**************************************************************************** File name: 6erp.pdb no. of DNA/RNA chains: 4 [D=46,E=45,H=46,I=45] no. of nucleotides: 182 no. of atoms: 27644 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 86 base pairs nt1 nt2 bp name Saenger LW DSSR 1 D.DT1 E.DA50 T-A WC 20-XX cWW cW-W 2 D.DG2 E.DC49 G-C WC 19-XIX cWW cW-W 3 D.DT3 E.DA48 T-A WC 20-XX cWW cW-W 4 D.DT4 E.DA47 T-A WC 20-XX cWW cW-W 5 D.DA5 E.DT46 A-T WC 20-XX cWW cW-W 6 D.DG6 E.DC45 G-C WC 19-XIX cWW cW-W 7 D.DT7 E.DA44 T-A WC 20-XX cWW cW-W 8 D.DT8 E.DA43 T-A WC 20-XX cWW cW-W 9 D.DG9 E.DC42 G-C WC 19-XIX cWW cW-W 10 D.DG10 E.DC41 G-C WC 19-XIX cWW cW-W 11 D.DG11 E.DC40 G-C WC 19-XIX cWW cW-W 12 D.DG12 E.DC39 G-C WC 19-XIX cWW cW-W 13 D.DG13 E.DC38 G-C WC 19-XIX cWW cW-W 14 D.DG14 E.DC37 G-C WC 19-XIX cWW cW-W 15 D.DT15 E.DA36 T-A WC 20-XX cWW cW-W 16 D.DG16 E.DC35 G-C WC 19-XIX cWW cW-W 17 D.DA17 E.DT34 A-T WC 20-XX cWW cW-W 18 D.DC18 E.DG33 C-G WC 19-XIX cWW cW-W 19 D.DT19 E.DA32 T-A WC 20-XX cWW cW-W 20 D.DG20 E.DC31 G-C WC 19-XIX cWW cW-W 21 D.DT21 E.DA30 T-A WC 20-XX cWW cW-W 22 D.DT22 E.DA29 T-A WC 20-XX cWW cW-W 23 D.DA23 E.DT28 A-T WC 20-XX cWW cW-W 24 D.DA24 E.DT27 A-T WC 20-XX cWW cW-W 25 D.DA25 E.DT26 A-T WC 20-XX cWW cW-W 26 D.DA26 E.DT25 A-T WC 20-XX cWW cW-W 27 D.DG27 E.DC24 G-C WC 19-XIX cWW cW-W 28 D.DT28 E.DA23 T-A WC 20-XX cWW cW-W 29 D.DG29 E.DC22 G-C WC 19-XIX cWW cW-W 30 D.DC30 E.DG21 C-G WC 19-XIX cWW cW-W 31 D.DA31 E.DT20 A-T WC 20-XX cWW cW-W 32 D.DT32 E.DA19 T-A WC 20-XX cWW cW-W 33 D.DA33 E.DT18 A-T WC 20-XX cWW cW-W 34 D.DC34 E.DG17 C-G WC 19-XIX cWW cW-W 35 D.DC35 E.DG16 C-G WC 19-XIX cWW cW-W 36 D.DG43 E.DC8 G-C WC 19-XIX cWW cW-W 37 D.DA44 E.DT7 A-T WC 20-XX cWW cW-W 38 D.DT45 E.DA6 T-A WC 20-XX cWW cW-W 39 D.DA46 E.DT5 A-T WC 20-XX cWW cW-W 40 D.DG47 E.DC4 G-C WC 19-XIX cWW cW-W 41 D.DG48 E.DC3 G-C WC 19-XIX cWW cW-W 42 D.DC49 E.DG2 C-G WC 19-XIX cWW cW-W 43 D.DC50 E.DG1 C-G WC 19-XIX cWW cW-W 44 H.DT1 I.DA50 T-A WC 20-XX cWW cW-W 45 H.DG2 I.DC49 G-C WC 19-XIX cWW cW-W 46 H.DT3 I.DA48 T-A WC 20-XX cWW cW-W 47 H.DT4 I.DA47 T-A WC 20-XX cWW cW-W 48 H.DA5 I.DT46 A-T WC 20-XX cWW cW-W 49 H.DG6 I.DC45 G-C WC 19-XIX cWW cW-W 50 H.DT7 I.DA44 T-A WC 20-XX cWW cW-W 51 H.DT8 I.DA43 T-A WC 20-XX cWW cW-W 52 H.DG9 I.DC42 G-C WC 19-XIX cWW cW-W 53 H.DG10 I.DC41 G-C WC 19-XIX cWW cW-W 54 H.DG11 I.DC40 G-C WC 19-XIX cWW cW-W 55 H.DG12 I.DC39 G-C WC 19-XIX cWW cW-W 56 H.DG13 I.DC38 G-C WC 19-XIX cWW cW-W 57 H.DG14 I.DC37 G-C WC 19-XIX cWW cW-W 58 H.DT15 I.DA36 T-A WC 20-XX cWW cW-W 59 H.DG16 I.DC35 G-C WC 19-XIX cWW cW-W 60 H.DA17 I.DT34 A-T WC 20-XX cWW cW-W 61 H.DC18 I.DG33 C-G WC 19-XIX cWW cW-W 62 H.DT19 I.DA32 T-A WC 20-XX cWW cW-W 63 H.DG20 I.DC31 G-C WC 19-XIX cWW cW-W 64 H.DT21 I.DA30 T-A WC 20-XX cWW cW-W 65 H.DT22 I.DA29 T-A WC 20-XX cWW cW-W 66 H.DA23 I.DT28 A-T WC 20-XX cWW cW-W 67 H.DA24 I.DT27 A-T WC 20-XX cWW cW-W 68 H.DA25 I.DT26 A-T WC 20-XX cWW cW-W 69 H.DA26 I.DT25 A-T WC 20-XX cWW cW-W 70 H.DG27 I.DC24 G-C WC 19-XIX cWW cW-W 71 H.DT28 I.DA23 T-A WC 20-XX cWW cW-W 72 H.DG29 I.DC22 G-C WC 19-XIX cWW cW-W 73 H.DC30 I.DG21 C-G WC 19-XIX cWW cW-W 74 H.DA31 I.DT20 A-T WC 20-XX cWW cW-W 75 H.DT32 I.DA19 T-A WC 20-XX cWW cW-W 76 H.DA33 I.DT18 A-T WC 20-XX cWW cW-W 77 H.DC34 I.DG17 C-G WC 19-XIX cWW cW-W 78 H.DC35 I.DG16 C-G WC 19-XIX cWW cW-W 79 H.DG43 I.DC8 G-C WC 19-XIX cWW cW-W 80 H.DA44 I.DT7 A-T WC 20-XX cWW cW-W 81 H.DT45 I.DA6 T-A WC 20-XX cWW cW-W 82 H.DA46 I.DT5 A-T WC 20-XX cWW cW-W 83 H.DG47 I.DC4 G-C WC 19-XIX cWW cW-W 84 H.DG48 I.DC3 G-C WC 19-XIX cWW cW-W 85 H.DC49 I.DG2 C-G WC 19-XIX cWW cW-W 86 H.DC50 I.DG1 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 4 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[1] bps=35 strand-1 5'-TGTTAGTTGGGGGGTGACTGTTAAAAGTGCATACC-3' bp-type ||||||||||||||||||||||||||||||||||| strand-2 3'-ACAATCAACCCCCCACTGACAATTTTCACGTATGG-5' helix-form BBB.BBB..BBBBBB......BBB...BBB.BBB 1 D.DT1 E.DA50 T-A WC 20-XX cWW cW-W 2 D.DG2 E.DC49 G-C WC 19-XIX cWW cW-W 3 D.DT3 E.DA48 T-A WC 20-XX cWW cW-W 4 D.DT4 E.DA47 T-A WC 20-XX cWW cW-W 5 D.DA5 E.DT46 A-T WC 20-XX cWW cW-W 6 D.DG6 E.DC45 G-C WC 19-XIX cWW cW-W 7 D.DT7 E.DA44 T-A WC 20-XX cWW cW-W 8 D.DT8 E.DA43 T-A WC 20-XX cWW cW-W 9 D.DG9 E.DC42 G-C WC 19-XIX cWW cW-W 10 D.DG10 E.DC41 G-C WC 19-XIX cWW cW-W 11 D.DG11 E.DC40 G-C WC 19-XIX cWW cW-W 12 D.DG12 E.DC39 G-C WC 19-XIX cWW cW-W 13 D.DG13 E.DC38 G-C WC 19-XIX cWW cW-W 14 D.DG14 E.DC37 G-C WC 19-XIX cWW cW-W 15 D.DT15 E.DA36 T-A WC 20-XX cWW cW-W 16 D.DG16 E.DC35 G-C WC 19-XIX cWW cW-W 17 D.DA17 E.DT34 A-T WC 20-XX cWW cW-W 18 D.DC18 E.DG33 C-G WC 19-XIX cWW cW-W 19 D.DT19 E.DA32 T-A WC 20-XX cWW cW-W 20 D.DG20 E.DC31 G-C WC 19-XIX cWW cW-W 21 D.DT21 E.DA30 T-A WC 20-XX cWW cW-W 22 D.DT22 E.DA29 T-A WC 20-XX cWW cW-W 23 D.DA23 E.DT28 A-T WC 20-XX cWW cW-W 24 D.DA24 E.DT27 A-T WC 20-XX cWW cW-W 25 D.DA25 E.DT26 A-T WC 20-XX cWW cW-W 26 D.DA26 E.DT25 A-T WC 20-XX cWW cW-W 27 D.DG27 E.DC24 G-C WC 19-XIX cWW cW-W 28 D.DT28 E.DA23 T-A WC 20-XX cWW cW-W 29 D.DG29 E.DC22 G-C WC 19-XIX cWW cW-W 30 D.DC30 E.DG21 C-G WC 19-XIX cWW cW-W 31 D.DA31 E.DT20 A-T WC 20-XX cWW cW-W 32 D.DT32 E.DA19 T-A WC 20-XX cWW cW-W 33 D.DA33 E.DT18 A-T WC 20-XX cWW cW-W 34 D.DC34 E.DG17 C-G WC 19-XIX cWW cW-W 35 D.DC35 E.DG16 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=8 strand-1 5'-GATAGGCC-3' bp-type |||||||| strand-2 3'-CTATCCGG-5' helix-form .BBBBBB 1 D.DG43 E.DC8 G-C WC 19-XIX cWW cW-W 2 D.DA44 E.DT7 A-T WC 20-XX cWW cW-W 3 D.DT45 E.DA6 T-A WC 20-XX cWW cW-W 4 D.DA46 E.DT5 A-T WC 20-XX cWW cW-W 5 D.DG47 E.DC4 G-C WC 19-XIX cWW cW-W 6 D.DG48 E.DC3 G-C WC 19-XIX cWW cW-W 7 D.DC49 E.DG2 C-G WC 19-XIX cWW cW-W 8 D.DC50 E.DG1 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#3[1] bps=35 strand-1 5'-TGTTAGTTGGGGGGTGACTGTTAAAAGTGCATACC-3' bp-type ||||||||||||||||||||||||||||||||||| strand-2 3'-ACAATCAACCCCCCACTGACAATTTTCACGTATGG-5' helix-form BBB.BBB..BBBBB........BB...BBB.BBB 1 H.DT1 I.DA50 T-A WC 20-XX cWW cW-W 2 H.DG2 I.DC49 G-C WC 19-XIX cWW cW-W 3 H.DT3 I.DA48 T-A WC 20-XX cWW cW-W 4 H.DT4 I.DA47 T-A WC 20-XX cWW cW-W 5 H.DA5 I.DT46 A-T WC 20-XX cWW cW-W 6 H.DG6 I.DC45 G-C WC 19-XIX cWW cW-W 7 H.DT7 I.DA44 T-A WC 20-XX cWW cW-W 8 H.DT8 I.DA43 T-A WC 20-XX cWW cW-W 9 H.DG9 I.DC42 G-C WC 19-XIX cWW cW-W 10 H.DG10 I.DC41 G-C WC 19-XIX cWW cW-W 11 H.DG11 I.DC40 G-C WC 19-XIX cWW cW-W 12 H.DG12 I.DC39 G-C WC 19-XIX cWW cW-W 13 H.DG13 I.DC38 G-C WC 19-XIX cWW cW-W 14 H.DG14 I.DC37 G-C WC 19-XIX cWW cW-W 15 H.DT15 I.DA36 T-A WC 20-XX cWW cW-W 16 H.DG16 I.DC35 G-C WC 19-XIX cWW cW-W 17 H.DA17 I.DT34 A-T WC 20-XX cWW cW-W 18 H.DC18 I.DG33 C-G WC 19-XIX cWW cW-W 19 H.DT19 I.DA32 T-A WC 20-XX cWW cW-W 20 H.DG20 I.DC31 G-C WC 19-XIX cWW cW-W 21 H.DT21 I.DA30 T-A WC 20-XX cWW cW-W 22 H.DT22 I.DA29 T-A WC 20-XX cWW cW-W 23 H.DA23 I.DT28 A-T WC 20-XX cWW cW-W 24 H.DA24 I.DT27 A-T WC 20-XX cWW cW-W 25 H.DA25 I.DT26 A-T WC 20-XX cWW cW-W 26 H.DA26 I.DT25 A-T WC 20-XX cWW cW-W 27 H.DG27 I.DC24 G-C WC 19-XIX cWW cW-W 28 H.DT28 I.DA23 T-A WC 20-XX cWW cW-W 29 H.DG29 I.DC22 G-C WC 19-XIX cWW cW-W 30 H.DC30 I.DG21 C-G WC 19-XIX cWW cW-W 31 H.DA31 I.DT20 A-T WC 20-XX cWW cW-W 32 H.DT32 I.DA19 T-A WC 20-XX cWW cW-W 33 H.DA33 I.DT18 A-T WC 20-XX cWW cW-W 34 H.DC34 I.DG17 C-G WC 19-XIX cWW cW-W 35 H.DC35 I.DG16 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#4[1] bps=8 strand-1 5'-GATAGGCC-3' bp-type |||||||| strand-2 3'-CTATCCGG-5' helix-form BBBBBBB 1 H.DG43 I.DC8 G-C WC 19-XIX cWW cW-W 2 H.DA44 I.DT7 A-T WC 20-XX cWW cW-W 3 H.DT45 I.DA6 T-A WC 20-XX cWW cW-W 4 H.DA46 I.DT5 A-T WC 20-XX cWW cW-W 5 H.DG47 I.DC4 G-C WC 19-XIX cWW cW-W 6 H.DG48 I.DC3 G-C WC 19-XIX cWW cW-W 7 H.DC49 I.DG2 C-G WC 19-XIX cWW cW-W 8 H.DC50 I.DG1 C-G WC 19-XIX 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=35 strand-1 5'-TGTTAGTTGGGGGGTGACTGTTAAAAGTGCATACC-3' bp-type ||||||||||||||||||||||||||||||||||| strand-2 3'-ACAATCAACCCCCCACTGACAATTTTCACGTATGG-5' helix-form BBB.BBB..BBBBBB......BBB...BBB.BBB 1 D.DT1 E.DA50 T-A WC 20-XX cWW cW-W 2 D.DG2 E.DC49 G-C WC 19-XIX cWW cW-W 3 D.DT3 E.DA48 T-A WC 20-XX cWW cW-W 4 D.DT4 E.DA47 T-A WC 20-XX cWW cW-W 5 D.DA5 E.DT46 A-T WC 20-XX cWW cW-W 6 D.DG6 E.DC45 G-C WC 19-XIX cWW cW-W 7 D.DT7 E.DA44 T-A WC 20-XX cWW cW-W 8 D.DT8 E.DA43 T-A WC 20-XX cWW cW-W 9 D.DG9 E.DC42 G-C WC 19-XIX cWW cW-W 10 D.DG10 E.DC41 G-C WC 19-XIX cWW cW-W 11 D.DG11 E.DC40 G-C WC 19-XIX cWW cW-W 12 D.DG12 E.DC39 G-C WC 19-XIX cWW cW-W 13 D.DG13 E.DC38 G-C WC 19-XIX cWW cW-W 14 D.DG14 E.DC37 G-C WC 19-XIX cWW cW-W 15 D.DT15 E.DA36 T-A WC 20-XX cWW cW-W 16 D.DG16 E.DC35 G-C WC 19-XIX cWW cW-W 17 D.DA17 E.DT34 A-T WC 20-XX cWW cW-W 18 D.DC18 E.DG33 C-G WC 19-XIX cWW cW-W 19 D.DT19 E.DA32 T-A WC 20-XX cWW cW-W 20 D.DG20 E.DC31 G-C WC 19-XIX cWW cW-W 21 D.DT21 E.DA30 T-A WC 20-XX cWW cW-W 22 D.DT22 E.DA29 T-A WC 20-XX cWW cW-W 23 D.DA23 E.DT28 A-T WC 20-XX cWW cW-W 24 D.DA24 E.DT27 A-T WC 20-XX cWW cW-W 25 D.DA25 E.DT26 A-T WC 20-XX cWW cW-W 26 D.DA26 E.DT25 A-T WC 20-XX cWW cW-W 27 D.DG27 E.DC24 G-C WC 19-XIX cWW cW-W 28 D.DT28 E.DA23 T-A WC 20-XX cWW cW-W 29 D.DG29 E.DC22 G-C WC 19-XIX cWW cW-W 30 D.DC30 E.DG21 C-G WC 19-XIX cWW cW-W 31 D.DA31 E.DT20 A-T WC 20-XX cWW cW-W 32 D.DT32 E.DA19 T-A WC 20-XX cWW cW-W 33 D.DA33 E.DT18 A-T WC 20-XX cWW cW-W 34 D.DC34 E.DG17 C-G WC 19-XIX cWW cW-W 35 D.DC35 E.DG16 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=8 strand-1 5'-GATAGGCC-3' bp-type |||||||| strand-2 3'-CTATCCGG-5' helix-form .BBBBBB 1 D.DG43 E.DC8 G-C WC 19-XIX cWW cW-W 2 D.DA44 E.DT7 A-T WC 20-XX cWW cW-W 3 D.DT45 E.DA6 T-A WC 20-XX cWW cW-W 4 D.DA46 E.DT5 A-T WC 20-XX cWW cW-W 5 D.DG47 E.DC4 G-C WC 19-XIX cWW cW-W 6 D.DG48 E.DC3 G-C WC 19-XIX cWW cW-W 7 D.DC49 E.DG2 C-G WC 19-XIX cWW cW-W 8 D.DC50 E.DG1 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#3[#3] bps=35 strand-1 5'-TGTTAGTTGGGGGGTGACTGTTAAAAGTGCATACC-3' bp-type ||||||||||||||||||||||||||||||||||| strand-2 3'-ACAATCAACCCCCCACTGACAATTTTCACGTATGG-5' helix-form BBB.BBB..BBBBB........BB...BBB.BBB 1 H.DT1 I.DA50 T-A WC 20-XX cWW cW-W 2 H.DG2 I.DC49 G-C WC 19-XIX cWW cW-W 3 H.DT3 I.DA48 T-A WC 20-XX cWW cW-W 4 H.DT4 I.DA47 T-A WC 20-XX cWW cW-W 5 H.DA5 I.DT46 A-T WC 20-XX cWW cW-W 6 H.DG6 I.DC45 G-C WC 19-XIX cWW cW-W 7 H.DT7 I.DA44 T-A WC 20-XX cWW cW-W 8 H.DT8 I.DA43 T-A WC 20-XX cWW cW-W 9 H.DG9 I.DC42 G-C WC 19-XIX cWW cW-W 10 H.DG10 I.DC41 G-C WC 19-XIX cWW cW-W 11 H.DG11 I.DC40 G-C WC 19-XIX cWW cW-W 12 H.DG12 I.DC39 G-C WC 19-XIX cWW cW-W 13 H.DG13 I.DC38 G-C WC 19-XIX cWW cW-W 14 H.DG14 I.DC37 G-C WC 19-XIX cWW cW-W 15 H.DT15 I.DA36 T-A WC 20-XX cWW cW-W 16 H.DG16 I.DC35 G-C WC 19-XIX cWW cW-W 17 H.DA17 I.DT34 A-T WC 20-XX cWW cW-W 18 H.DC18 I.DG33 C-G WC 19-XIX cWW cW-W 19 H.DT19 I.DA32 T-A WC 20-XX cWW cW-W 20 H.DG20 I.DC31 G-C WC 19-XIX cWW cW-W 21 H.DT21 I.DA30 T-A WC 20-XX cWW cW-W 22 H.DT22 I.DA29 T-A WC 20-XX cWW cW-W 23 H.DA23 I.DT28 A-T WC 20-XX cWW cW-W 24 H.DA24 I.DT27 A-T WC 20-XX cWW cW-W 25 H.DA25 I.DT26 A-T WC 20-XX cWW cW-W 26 H.DA26 I.DT25 A-T WC 20-XX cWW cW-W 27 H.DG27 I.DC24 G-C WC 19-XIX cWW cW-W 28 H.DT28 I.DA23 T-A WC 20-XX cWW cW-W 29 H.DG29 I.DC22 G-C WC 19-XIX cWW cW-W 30 H.DC30 I.DG21 C-G WC 19-XIX cWW cW-W 31 H.DA31 I.DT20 A-T WC 20-XX cWW cW-W 32 H.DT32 I.DA19 T-A WC 20-XX cWW cW-W 33 H.DA33 I.DT18 A-T WC 20-XX cWW cW-W 34 H.DC34 I.DG17 C-G WC 19-XIX cWW cW-W 35 H.DC35 I.DG16 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#4[#4] bps=8 strand-1 5'-GATAGGCC-3' bp-type |||||||| strand-2 3'-CTATCCGG-5' helix-form BBBBBBB 1 H.DG43 I.DC8 G-C WC 19-XIX cWW cW-W 2 H.DA44 I.DT7 A-T WC 20-XX cWW cW-W 3 H.DT45 I.DA6 T-A WC 20-XX cWW cW-W 4 H.DA46 I.DT5 A-T WC 20-XX cWW cW-W 5 H.DG47 I.DC4 G-C WC 19-XIX cWW cW-W 6 H.DG48 I.DC3 G-C WC 19-XIX cWW cW-W 7 H.DC49 I.DG2 C-G WC 19-XIX cWW cW-W 8 H.DC50 I.DG1 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 3 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 GR E.DG14,A.ARG502 2 nts=3 CTA H.DC35,H.DT36,H.DA37 3 nts=4 CTAT D.DC35,D.DT36,D.DA37,D.DT38 **************************************************************************** Nucleotides not involved in stacking interactions nts=3 CTC E.DC15,H.DT38,I.DC15 **************************************************************************** List of 4 non-loop single-stranded segments 1 nts=3 TAT D.DT36,D.DA37,D.DT38 2 nts=2 GC E.DG14,E.DC15 3 nts=3 TAT H.DT36,H.DA37,H.DT38 4 nts=2 GC I.DG14,I.DC15 **************************************************************************** List of 2 splayed-apart dinucleotides 1 E.DG14 E.DC15 angle=134 distance=19.4 ratio=0.92 2 I.DC15 I.DG16 angle=99 distance=13.7 ratio=0.76 ---------------------------------------------------------------- Summary of 2 splayed-apart units 1 nts=2 GC E.DG14,E.DC15 2 nts=2 CG I.DC15,I.DG16 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >6erp nts=182 [whole] TGTTAGTTGGGGGGTGACTGTTAAAAGTGCATACCTAT&GATAGGCC&GGCCTATC&GCGGTATGCACTTTTAACAGTCACCCCCCAACTAACA&TGTTAGTTGGGGGGTGACTGTTAAAAGTGCATACCTAT&GATAGGCC&GGCCTATC&GCGGTATGCACTTTTAACAGTCACCCCCCAACTAACA (((((((((((((((((((((((((((((((((((...&((((((((&))))))))&..)))))))))))))))))))))))))))))))))))&(((((((((((((((((((((((((((((((((((...&((((((((&))))))))&..))))))))))))))))))))))))))))))))))) >6erp-D #1 nts=46 1.49(2.25) [chain] DNA* TGTTAGTTGGGGGGTGACTGTTAAAAGTGCATACCTAT&GATAGGCC (((((((((((((((((((((((((((((((((((...&(((((((( >6erp-E #2 nts=45 0.89(2.57) [chain] DNA* GGCCTATC&GCGGTATGCACTTTTAACAGTCACCCCCCAACTAACA ))))))))&..))))))))))))))))))))))))))))))))))) >6erp-H #3 nts=46 1.66(2.24) [chain] DNA* TGTTAGTTGGGGGGTGACTGTTAAAAGTGCATACCTAT&GATAGGCC (((((((((((((((((((((((((((((((((((...&(((((((( >6erp-I #4 nts=45 0.54(2.60) [chain] DNA* GGCCTATC&GCGGTATGCACTTTTAACAGTCACCCCCCAACTAACA ))))))))&..))))))))))))))))))))))))))))))))))) **************************************************************************** Summary of structural features of 182 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 T ( D.DT1 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 G ( D.DG2 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 3 T ( D.DT3 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 4 T ( D.DT4 0.003 anti,canonical,non-pair-contact,helix,stem 5 A ( D.DA5 0.007 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 6 G ( D.DG6 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 7 T ( D.DT7 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 8 T ( D.DT8 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,phosphate 9 G ( D.DG9 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 10 G ( D.DG10 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 11 G ( D.DG11 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 12 G ( D.DG12 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 13 G ( D.DG13 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 14 G ( D.DG14 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 15 T ( D.DT15 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 16 G ( D.DG16 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 17 A ( D.DA17 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 18 C ( D.DC18 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 19 T ( D.DT19 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 20 G ( D.DG20 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 21 T ( D.DT21 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 22 T ( D.DT22 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 23 A ( D.DA23 0.007 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,phosphate 24 A ( D.DA24 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 25 A ( D.DA25 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 26 A ( D.DA26 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 27 G ( D.DG27 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 28 T ( D.DT28 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 29 G ( D.DG29 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 30 C ( D.DC30 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 31 A ( D.DA31 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 32 T ( D.DT32 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 33 A ( D.DA33 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 34 C ( D.DC34 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 35 C ( D.DC35 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 36 T . D.DT36 0.003 anti,~C2'-endo,non-pair-contact,ss-non-loop 37 A . D.DA37 0.004 anti,~C2'-endo,non-pair-contact,ss-non-loop 38 T . D.DT38 0.002 break,anti,~C2'-endo,non-pair-contact,ss-non-loop 39 G ( D.DG43 0.010 ~C2'-endo,BII,canonical,non-pair-contact,helix-end,stem-end 40 A ( D.DA44 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 41 T ( D.DT45 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 42 A ( D.DA46 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 43 G ( D.DG47 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 44 G ( D.DG48 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 45 C ( D.DC49 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 46 C ( D.DC50 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 47 G ) E.DG1 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 48 G ) E.DG2 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 49 C ) E.DC3 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 50 C ) E.DC4 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 51 T ) E.DT5 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 52 A ) E.DA6 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 53 T ) E.DT7 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 54 C ) E.DC8 0.002 break,anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 55 G . E.DG14 0.005 syn,~C2'-endo,ss-non-loop,phosphate,splayed-apart 56 C . E.DC15 0.003 anti,non-stack,ss-non-loop,splayed-apart 57 G ) E.DG16 0.006 ~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 58 G ) E.DG17 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 59 T ) E.DT18 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 60 A ) E.DA19 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 61 T ) E.DT20 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 62 G ) E.DG21 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 63 C ) E.DC22 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 64 A ) E.DA23 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 65 C ) E.DC24 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 66 T ) E.DT25 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 67 T ) E.DT26 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 68 T ) E.DT27 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 69 T ) E.DT28 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 70 A ) E.DA29 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 71 A ) E.DA30 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 72 C ) E.DC31 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 73 A ) E.DA32 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 74 G ) E.DG33 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 75 T ) E.DT34 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 76 C ) E.DC35 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 77 A ) E.DA36 0.004 anti,canonical,non-pair-contact,helix,stem 78 C ) E.DC37 0.005 anti,BI,canonical,non-pair-contact,helix,stem 79 C ) E.DC38 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 80 C ) E.DC39 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 81 C ) E.DC40 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 82 C ) E.DC41 0.004 anti,canonical,non-pair-contact,helix,stem 83 C ) E.DC42 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 84 A ) E.DA43 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 85 A ) E.DA44 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 86 C ) E.DC45 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 87 T ) E.DT46 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 88 A ) E.DA47 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 89 A ) E.DA48 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 90 C ) E.DC49 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 91 A ) E.DA50 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 92 T ( H.DT1 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 93 G ( H.DG2 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 94 T ( H.DT3 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 95 T ( H.DT4 0.003 anti,canonical,non-pair-contact,helix,stem 96 A ( H.DA5 0.006 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 97 G ( H.DG6 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 98 T ( H.DT7 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 99 T ( H.DT8 0.002 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,phosphate 100 G ( H.DG9 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 101 G ( H.DG10 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 102 G ( H.DG11 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 103 G ( H.DG12 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 104 G ( H.DG13 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 105 G ( H.DG14 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 106 T ( H.DT15 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 107 G ( H.DG16 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 108 A ( H.DA17 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 109 C ( H.DC18 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 110 T ( H.DT19 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 111 G ( H.DG20 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 112 T ( H.DT21 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 113 T ( H.DT22 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 114 A ( H.DA23 0.009 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 115 A ( H.DA24 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 116 A ( H.DA25 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 117 A ( H.DA26 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 118 G ( H.DG27 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 119 T ( H.DT28 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 120 G ( H.DG29 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 121 C ( H.DC30 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 122 A ( H.DA31 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 123 T ( H.DT32 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 124 A ( H.DA33 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 125 C ( H.DC34 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 126 C ( H.DC35 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 127 T . H.DT36 0.003 anti,~C2'-endo,non-pair-contact,ss-non-loop 128 A . H.DA37 0.003 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate 129 T . H.DT38 0.002 break,anti,~C2'-endo,non-stack,ss-non-loop 130 G ( H.DG43 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 131 A ( H.DA44 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 132 T ( H.DT45 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 133 A ( H.DA46 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 134 G ( H.DG47 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 135 G ( H.DG48 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 136 C ( H.DC49 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 137 C ( H.DC50 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 138 G ) I.DG1 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 139 G ) I.DG2 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 140 C ) I.DC3 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 141 C ) I.DC4 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 142 T ) I.DT5 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 143 A ) I.DA6 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 144 T ) I.DT7 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 145 C ) I.DC8 0.004 break,anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 146 G . I.DG14 0.003 anti,~C2'-endo,ss-non-loop 147 C . I.DC15 0.003 syn,non-stack,ss-non-loop,splayed-apart 148 G ) I.DG16 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,splayed-apart 149 G ) I.DG17 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 150 T ) I.DT18 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 151 A ) I.DA19 0.009 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 152 T ) I.DT20 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 153 G ) I.DG21 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 154 C ) I.DC22 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 155 A ) I.DA23 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 156 C ) I.DC24 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 157 T ) I.DT25 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 158 T ) I.DT26 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 159 T ) I.DT27 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 160 T ) I.DT28 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 161 A ) I.DA29 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 162 A ) I.DA30 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 163 C ) I.DC31 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 164 A ) I.DA32 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 165 G ) I.DG33 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 166 T ) I.DT34 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 167 C ) I.DC35 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 168 A ) I.DA36 0.004 anti,canonical,non-pair-contact,helix,stem 169 C ) I.DC37 0.004 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 170 C ) I.DC38 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 171 C ) I.DC39 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 172 C ) I.DC40 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 173 C ) I.DC41 0.004 anti,canonical,non-pair-contact,helix,stem 174 C ) I.DC42 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 175 A ) I.DA43 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 176 A ) I.DA44 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 177 C ) I.DC45 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 178 T ) I.DT46 0.006 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 179 A ) I.DA47 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 180 A ) I.DA48 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 181 C ) I.DC49 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 182 A ) I.DA50 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** List of 13 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-2ndstrs.bpseq -- secondary structure in bpseq format 5 dssr-2ndstrs.ct -- secondary structure in connectivity table format 6 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 7 dssr-torsions.txt -- backbone torsion angles and suite names 8 dssr-splays.pdb -- an ensemble of splayed-apart units 9 dssr-stacks.pdb -- an ensemble of base stacks 10 dssr-rotmat.txt -- position vector and rotation matrix 11 dssr-viewV.pdb -- vertical view of the principal moment of inertia 12 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 13 dssr-viewT.pdb -- top view of the principal moment of inertia