J.DG130 C-G WC 19-XIX cWW cW-W 8 I.DG19 J.DC129 G-C WC 19-XIX cWW cW-W 9 I.DA20 J.DT128 A-T WC 20-XX cWW cW-W 10 I.DA20 J.DC129 A-C -- -- cWW cW-W 11 I.DG21 J.DC127 G-C WC 19-XIX cWW cW-W 12 I.DG22 J.DC126 G-C WC 19-XIX cWW cW-W 13 I.DG22 J.DC127 G-C -- -- cWW cW-W 14 I.DC23 J.DG125 C-G WC 19-XIX cWW cW-W 15 I.DC24 J.DG124 C-G WC 19-XIX cWW cW-W 16 I.DG25 J.DC123 G-C WC 19-XIX cWW cW-W 17 I.DC26 J.DA121 C-A ~Wobble -- cWW cW-W 18 I.DC26 J.DG122 C-G WC 19-XIX cWW cW-W 19 I.DT27 J.DA121 T-A WC 20-XX cWW cW-W 20 I.DC28 J.DG120 C-G WC 19-XIX cWW cW-W 21 I.DA29 J.DT119 A-T WC 20-XX cWW cW-W 22 I.DA30 J.DA117 A-A -- -- cWW cW-W 23 I.DA30 J.DT118 A-T WC 20-XX cWW cW-W 24 I.DT31 J.DA117 T-A WC 20-XX cWW cW-W 25 I.DT32 J.DA116 T-A WC 20-XX cWW cW-W 26 I.DG33 J.DC115 G-C WC 19-XIX cWW cW-W 27 I.DG34 J.DC114 G-C WC 19-XIX cWW cW-W 28 I.DT35 J.DA113 T-A WC 20-XX cWW cW-W 29 I.DC36 J.DG112 C-G WC 19-XIX cWW cW-W 30 I.DG37 J.DC111 G-C WC 19-XIX cWW cW-W 31 I.DT38 J.DA110 T-A WC 20-XX cWW cW-W 32 I.DA39 J.DT109 A-T WC 20-XX cWW cW-W 33 I.DG40 J.DC108 G-C WC 19-XIX cWW cW-W 34 I.DA41 J.DT107 A-T WC 20-XX cWW cW-W 35 I.DC42 J.DT105 C-T -- -- cWW cW-W 36 I.DC42 J.DG106 C-G WC 19-XIX cWW cW-W 37 I.DA43 J.DT105 A-T WC 20-XX cWW cW-W 38 I.DG44 J.DC104 G-C WC 19-XIX cWW cW-W 39 I.DC45 J.DG103 C-G WC 19-XIX cWW cW-W 40 I.DT46 J.DA102 T-A WC 20-XX cWW cW-W 41 I.DC47 J.DG101 C-G WC 19-XIX cWW cW-W 42 I.DT48 J.DA100 T-A WC 20-XX cWW cW-W 43 I.DA49 J.DT99 A-T WC 20-XX cWW cW-W 44 I.DG50 J.DC98 G-C WC 19-XIX cWW cW-W 45 I.DC51 J.DG97 C-G WC 19-XIX cWW cW-W 46 I.DA52 J.DG95 A-G -- -- cWW cW-W 47 I.DA52 J.DT96 A-T WC 20-XX cWW cW-W 48 I.DC53 J.DG95 C-G WC 19-XIX cWW cW-W 49 I.DC54 J.DG94 C-G WC 19-XIX cWW cW-W 50 I.DG55 J.DC93 G-C WC 19-XIX cWW cW-W 51 I.DC56 J.DG92 C-G WC 19-XIX cWW cW-W 52 I.DT57 J.DA91 T-A WC 20-XX cWW cW-W 53 I.DT57 J.DG92 T-G -- -- cWW cW-W 54 I.DT58 J.DT89 T-T -- -- cWW cW-W 55 I.DT58 J.DA90 T-A WC 20-XX cWW cW-W 56 I.DA59 J.DT88 A-T -- -- cWW cW-W 57 I.DA59 J.DT89 A-T WC 20-XX cWW cW-W 58 I.DA60 J.DT88 A-T WC 20-XX cWW cW-W 59 I.DC62 J.DG86 C-G WC 19-XIX cWW cW-W 60 I.DG63 J.DC85 G-C WC 19-XIX cWW cW-W 61 I.DC64 J.DG84 C-G WC 19-XIX cWW cW-W 62 I.DA65 J.DT83 A-T WC 20-XX cWW cW-W 63 I.DC66 J.DC81 C-C -- -- cWW cW-W 64 I.DC66 J.DG82 C-G WC 19-XIX cWW cW-W 65 I.DG67 J.DC81 G-C WC 19-XIX cWW cW-W 66 I.DT68 J.DA80 T-A WC 20-XX cWW cW-W 67 I.DA69 J.DT79 A-T WC 20-XX cWW cW-W 68 I.DC70 J.DG78 C-G WC 19-XIX cWW cW-W 69 I.DG71 J.DC77 G-C WC 19-XIX cWW cW-W 70 I.DC72 J.DG76 C-G WC 19-XIX cWW cW-W 71 I.DG73 J.DC75 G-C WC 19-XIX cWW cW-W 72 I.DC74 J.DG74 C-G WC 19-XIX cWW cW-W 73 I.DT75 J.DA73 T-A WC 20-XX cWW cW-W 74 I.DG76 J.DC72 G-C WC 19-XIX cWW cW-W 75 I.DT77 J.DA71 T-A WC 20-XX cWW cW-W 76 I.DC78 J.DG70 C-G WC 19-XIX cWW cW-W 77 I.DC79 J.DG69 C-G WC 19-XIX cWW cW-W 78 I.DC80 J.DG68 C-G WC 19-XIX cWW cW-W 79 I.DC81 J.DG66 C-G -- -- cWW cW-W 80 I.DC81 J.DG67 C-G WC 19-XIX cWW cW-W 81 I.DC82 J.DG66 C-G WC 19-XIX cWW cW-W 82 I.DG83 J.DC65 G-C WC 19-XIX cWW cW-W 83 I.DC84 J.DG64 C-G WC 19-XIX cWW cW-W 84 I.DG85 J.DC63 G-C WC 19-XIX cWW cW-W 85 I.DT86 J.DA62 T-A WC 20-XX cWW cW-W 86 I.DT87 J.DA61 T-A WC 20-XX cWW cW-W 87 I.DT88 J.DA60 T-A WC 20-XX cWW cW-W 88 I.DT89 J.DA59 T-A WC 20-XX cWW cW-W 89 I.DA90 J.DT58 A-T WC 20-XX cWW cW-W 90 I.DA91 J.DT57 A-T WC 20-XX cWW cW-W 91 I.DC92 J.DG56 C-G WC 19-XIX cWW cW-W 92 I.DC93 J.DG55 C-G WC 19-XIX cWW cW-W 93 I.DC93 J.DG56 C-G -- -- cWW cW-W 94 I.DG94 J.DC54 G-C WC 19-XIX cWW cW-W 95 I.DC95 J.DG53 C-G WC 19-XIX cWW cW-W 96 I.DC96 J.DG52 C-G WC 19-XIX cWW cW-W 97 I.DA98 J.DT50 A-T -- -- cWW cW-W 98 I.DA98 J.DT51 A-T WC 20-XX cWW cW-W 99 I.DG99 J.DC49 G-C WC 19-XIX cWW cW-W 100 I.DG100 J.DC48 G-C WC 19-XIX cWW cW-W 101 I.DG101 J.DC47 G-C WC 19-XIX cWW cW-W 102 I.DG102 J.DC46 G-C WC 19-XIX cWW cW-W 103 I.DA103 J.DT45 A-T WC 20-XX cWW cW-W 104 I.DT104 J.DA44 T-A WC 20-XX cWW cW-W 105 I.DT105 J.DA43 T-A WC 20-XX cWW cW-W 106 I.DA106 J.DT42 A-T WC 20-XX cWW cW-W 107 I.DC107 J.DG41 C-G WC 19-XIX cWW cW-W 108 I.DT108 J.DA40 T-A WC 20-XX cWW cW-W 109 I.DC109 J.DG38 C-G -- -- cWW cW-W 110 I.DC110 J.DG37 C-G -- -- .WW .W-W 111 I.DC110 J.DG38 C-G WC 19-XIX cWW cW-W 112 I.DC111 J.DA36 C-A ~Wobble -- cWW cW-W 113 I.DC111 J.DG37 C-G WC 19-XIX cWW cW-W 114 I.DT112 J.DT35 T-T -- -- cWW cW-W 115 I.DT112 J.DA36 T-A WC 20-XX cWW cW-W 116 I.DA113 J.DT35 A-T WC 20-XX cWW cW-W 117 I.DG114 J.DA33 G-A -- -- cWW cW-W 118 I.DG114 J.DC34 G-C WC 19-XIX cWW cW-W 119 I.DT115 J.DA33 T-A WC 20-XX cWW cW-W 120 I.DC116 J.DG32 C-G WC 19-XIX cWW cW-W 121 I.DT117 J.DA31 T-A WC 20-XX cWW cW-W 122 I.DC118 J.DG30 C-G WC 19-XIX cWW cW-W 123 I.DC119 J.DG29 C-G WC 19-XIX cWW cW-W 124 I.DC119 J.DG30 C-G -- -- cWW cW-W 125 I.DA120 J.DT28 A-T WC 20-XX cWW cW-W 126 I.DG121 J.DC27 G-C WC 19-XIX cWW cW-W 127 I.DG122 J.DC26 G-C WC 19-XIX cWW cW-W 128 I.DC123 J.DG25 C-G WC 19-XIX cWW cW-W 129 I.DA124 J.DT24 A-T WC 20-XX cWW cW-W 130 I.DC125 J.DG23 C-G WC 19-XIX cWW cW-W 131 I.DG126 J.DC22 G-C WC 19-XIX cWW cW-W 132 I.DT127 J.DA21 T-A WC 20-XX cWW cW-W 133 I.DG128 J.DC20 G-C WC 19-XIX cWW cW-W 134 I.DT129 J.DA19 T-A WC 20-XX cWW cW-W 135 I.DC130 J.DG18 C-G WC 19-XIX cWW cW-W 136 I.DA131 J.DT17 A-T WC 20-XX cWW cW-W 137 I.DG132 J.DC16 G-C WC 19-XIX cWW cW-W 138 I.DA133 J.DT15 A-T WC 20-XX cWW cW-W 139 I.DT134 J.DA14 T-A WC 20-XX cWW cW-W 140 I.DA135 J.DT13 A-T WC 20-XX cWW cW-W 141 I.DT136 J.DA12 T-A WC 20-XX cWW cW-W 142 I.DA137 J.DT11 A-T WC 20-XX cWW cW-W 143 I.DT138 J.DA10 T-A WC 20-XX cWW cW-W 144 I.DA139 J.DT9 A-T WC 20-XX cWW cW-W 145 I.DC140 J.DG8 C-G WC 19-XIX cWW cW-W 146 I.DA141 J.DT7 A-T WC 20-XX cWW cW-W 147 I.DT142 J.DA6 T-A WC 20-XX cWW cW-W 148 I.DC143 J.DG5 C-G WC 19-XIX cWW cW-W 149 I.DC144 J.DG4 C-G WC 19-XIX cWW cW-W 150 I.DT145 J.DA3 T-A WC 20-XX cWW cW-W 151 I.DG146 J.DC2 G-C WC 19-XIX cWW cW-W 152 I.DA147 J.DT1 A-T WC 20-XX cWW cW-W **************************************************************************** List of 1 helix 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[4] bps=132 strand-1 5'-GGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAGGGGATTACTCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGA-3' bp-type |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| strand-2 3'-CCACGGCTCCGGCGAGTTAACCAGCATCTGTCGAGATCGTGGCGAATTGCGTGCATGCGCGACAGGGGGCGCAAAATTGGCGGTCCCCTAATGAGGATCAGAGGTCCGTGCACAGTCTATATATGTAGGACT-5' helix-form .BBB.........B..B...B..BB...BBBBBBB.B...BB.B...x.BB..B.B..BB...BB..BBB...BB.B.....xx..BB..BBBx.....BB.....................BBB.BB... 1 I.DG13 J.DC135 G-C WC 19-XIX cWW cW-W 2 I.DG14 J.DC134 G-C WC 19-XIX cWW cW-W 3 I.DT15 J.DA133 T-A WC 20-XX cWW cW-W 4 I.DG16 J.DC132 G-C WC 19-XIX cWW cW-W 5 I.DC17 J.DG131 C-G WC 19-XIX cWW cW-W 6 I.DC18 J.DG130 C-G WC 19-XIX cWW cW-W 7 I.DG19 J.DC129 G-C WC 19-XIX cWW cW-W 8 I.DA20 J.DT128 A-T WC 20-XX cWW cW-W 9 I.DG21 J.DC127 G-C WC 19-XIX cWW cW-W 10 I.DG22 J.DC126 G-C WC 19-XIX cWW cW-W 11 I.DC23 J.DG125 C-G WC 19-XIX cWW cW-W 12 I.DC24 J.DG124 C-G WC 19-XIX cWW cW-W 13 I.DG25 J.DC123 G-C WC 19-XIX cWW cW-W 14 I.DC26 J.DG122 C-G WC 19-XIX cWW cW-W 15 I.DT27 J.DA121 T-A WC 20-XX cWW cW-W 16 I.DC28 J.DG120 C-G WC 19-XIX cWW cW-W 17 I.DA29 J.DT119 A-T WC 20-XX cWW cW-W 18 I.DA30 J.DT118 A-T WC 20-XX cWW cW-W 19 I.DT31 J.DA117 T-A WC 20-XX cWW cW-W 20 I.DT32 J.DA116 T-A WC 20-XX cWW cW-W 21 I.DG33 J.DC115 G-C WC 19-XIX cWW cW-W 22 I.DG34 J.DC114 G-C WC 19-XIX cWW cW-W 23 I.DT35 J.DA113 T-A WC 20-XX cWW cW-W 24 I.DC36 J.DG112 C-G WC 19-XIX cWW cW-W 25 I.DG37 J.DC111 G-C WC 19-XIX cWW cW-W 26 I.DT38 J.DA110 T-A WC 20-XX cWW cW-W 27 I.DA39 J.DT109 A-T WC 20-XX cWW cW-W 28 I.DG40 J.DC108 G-C WC 19-XIX cWW cW-W 29 I.DA41 J.DT107 A-T WC 20-XX cWW cW-W 30 I.DC42 J.DG106 C-G WC 19-XIX cWW cW-W 31 I.DA43 J.DT105 A-T WC 20-XX cWW cW-W 32 I.DG44 J.DC104 G-C WC 19-XIX cWW cW-W 33 I.DC45 J.DG103 C-G WC 19-XIX cWW cW-W 34 I.DT46 J.DA102 T-A WC 20-XX cWW cW-W 35 I.DC47 J.DG101 C-G WC 19-XIX cWW cW-W 36 I.DT48 J.DA100 T-A WC 20-XX cWW cW-W 37 I.DA49 J.DT99 A-T WC 20-XX cWW cW-W 38 I.DG50 J.DC98 G-C WC 19-XIX cWW cW-W 39 I.DC51 J.DG97 C-G WC 19-XIX cWW cW-W 40 I.DA52 J.DT96 A-T WC 20-XX cWW cW-W 41 I.DC53 J.DG95 C-G WC 19-XIX cWW cW-W 42 I.DC54 J.DG94 C-G WC 19-XIX cWW cW-W 43 I.DG55 J.DC93 G-C WC 19-XIX cWW cW-W 44 I.DC56 J.DG92 C-G WC 19-XIX cWW cW-W 45 I.DT57 J.DA91 T-A WC 20-XX cWW cW-W 46 I.DT58 J.DA90 T-A WC 20-XX cWW cW-W 47 I.DA59 J.DT89 A-T WC 20-XX cWW cW-W 48 I.DA60 J.DT88 A-T WC 20-XX cWW cW-W 49 I.DC62 J.DG86 C-G WC 19-XIX cWW cW-W 50 I.DG63 J.DC85 G-C WC 19-XIX cWW cW-W 51 I.DC64 J.DG84 C-G WC 19-XIX cWW cW-W 52 I.DA65 J.DT83 A-T WC 20-XX cWW cW-W 53 I.DC66 J.DG82 C-G WC 19-XIX cWW cW-W 54 I.DG67 J.DC81 G-C WC 19-XIX cWW cW-W 55 I.DT68 J.DA80 T-A WC 20-XX cWW cW-W 56 I.DA69 J.DT79 A-T WC 20-XX cWW cW-W 57 I.DC70 J.DG78 C-G WC 19-XIX cWW cW-W 58 I.DG71 J.DC77 G-C WC 19-XIX cWW cW-W 59 I.DC72 J.DG76 C-G WC 19-XIX cWW cW-W 60 I.DG73 J.DC75 G-C WC 19-XIX cWW cW-W 61 I.DC74 J.DG74 C-G WC 19-XIX cWW cW-W 62 I.DT75 J.DA73 T-A WC 20-XX cWW cW-W 63 I.DG76 J.DC72 G-C WC 19-XIX cWW cW-W 64 I.DT77 J.DA71 T-A WC 20-XX cWW cW-W 65 I.DC78 J.DG70 C-G WC 19-XIX cWW cW-W 66 I.DC79 J.DG69 C-G WC 19-XIX cWW cW-W 67 I.DC80 J.DG68 C-G WC 19-XIX cWW cW-W 68 I.DC81 J.DG67 C-G WC 19-XIX cWW cW-W 69 I.DC82 J.DG66 C-G WC 19-XIX cWW cW-W 70 I.DG83 J.DC65 G-C WC 19-XIX cWW cW-W 71 I.DC84 J.DG64 C-G WC 19-XIX cWW cW-W 72 I.DG85 J.DC63 G-C WC 19-XIX cWW cW-W 73 I.DT86 J.DA62 T-A WC 20-XX cWW cW-W 74 I.DT87 J.DA61 T-A WC 20-XX cWW cW-W 75 I.DT88 J.DA60 T-A WC 20-XX cWW cW-W 76 I.DT89 J.DA59 T-A WC 20-XX cWW cW-W 77 I.DA90 J.DT58 A-T WC 20-XX cWW cW-W 78 I.DA91 J.DT57 A-T WC 20-XX cWW cW-W 79 I.DC92 J.DG56 C-G WC 19-XIX cWW cW-W 80 I.DC93 J.DG55 C-G WC 19-XIX cWW cW-W 81 I.DG94 J.DC54 G-C WC 19-XIX cWW cW-W 82 I.DC95 J.DG53 C-G WC 19-XIX cWW cW-W 83 I.DC96 J.DG52 C-G WC 19-XIX cWW cW-W 84 I.DA98 J.DT51 A-T WC 20-XX cWW cW-W 85 I.DG99 J.DC49 G-C WC 19-XIX cWW cW-W 86 I.DG100 J.DC48 G-C WC 19-XIX cWW cW-W 87 I.DG101 J.DC47 G-C WC 19-XIX cWW cW-W 88 I.DG102 J.DC46 G-C WC 19-XIX cWW cW-W 89 I.DA103 J.DT45 A-T WC 20-XX cWW cW-W 90 I.DT104 J.DA44 T-A WC 20-XX cWW cW-W 91 I.DT105 J.DA43 T-A WC 20-XX cWW cW-W 92 I.DA106 J.DT42 A-T WC 20-XX cWW cW-W 93 I.DC107 J.DG41 C-G WC 19-XIX cWW cW-W 94 I.DT108 J.DA40 T-A WC 20-XX cWW cW-W 95 I.DC110 J.DG38 C-G WC 19-XIX cWW cW-W 96 I.DC111 J.DG37 C-G WC 19-XIX cWW cW-W 97 I.DT112 J.DA36 T-A WC 20-XX cWW cW-W 98 I.DA113 J.DT35 A-T WC 20-XX cWW cW-W 99 I.DG114 J.DC34 G-C WC 19-XIX cWW cW-W 100 I.DT115 J.DA33 T-A WC 20-XX cWW cW-W 101 I.DC116 J.DG32 C-G WC 19-XIX cWW cW-W 102 I.DT117 J.DA31 T-A WC 20-XX cWW cW-W 103 I.DC118 J.DG30 C-G WC 19-XIX cWW cW-W 104 I.DC119 J.DG29 C-G WC 19-XIX cWW cW-W 105 I.DA120 J.DT28 A-T WC 20-XX cWW cW-W 106 I.DG121 J.DC27 G-C WC 19-XIX cWW cW-W 107 I.DG122 J.DC26 G-C WC 19-XIX cWW cW-W 108 I.DC123 J.DG25 C-G WC 19-XIX cWW cW-W 109 I.DA124 J.DT24 A-T WC 20-XX cWW cW-W 110 I.DC125 J.DG23 C-G WC 19-XIX cWW cW-W 111 I.DG126 J.DC22 G-C WC 19-XIX cWW cW-W 112 I.DT127 J.DA21 T-A WC 20-XX cWW cW-W 113 I.DG128 J.DC20 G-C WC 19-XIX cWW cW-W 114 I.DT129 J.DA19 T-A WC 20-XX cWW cW-W 115 I.DC130 J.DG18 C-G WC 19-XIX cWW cW-W 116 I.DA131 J.DT17 A-T WC 20-XX cWW cW-W 117 I.DG132 J.DC16 G-C WC 19-XIX cWW cW-W 118 I.DA133 J.DT15 A-T WC 20-XX cWW cW-W 119 I.DT134 J.DA14 T-A WC 20-XX cWW cW-W 120 I.DA135 J.DT13 A-T WC 20-XX cWW cW-W 121 I.DT136 J.DA12 T-A WC 20-XX cWW cW-W 122 I.DA137 J.DT11 A-T WC 20-XX cWW cW-W 123 I.DT138 J.DA10 T-A WC 20-XX cWW cW-W 124 I.DA139 J.DT9 A-T WC 20-XX cWW cW-W 125 I.DC140 J.DG8 C-G WC 19-XIX cWW cW-W 126 I.DA141 J.DT7 A-T WC 20-XX cWW cW-W 127 I.DT142 J.DA6 T-A WC 20-XX cWW cW-W 128 I.DC143 J.DG5 C-G WC 19-XIX cWW cW-W 129 I.DC144 J.DG4 C-G WC 19-XIX cWW cW-W 130 I.DT145 J.DA3 T-A WC 20-XX cWW cW-W 131 I.DG146 J.DC2 G-C WC 19-XIX cWW cW-W 132 I.DA147 J.DT1 A-T WC 20-XX cWW cW-W **************************************************************************** List of 4 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=48 strand-1 5'-GGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA-3' bp-type |||||||||||||||||||||||||||||||||||||||||||||||| strand-2 3'-CCACGGCTCCGGCGAGTTAACCAGCATCTGTCGAGATCGTGGCGAATT-5' helix-form .BBB.........B..B...B..BB...BBBBBBB.B...BB.B... 1 I.DG13 J.DC135 G-C WC 19-XIX cWW cW-W 2 I.DG14 J.DC134 G-C WC 19-XIX cWW cW-W 3 I.DT15 J.DA133 T-A WC 20-XX cWW cW-W 4 I.DG16 J.DC132 G-C WC 19-XIX cWW cW-W 5 I.DC17 J.DG131 C-G WC 19-XIX cWW cW-W 6 I.DC18 J.DG130 C-G WC 19-XIX cWW cW-W 7 I.DG19 J.DC129 G-C WC 19-XIX cWW cW-W 8 I.DA20 J.DT128 A-T WC 20-XX cWW cW-W 9 I.DG21 J.DC127 G-C WC 19-XIX cWW cW-W 10 I.DG22 J.DC126 G-C WC 19-XIX cWW cW-W 11 I.DC23 J.DG125 C-G WC 19-XIX cWW cW-W 12 I.DC24 J.DG124 C-G WC 19-XIX cWW cW-W 13 I.DG25 J.DC123 G-C WC 19-XIX cWW cW-W 14 I.DC26 J.DG122 C-G WC 19-XIX cWW cW-W 15 I.DT27 J.DA121 T-A WC 20-XX cWW cW-W 16 I.DC28 J.DG120 C-G WC 19-XIX cWW cW-W 17 I.DA29 J.DT119 A-T WC 20-XX cWW cW-W 18 I.DA30 J.DT118 A-T WC 20-XX cWW cW-W 19 I.DT31 J.DA117 T-A WC 20-XX cWW cW-W 20 I.DT32 J.DA116 T-A WC 20-XX cWW cW-W 21 I.DG33 J.DC115 G-C WC 19-XIX cWW cW-W 22 I.DG34 J.DC114 G-C WC 19-XIX cWW cW-W 23 I.DT35 J.DA113 T-A WC 20-XX cWW cW-W 24 I.DC36 J.DG112 C-G WC 19-XIX cWW cW-W 25 I.DG37 J.DC111 G-C WC 19-XIX cWW cW-W 26 I.DT38 J.DA110 T-A WC 20-XX cWW cW-W 27 I.DA39 J.DT109 A-T WC 20-XX cWW cW-W 28 I.DG40 J.DC108 G-C WC 19-XIX cWW cW-W 29 I.DA41 J.DT107 A-T WC 20-XX cWW cW-W 30 I.DC42 J.DG106 C-G WC 19-XIX cWW cW-W 31 I.DA43 J.DT105 A-T WC 20-XX cWW cW-W 32 I.DG44 J.DC104 G-C WC 19-XIX cWW cW-W 33 I.DC45 J.DG103 C-G WC 19-XIX cWW cW-W 34 I.DT46 J.DA102 T-A WC 20-XX cWW cW-W 35 I.DC47 J.DG101 C-G WC 19-XIX cWW cW-W 36 I.DT48 J.DA100 T-A WC 20-XX cWW cW-W 37 I.DA49 J.DT99 A-T WC 20-XX cWW cW-W 38 I.DG50 J.DC98 G-C WC 19-XIX cWW cW-W 39 I.DC51 J.DG97 C-G WC 19-XIX cWW cW-W 40 I.DA52 J.DT96 A-T WC 20-XX cWW cW-W 41 I.DC53 J.DG95 C-G WC 19-XIX cWW cW-W 42 I.DC54 J.DG94 C-G WC 19-XIX cWW cW-W 43 I.DG55 J.DC93 G-C WC 19-XIX cWW cW-W 44 I.DC56 J.DG92 C-G WC 19-XIX cWW cW-W 45 I.DT57 J.DA91 T-A WC 20-XX cWW cW-W 46 I.DT58 J.DA90 T-A WC 20-XX cWW cW-W 47 I.DA59 J.DT89 A-T WC 20-XX cWW cW-W 48 I.DA60 J.DT88 A-T WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=35 strand-1 5'-CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCC-3' bp-type ||||||||||||||||||||||||||||||||||| strand-2 3'-GCGTGCATGCGCGACAGGGGGCGCAAAATTGGCGG-5' helix-form .BB..B.B..BB...BB..BBB...BB.B..... 1 I.DC62 J.DG86 C-G WC 19-XIX cWW cW-W 2 I.DG63 J.DC85 G-C WC 19-XIX cWW cW-W 3 I.DC64 J.DG84 C-G WC 19-XIX cWW cW-W 4 I.DA65 J.DT83 A-T WC 20-XX cWW cW-W 5 I.DC66 J.DG82 C-G WC 19-XIX cWW cW-W 6 I.DG67 J.DC81 G-C WC 19-XIX cWW cW-W 7 I.DT68 J.DA80 T-A WC 20-XX cWW cW-W 8 I.DA69 J.DT79 A-T WC 20-XX cWW cW-W 9 I.DC70 J.DG78 C-G WC 19-XIX cWW cW-W 10 I.DG71 J.DC77 G-C WC 19-XIX cWW cW-W 11 I.DC72 J.DG76 C-G WC 19-XIX cWW cW-W 12 I.DG73 J.DC75 G-C WC 19-XIX cWW cW-W 13 I.DC74 J.DG74 C-G WC 19-XIX cWW cW-W 14 I.DT75 J.DA73 T-A WC 20-XX cWW cW-W 15 I.DG76 J.DC72 G-C WC 19-XIX cWW cW-W 16 I.DT77 J.DA71 T-A WC 20-XX cWW cW-W 17 I.DC78 J.DG70 C-G WC 19-XIX cWW cW-W 18 I.DC79 J.DG69 C-G WC 19-XIX cWW cW-W 19 I.DC80 J.DG68 C-G WC 19-XIX cWW cW-W 20 I.DC81 J.DG67 C-G WC 19-XIX cWW cW-W 21 I.DC82 J.DG66 C-G WC 19-XIX cWW cW-W 22 I.DG83 J.DC65 G-C WC 19-XIX cWW cW-W 23 I.DC84 J.DG64 C-G WC 19-XIX cWW cW-W 24 I.DG85 J.DC63 G-C WC 19-XIX cWW cW-W 25 I.DT86 J.DA62 T-A WC 20-XX cWW cW-W 26 I.DT87 J.DA61 T-A WC 20-XX cWW cW-W 27 I.DT88 J.DA60 T-A WC 20-XX cWW cW-W 28 I.DT89 J.DA59 T-A WC 20-XX cWW cW-W 29 I.DA90 J.DT58 A-T WC 20-XX cWW cW-W 30 I.DA91 J.DT57 A-T WC 20-XX cWW cW-W 31 I.DC92 J.DG56 C-G WC 19-XIX cWW cW-W 32 I.DC93 J.DG55 C-G WC 19-XIX cWW cW-W 33 I.DG94 J.DC54 G-C WC 19-XIX cWW cW-W 34 I.DC95 J.DG53 C-G WC 19-XIX cWW cW-W 35 I.DC96 J.DG52 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#3[#1] bps=10 strand-1 5'-GGGGATTACT-3' bp-type |||||||||| strand-2 3'-CCCCTAATGA-5' helix-form ..BB..BBB 1 I.DG99 J.DC49 G-C WC 19-XIX cWW cW-W 2 I.DG100 J.DC48 G-C WC 19-XIX cWW cW-W 3 I.DG101 J.DC47 G-C WC 19-XIX cWW cW-W 4 I.DG102 J.DC46 G-C WC 19-XIX cWW cW-W 5 I.DA103 J.DT45 A-T WC 20-XX cWW cW-W 6 I.DT104 J.DA44 T-A WC 20-XX cWW cW-W 7 I.DT105 J.DA43 T-A WC 20-XX cWW cW-W 8 I.DA106 J.DT42 A-T WC 20-XX cWW cW-W 9 I.DC107 J.DG41 C-G WC 19-XIX cWW cW-W 10 I.DT108 J.DA40 T-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#4[#1] bps=38 strand-1 5'-CCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGA-3' bp-type |||||||||||||||||||||||||||||||||||||| strand-2 3'-GGATCAGAGGTCCGTGCACAGTCTATATATGTAGGACT-5' helix-form .....BB.....................BBB.BB... 1 I.DC110 J.DG38 C-G WC 19-XIX cWW cW-W 2 I.DC111 J.DG37 C-G WC 19-XIX cWW cW-W 3 I.DT112 J.DA36 T-A WC 20-XX cWW cW-W 4 I.DA113 J.DT35 A-T WC 20-XX cWW cW-W 5 I.DG114 J.DC34 G-C WC 19-XIX cWW cW-W 6 I.DT115 J.DA33 T-A WC 20-XX cWW cW-W 7 I.DC116 J.DG32 C-G WC 19-XIX cWW cW-W 8 I.DT117 J.DA31 T-A WC 20-XX cWW cW-W 9 I.DC118 J.DG30 C-G WC 19-XIX cWW cW-W 10 I.DC119 J.DG29 C-G WC 19-XIX cWW cW-W 11 I.DA120 J.DT28 A-T WC 20-XX cWW cW-W 12 I.DG121 J.DC27 G-C WC 19-XIX cWW cW-W 13 I.DG122 J.DC26 G-C WC 19-XIX cWW cW-W 14 I.DC123 J.DG25 C-G WC 19-XIX cWW cW-W 15 I.DA124 J.DT24 A-T WC 20-XX cWW cW-W 16 I.DC125 J.DG23 C-G WC 19-XIX cWW cW-W 17 I.DG126 J.DC22 G-C WC 19-XIX cWW cW-W 18 I.DT127 J.DA21 T-A WC 20-XX cWW cW-W 19 I.DG128 J.DC20 G-C WC 19-XIX cWW cW-W 20 I.DT129 J.DA19 T-A WC 20-XX cWW cW-W 21 I.DC130 J.DG18 C-G WC 19-XIX cWW cW-W 22 I.DA131 J.DT17 A-T WC 20-XX cWW cW-W 23 I.DG132 J.DC16 G-C WC 19-XIX cWW cW-W 24 I.DA133 J.DT15 A-T WC 20-XX cWW cW-W 25 I.DT134 J.DA14 T-A WC 20-XX cWW cW-W 26 I.DA135 J.DT13 A-T WC 20-XX cWW cW-W 27 I.DT136 J.DA12 T-A WC 20-XX cWW cW-W 28 I.DA137 J.DT11 A-T WC 20-XX cWW cW-W 29 I.DT138 J.DA10 T-A WC 20-XX cWW cW-W 30 I.DA139 J.DT9 A-T WC 20-XX cWW cW-W 31 I.DC140 J.DG8 C-G WC 19-XIX cWW cW-W 32 I.DA141 J.DT7 A-T WC 20-XX cWW cW-W 33 I.DT142 J.DA6 T-A WC 20-XX cWW cW-W 34 I.DC143 J.DG5 C-G WC 19-XIX cWW cW-W 35 I.DC144 J.DG4 C-G WC 19-XIX cWW cW-W 36 I.DT145 J.DA3 T-A WC 20-XX cWW cW-W 37 I.DG146 J.DC2 G-C WC 19-XIX cWW cW-W 38 I.DA147 J.DT1 A-T WC 20-XX 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. -------------------------------------------------------------------- [#1] -1 I.DA98 J.DT51 A-T WC 20-XX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#1 contains 4 stems: [#1,#2,#3,#4] **************************************************************************** List of 7 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 GG I.DG13,J.DG136 2 nts=3 AAC I.DA60,I.DA61,I.DC62 3 nts=3 TCC I.DT108,I.DC109,I.DC110 4 nts=3 GGA J.DG38,J.DG39,J.DA40 5 nts=3 GTT J.DG86,J.DT87,J.DT88 6 nts=4 CAAG I.DC96,I.DA97,I.DA98,I.DG99 7 nts=4 CTTG J.DC49,J.DT50,J.DT51,J.DG52 **************************************************************************** Nucleotides not involved in stacking interactions nts=2 Ga J.DG137,A.ADP1703 **************************************************************************** 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 2 bulges 1 bulge: nts=5; [1,0]; linked by [#2,#-1] summary: [2] 1 0 [I.96 J.52 I.98 J.51] 35 1 nts=5 CAATG I.DC96,I.DA97,I.DA98,J.DT51,J.DG52 nts=1 A I.DA97 nts=0 2 bulge: nts=5; [0,1]; linked by [#-1,#3] summary: [2] 0 1 [I.98 J.51 I.99 J.49] 1 10 nts=5 AGCTT I.DA98,I.DG99,J.DC49,J.DT50,J.DT51 nts=0 nts=1 T J.DT50 **************************************************************************** List of 2 internal loops 1 symmetric internal loop: nts=6; [1,1]; linked by [#1,#2] summary: [2] 1 1 [I.60 J.88 I.62 J.86] 48 35 nts=6 AACGTT I.DA60,I.DA61,I.DC62,J.DG86,J.DT87,J.DT88 nts=1 A I.DA61 nts=1 T J.DT87 2 symmetric internal loop: nts=6; [1,1]; linked by [#3,#4] summary: [2] 1 1 [I.108 J.40 I.110 J.38] 10 38 nts=6 TCCGGA I.DT108,I.DC109,I.DC110,J.DG38,J.DG39,J.DA40 nts=1 C I.DC109 nts=1 G J.DG39 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=2 GG J.DG136,J.DG137 2 nts=1 a A.ADP1703 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >7vdv nts=273 [whole] GGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGA&TCAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGG&a ((((((((((((((((((((((((((((((((((((((((((((((((.(((((((((((((((((((((((((((((((((((.(((((((((((.((((((((((((((((((((((((((((((((((((((&)))))))))))))))))))))))))))))))))))))).)))))))))).)))))))))))))))))))))))))))))))))))).))))))))))))))))))))))))))))))))))))))))))))))))..&. >7vdv-I #1 nts=135 0.37(2.23) [chain] DNA GGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGA ((((((((((((((((((((((((((((((((((((((((((((((((.(((((((((((((((((((((((((((((((((((.(((((((((((.(((((((((((((((((((((((((((((((((((((( >7vdv-J #2 nts=137 0.35(2.24) [chain] DNA TCAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGG )))))))))))))))))))))))))))))))))))))).)))))))))).)))))))))))))))))))))))))))))))))))).)))))))))))))))))))))))))))))))))))))))))))))))).. **************************************************************************** Summary of structural features of 273 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 ( I.DG13 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 2 G ( I.DG14 0.006 anti,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 3 T ( I.DT15 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 4 G ( I.DG16 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 5 C ( I.DC17 0.007 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 6 C ( I.DC18 0.006 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 7 G ( I.DG19 0.007 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 8 A ( I.DA20 0.007 anti,~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 9 G ( I.DG21 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 10 G ( I.DG22 0.006 anti,~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 11 C ( I.DC23 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 12 C ( I.DC24 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 13 G ( I.DG25 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 14 C ( I.DC26 0.010 anti,~C2'-endo,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 15 T ( I.DT27 0.012 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 16 C ( I.DC28 0.011 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 17 A ( I.DA29 0.014 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 18 A ( I.DA30 0.015 anti,~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 19 T ( I.DT31 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 20 T ( I.DT32 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 21 G ( I.DG33 0.013 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 22 G ( I.DG34 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 23 T ( I.DT35 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 24 C ( I.DC36 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 25 G ( I.DG37 0.018 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 26 T ( I.DT38 0.017 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 27 A ( I.DA39 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 28 G ( I.DG40 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 29 A ( I.DA41 0.020 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 30 C ( I.DC42 0.012 anti,~C2'-endo,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 31 A ( I.DA43 0.015 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 32 G ( I.DG44 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 33 C ( I.DC45 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 34 T ( I.DT46 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 35 C ( I.DC47 0.013 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 36 T ( I.DT48 0.012 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 37 A ( I.DA49 0.013 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 38 G ( I.DG50 0.023 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 39 C ( I.DC51 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 40 A ( I.DA52 0.018 anti,~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 41 C ( I.DC53 0.015 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 42 C ( I.DC54 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 43 G ( I.DG55 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 44 C ( I.DC56 0.010 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 45 T ( I.DT57 0.014 anti,~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 46 T ( I.DT58 0.016 anti,~C2'-endo,BII,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 47 A ( I.DA59 0.018 anti,~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 48 A ( I.DA60 0.017 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 49 A . I.DA61 0.020 anti,~C2'-endo,BI,non-pair-contact,internal-loop,phosphate 50 C ( I.DC62 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 51 G ( I.DG63 0.013 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 52 C ( I.DC64 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 53 A ( I.DA65 0.013 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 54 C ( I.DC66 0.011 anti,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 55 G ( I.DG67 0.016 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 56 T ( I.DT68 0.018 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 57 A ( I.DA69 0.018 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 58 C ( I.DC70 0.017 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 59 G ( I.DG71 0.019 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 60 C ( I.DC72 0.016 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 61 G ( I.DG73 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 62 C ( I.DC74 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 63 T ( I.DT75 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 64 G ( I.DG76 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 65 T ( I.DT77 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 66 C ( I.DC78 0.019 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 67 C ( I.DC79 0.013 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 68 C ( I.DC80 0.014 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 69 C ( I.DC81 0.013 anti,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 70 C ( I.DC82 0.016 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 71 G ( I.DG83 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 72 C ( I.DC84 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 73 G ( I.DG85 0.012 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 74 T ( I.DT86 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 75 T ( I.DT87 0.018 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 76 T ( I.DT88 0.022 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 77 T ( I.DT89 0.018 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 78 A ( I.DA90 0.023 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 79 A ( I.DA91 0.026 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 80 C ( I.DC92 0.016 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 81 C ( I.DC93 0.019 ~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 82 G ( I.DG94 0.021 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 83 C ( I.DC95 0.017 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 84 C ( I.DC96 0.019 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 85 A . I.DA97 0.020 anti,~C2'-endo,BI,non-pair-contact,bulge,phosphate 86 A ( I.DA98 0.023 anti,~C2'-endo,BI,isolated-canonical,non-canonical,non-pair-contact,helix,bulge,phosphate 87 G ( I.DG99 0.026 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 88 G ( I.DG100 0.024 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 89 G ( I.DG101 0.021 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 90 G ( I.DG102 0.025 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 91 A ( I.DA103 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 92 T ( I.DT104 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 93 T ( I.DT105 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 94 A ( I.DA106 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 95 C ( I.DC107 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 96 T ( I.DT108 0.015 ~C2'-endo,BII,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 97 C . I.DC109 0.016 anti,~C2'-endo,BII,non-canonical,non-pair-contact,internal-loop 98 C ( I.DC110 0.015 anti,~C2'-endo,BII,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 99 C ( I.DC111 0.013 anti,~C2'-endo,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 100 T ( I.DT112 0.015 anti,~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 101 A ( I.DA113 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 102 G ( I.DG114 0.013 anti,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 103 T ( I.DT115 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 104 C ( I.DC116 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 105 T ( I.DT117 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 106 C ( I.DC118 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 107 C ( I.DC119 0.009 ~C2'-endo,BII,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 108 A ( I.DA120 0.016 ~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 109 G ( I.DG121 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 110 G ( I.DG122 0.014 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 111 C ( I.DC123 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 112 A ( I.DA124 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 113 C ( I.DC125 0.010 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 114 G ( I.DG126 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 115 T ( I.DT127 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 116 G ( I.DG128 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 117 T ( I.DT129 0.009 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 118 C ( I.DC130 0.011 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 119 A ( I.DA131 0.011 BI,canonical,non-pair-contact,helix,stem,coaxial-stack 120 G ( I.DG132 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 121 A ( I.DA133 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 122 T ( I.DT134 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 123 A ( I.DA135 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 124 T ( I.DT136 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 125 A ( I.DA137 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 126 T ( I.DT138 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 127 A ( I.DA139 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 128 C ( I.DC140 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 129 A ( I.DA141 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 130 T ( I.DT142 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 131 C ( I.DC143 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 132 C ( I.DC144 0.004 BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 133 T ( I.DT145 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 134 G ( I.DG146 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 135 A ( I.DA147 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 136 T ) J.DT1 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 137 C ) J.DC2 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 138 A ) J.DA3 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 139 G ) J.DG4 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 140 G ) J.DG5 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 141 A ) J.DA6 0.005 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 142 T ) J.DT7 0.005 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 143 G ) J.DG8 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 144 T ) J.DT9 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 145 A ) J.DA10 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 146 T ) J.DT11 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 147 A ) J.DA12 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 148 T ) J.DT13 0.009 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 149 A ) J.DA14 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 150 T ) J.DT15 0.006 anti,canonical,non-pair-contact,helix,stem,coaxial-stack 151 C ) J.DC16 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 152 T ) J.DT17 0.010 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 153 G ) J.DG18 0.010 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 154 A ) J.DA19 0.010 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 155 C ) J.DC20 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 156 A ) J.DA21 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 157 C ) J.DC22 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 158 G ) J.DG23 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 159 T ) J.DT24 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 160 G ) J.DG25 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 161 C ) J.DC26 0.010 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 162 C ) J.DC27 0.009 ~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 163 T ) J.DT28 0.013 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 164 G ) J.DG29 0.014 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 165 G ) J.DG30 0.016 anti,~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 166 A ) J.DA31 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 167 G ) J.DG32 0.011 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 168 A ) J.DA33 0.016 anti,~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 169 C ) J.DC34 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 170 T ) J.DT35 0.014 anti,~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 171 A ) J.DA36 0.019 anti,~C2'-endo,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 172 G ) J.DG37 0.019 anti,~C2'-endo,BII,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 173 G ) J.DG38 0.018 anti,~C2'-endo,BII,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 174 G . J.DG39 0.022 anti,~C2'-endo,BI,non-pair-contact,internal-loop 175 A ) J.DA40 0.018 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 176 G ) J.DG41 0.020 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 177 T ) J.DT42 0.016 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 178 A ) J.DA43 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 179 A ) J.DA44 0.017 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 180 T ) J.DT45 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 181 C ) J.DC46 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 182 C ) J.DC47 0.020 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 183 C ) J.DC48 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 184 C ) J.DC49 0.019 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 185 T . J.DT50 0.018 anti,~C2'-endo,BI,non-canonical,non-pair-contact,bulge,phosphate 186 T ) J.DT51 0.021 ~C2'-endo,BI,isolated-canonical,non-pair-contact,helix,bulge,phosphate 187 G ) J.DG52 0.026 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 188 G ) J.DG53 0.016 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 189 C ) J.DC54 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 190 G ) J.DG55 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 191 G ) J.DG56 0.023 anti,~C2'-endo,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 192 T ) J.DT57 0.021 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 193 T ) J.DT58 0.020 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 194 A ) J.DA59 0.022 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 195 A ) J.DA60 0.024 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 196 A ) J.DA61 0.021 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 197 A ) J.DA62 0.023 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 198 C ) J.DC63 0.019 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 199 G ) J.DG64 0.015 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 200 C ) J.DC65 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 201 G ) J.DG66 0.012 anti,~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 202 G ) J.DG67 0.018 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 203 G ) J.DG68 0.019 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 204 G ) J.DG69 0.021 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 205 G ) J.DG70 0.012 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 206 A ) J.DA71 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 207 C ) J.DC72 0.014 ~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 208 A ) J.DA73 0.018 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 209 G ) J.DG74 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 210 C ) J.DC75 0.014 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 211 G ) J.DG76 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 212 C ) J.DC77 0.010 ~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 213 G ) J.DG78 0.013 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 214 T ) J.DT79 0.017 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 215 A ) J.DA80 0.010 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 216 C ) J.DC81 0.013 anti,~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 217 G ) J.DG82 0.021 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 218 T ) J.DT83 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 219 G ) J.DG84 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 220 C ) J.DC85 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 221 G ) J.DG86 0.019 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 222 T . J.DT87 0.016 BI,non-pair-contact,internal-loop 223 T ) J.DT88 0.017 anti,~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 224 T ) J.DT89 0.016 anti,~C2'-endo,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 225 A ) J.DA90 0.017 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 226 A ) J.DA91 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 227 G ) J.DG92 0.021 anti,~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 228 C ) J.DC93 0.016 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 229 G ) J.DG94 0.018 anti,canonical,non-pair-contact,helix,stem,coaxial-stack 230 G ) J.DG95 0.011 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 231 T ) J.DT96 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 232 G ) J.DG97 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 233 C ) J.DC98 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 234 T ) J.DT99 0.017 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 235 A ) J.DA100 0.013 ~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 236 G ) J.DG101 0.019 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 237 A ) J.DA102 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 238 G ) J.DG103 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 239 C ) J.DC104 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 240 T ) J.DT105 0.016 anti,~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 241 G ) J.DG106 0.014 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 242 T ) J.DT107 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 243 C ) J.DC108 0.014 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 244 T ) J.DT109 0.016 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 245 A ) J.DA110 0.016 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 246 C ) J.DC111 0.011 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 247 G ) J.DG112 0.015 ~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 248 A ) J.DA113 0.020 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 249 C ) J.DC114 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 250 C ) J.DC115 0.012 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 251 A ) J.DA116 0.013 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 252 A ) J.DA117 0.012 anti,~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 253 T ) J.DT118 0.013 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 254 T ) J.DT119 0.014 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 255 G ) J.DG120 0.019 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 256 A ) J.DA121 0.018 anti,~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 257 G ) J.DG122 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 258 C ) J.DC123 0.012 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 259 G ) J.DG124 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 260 G ) J.DG125 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 261 C ) J.DC126 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 262 C ) J.DC127 0.005 anti,~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 263 T ) J.DT128 0.006 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 264 C ) J.DC129 0.006 ~C2'-endo,BII,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 265 G ) J.DG130 0.014 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 266 G ) J.DG131 0.008 BI,canonical,non-pair-contact,helix,stem,coaxial-stack 267 C ) J.DC132 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 268 A ) J.DA133 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 269 C ) J.DC134 0.005 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 270 C ) J.DC135 0.004 ~C2'-endo,canonical,non-canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 271 G . J.DG136 0.004 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 272 G . J.DG137 0.003 anti,~C3'-endo,non-stack,non-pair-contact,ss-non-loop 273 a . A.ADP1703 0.057 modified,anti,~C2'-endo,non-stack,ss-non-loop **************************************************************************** List of 14 additional files 1 dssr-pairs.pdb -- an ensemble of base pairs 2 dssr-stems.pdb -- an ensemble of stems 3 dssr-helices.pdb -- an ensemble of helices (coaxial stacking) 4 dssr-bulges.pdb -- an ensemble of bulges 5 dssr-iloops.pdb -- an ensemble of internal loops 6 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 7 dssr-2ndstrs.ct -- secondary structure in connectivity table format 8 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 9 dssr-torsions.txt -- backbone torsion angles and suite names 10 dssr-stacks.pdb -- an ensemble of base stacks 11 dssr-rotmat.txt -- position vector and rotation matrix 12 dssr-viewV.pdb -- vertical view of the principal moment of inertia 13 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 14 dssr-viewT.pdb -- top view of the principal moment of inertia