**************************************************************************** File name: 9d3q.pdb no. of DNA/RNA chains: 2 [I=109,J=109] no. of nucleotides: 218 no. of atoms: 10138 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 110 base pairs nt1 nt2 bp name Saenger LW DSSR 1 I.DT-58 J.DA58 T-A WC 20-XX cWW cW-W 2 I.DG-57 J.DC57 G-C WC 19-XIX cWW cW-W 3 I.DG-56 J.DC56 G-C WC 19-XIX cWW cW-W 4 I.DG-55 J.DC55 G-C WC 19-XIX cWW cW-W 5 I.DG-54 J.DC54 G-C WC 19-XIX cWW cW-W 6 I.DG-53 J.DC53 G-C WC 19-XIX cWW cW-W 7 I.DA-52 J.DT52 A-T WC 20-XX cWW cW-W 8 I.DA-51 J.DT51 A-T WC 20-XX cWW cW-W 9 I.DA-50 J.DT50 A-T WC 20-XX cWW cW-W 10 I.DA-49 J.DT49 A-T WC 20-XX cWW cW-W 11 I.DG-48 J.DC48 G-C WC 19-XIX cWW cW-W 12 I.DA-47 J.DT47 A-T WC 20-XX cWW cW-W 13 I.DC-46 J.DG46 C-G WC 19-XIX cWW cW-W 14 I.DC-45 J.DG45 C-G WC 19-XIX cWW cW-W 15 I.DC-44 J.DG44 C-G WC 19-XIX cWW cW-W 16 I.DT-43 J.DA43 T-A WC 20-XX cWW cW-W 17 I.DG-42 J.DC42 G-C WC 19-XIX cWW cW-W 18 I.DG-41 J.DC41 G-C WC 19-XIX cWW cW-W 19 I.DC-40 J.DG40 C-G WC 19-XIX cWW cW-W 20 I.DA-39 J.DT39 A-T WC 20-XX cWW cW-W 21 I.DT-38 J.DA38 T-A WC 20-XX cWW cW-W 22 I.DG-37 J.DC37 G+C -- -- cWH cW+M 23 I.DG-36 J.DC36 G-C WC 19-XIX cWW cW-W 24 I.DG-35 J.DC35 G-C WC 19-XIX cWW cW-W 25 I.DG-34 J.DC34 G-C WC 19-XIX cWW cW-W 26 I.DA-33 J.DT33 A-T WC 20-XX cWW cW-W 27 I.DG-32 J.DC32 G-C WC 19-XIX cWW cW-W 28 I.DG-31 J.DC31 G-C WC 19-XIX cWW cW-W 29 I.DA-30 J.DT30 A-T WC 20-XX cWW cW-W 30 I.DG-29 J.DC29 G-C WC 19-XIX cWW cW-W 31 I.DC-28 J.DG28 C-G WC 19-XIX cWW cW-W 32 I.DT-27 J.DA27 T-A WC 20-XX cWW cW-W 33 I.DG-26 J.DC26 G-C WC 19-XIX cWW cW-W 34 I.DG-25 J.DC25 G-C WC 19-XIX cWW cW-W 35 I.DG-24 J.DC24 G-C WC 19-XIX cWW cW-W 36 I.DC-23 J.DG23 C-G WC 19-XIX cWW cW-W 37 I.DC-22 J.DG22 C-G WC 19-XIX cWW cW-W 38 I.DC-21 J.DG21 C-G WC 19-XIX cWW cW-W 39 I.DC-20 J.DG20 C-G WC 19-XIX cWW cW-W 40 I.DC-19 J.DG19 C-G WC 19-XIX cWW cW-W 41 I.DC-18 J.DG18 C-G WC 19-XIX cWW cW-W 42 I.DC-17 J.DG17 C-G WC 19-XIX cWW cW-W 43 I.DC-16 J.DG16 C-G WC 19-XIX cWW cW-W 44 I.DA-15 J.DT15 A-T WC 20-XX cWW cW-W 45 I.DG-14 J.DC14 G-C WC 19-XIX cWW cW-W 46 I.DA-13 J.DT13 A-T WC 20-XX cWW cW-W 47 I.DA-12 J.DT12 A-T WC 20-XX cWW cW-W 48 I.DG-11 J.DC11 G-C WC 19-XIX cWW cW-W 49 I.DG-10 J.DC10 G-C WC 19-XIX cWW cW-W 50 I.DC-9 J.DG9 C-G WC 19-XIX cWW cW-W 51 I.DA-8 J.DT8 A-T WC 20-XX cWW cW-W 52 I.DG-7 J.DC7 G-C WC 19-XIX cWW cW-W 53 I.DC-6 J.DG6 C-G WC 19-XIX cWW cW-W 54 I.DA-5 J.DT5 A-T WC 20-XX cWW cW-W 55 I.DC-4 J.DG4 C-G WC 19-XIX cWW cW-W 56 I.DA-3 J.DT3 A-T WC 20-XX cWW cW-W 57 I.DA-2 J.DT2 A-T WC 20-XX cWW cW-W 58 I.DG-1 J.DC1 G-C WC 19-XIX cWW cW-W 59 I.DG0 J.DC0 G-C WC 19-XIX cWW cW-W 60 I.DG1 J.DC-1 G-C WC 19-XIX cWW cW-W 61 I.DG2 J.DC-2 G-C WC 19-XIX cWW cW-W 62 I.DA3 J.DT-3 A-T WC 20-XX cWW cW-W 63 I.DG4 J.DC-4 G-C WC 19-XIX cWW cW-W 64 I.DG5 J.DC-5 G-C WC 19-XIX cWW cW-W 65 I.DA6 J.DT-6 A-T WC 20-XX cWW cW-W 66 I.DA7 J.DT-7 A-T WC 20-XX cWW cW-W 67 I.DA8 J.DT-8 A-T WC 20-XX cWW cW-W 68 I.DA9 J.DT-9 A-T WC 20-XX cWW cW-W 69 I.DG10 J.DC-10 G-C WC 19-XIX cWW cW-W 70 I.DT11 J.DA-11 T-A WC 20-XX cWW cW-W 71 I.DC12 J.DG-12 C-G WC 19-XIX cWW cW-W 72 I.DA13 J.DT-13 A-T WC 20-XX cWW cW-W 73 I.DG14 J.DC-14 G-C WC 19-XIX cWW cW-W 74 I.DC15 J.DG-15 C-G WC 19-XIX cWW cW-W 75 I.DC16 J.DG-16 C-G WC 19-XIX cWW cW-W 76 I.DT17 J.DA-17 T-A WC 20-XX cWW cW-W 77 I.DT18 J.DA-18 T-A WC 20-XX cWW cW-W 78 I.DG19 J.DC-19 G-C WC 19-XIX cWW cW-W 79 I.DT20 J.DA-20 T-A WC 20-XX cWW cW-W 80 I.DG21 J.DC-21 G-C WC 19-XIX cWW cW-W 81 I.DC22 J.DG-22 C-G WC 19-XIX cWW cW-W 82 I.DT23 J.DA-23 T-A WC 20-XX cWW cW-W 83 I.DC24 J.DG-24 C-G WC 19-XIX cWW cW-W 84 I.DG25 J.DC-25 G-C WC 19-XIX cWW cW-W 85 I.DC26 J.DG-26 C-G WC 19-XIX cWW cW-W 86 I.DC27 J.DG-27 C-G WC 19-XIX cWW cW-W 87 I.DT28 J.DA-28 T-A WC 20-XX cWW cW-W 88 I.DA29 J.DT-29 A-T WC 20-XX cWW cW-W 89 I.DC30 J.DG-30 C-G WC 19-XIX cWW cW-W 90 I.DG31 J.DC-31 G-C WC 19-XIX cWW cW-W 91 I.DG32 J.DC-32 G-C WC 19-XIX cWW cW-W 92 I.DC33 J.DG-33 C-G WC 19-XIX cWW cW-W 93 I.DC34 J.DG-34 C-G WC 19-XIX cWW cW-W 94 I.DA35 J.DT-35 A-T WC 20-XX cWW cW-W 95 I.DT36 J.DA-36 T-A WC 20-XX cWW cW-W 96 I.DA37 J.DT-37 A-T WC 20-XX cWW cW-W 97 I.DC38 J.DG-38 C-G WC 19-XIX cWW cW-W 98 I.DC39 J.DG-39 C-G WC 19-XIX cWW cW-W 99 I.DA40 J.DT-40 A-T WC 20-XX cWW cW-W 100 I.DC41 J.DG-41 C-G WC 19-XIX cWW cW-W 101 I.DC42 J.DG-42 C-G WC 19-XIX cWW cW-W 102 I.DC43 J.DG-43 C-G WC 19-XIX cWW cW-W 103 I.DT44 J.DA-44 T-A WC 20-XX cWW cW-W 104 I.DG45 J.DC-45 G-C WC 19-XIX cWW cW-W 105 I.DA46 J.DT-46 A-T WC 20-XX cWW cW-W 106 I.DA47 J.DT-47 A-T WC 20-XX cWW cW-W 107 I.DA48 J.DT-48 A-T WC 20-XX cWW cW-W 108 I.DG49 J.DC-49 G-C WC 19-XIX cWW cW-W 109 I.DG49 J.DT-48 G-T -- -- cWW cW-W 110 I.DT50 J.DA-50 T-A 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[2] bps=109 strand-1 5'-TGGGGGAAAAGACCCTGGCATGGGGAGGAGCTGGGCCCCCCCCAGAAGGCAGCACAAGGGGAGGAAAAGTCAGCCTTGTGCTCGCCTACGGCCATACCACCCTGAAAGT-3' bp-type |||||||||||||||||||||.||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| strand-2 3'-ACCCCCTTTTCTGGGACCGTACCCCTCCTCGACCCGGGGGGGGTCTTCCGTCGTGTTCCCCTCCTTTTCAGTCGGAACACGAGCGGATGCCGGTATGGTGGGACTTTCA-5' helix-form BBB.....BBBBBBBBBBBB..BB..BBBBBBBBB.BBBBBB.B...BBBBBBBBBBBBBBBBB....BBBBBB.BB.BBBBBBBBBBBBBBBB.BBBBBBBBB.... 1 I.DT-58 J.DA58 T-A WC 20-XX cWW cW-W 2 I.DG-57 J.DC57 G-C WC 19-XIX cWW cW-W 3 I.DG-56 J.DC56 G-C WC 19-XIX cWW cW-W 4 I.DG-55 J.DC55 G-C WC 19-XIX cWW cW-W 5 I.DG-54 J.DC54 G-C WC 19-XIX cWW cW-W 6 I.DG-53 J.DC53 G-C WC 19-XIX cWW cW-W 7 I.DA-52 J.DT52 A-T WC 20-XX cWW cW-W 8 I.DA-51 J.DT51 A-T WC 20-XX cWW cW-W 9 I.DA-50 J.DT50 A-T WC 20-XX cWW cW-W 10 I.DA-49 J.DT49 A-T WC 20-XX cWW cW-W 11 I.DG-48 J.DC48 G-C WC 19-XIX cWW cW-W 12 I.DA-47 J.DT47 A-T WC 20-XX cWW cW-W 13 I.DC-46 J.DG46 C-G WC 19-XIX cWW cW-W 14 I.DC-45 J.DG45 C-G WC 19-XIX cWW cW-W 15 I.DC-44 J.DG44 C-G WC 19-XIX cWW cW-W 16 I.DT-43 J.DA43 T-A WC 20-XX cWW cW-W 17 I.DG-42 J.DC42 G-C WC 19-XIX cWW cW-W 18 I.DG-41 J.DC41 G-C WC 19-XIX cWW cW-W 19 I.DC-40 J.DG40 C-G WC 19-XIX cWW cW-W 20 I.DA-39 J.DT39 A-T WC 20-XX cWW cW-W 21 I.DT-38 J.DA38 T-A WC 20-XX cWW cW-W 22 I.DG-37 J.DC37 G+C -- -- cWH cW+M 23 I.DG-36 J.DC36 G-C WC 19-XIX cWW cW-W 24 I.DG-35 J.DC35 G-C WC 19-XIX cWW cW-W 25 I.DG-34 J.DC34 G-C WC 19-XIX cWW cW-W 26 I.DA-33 J.DT33 A-T WC 20-XX cWW cW-W 27 I.DG-32 J.DC32 G-C WC 19-XIX cWW cW-W 28 I.DG-31 J.DC31 G-C WC 19-XIX cWW cW-W 29 I.DA-30 J.DT30 A-T WC 20-XX cWW cW-W 30 I.DG-29 J.DC29 G-C WC 19-XIX cWW cW-W 31 I.DC-28 J.DG28 C-G WC 19-XIX cWW cW-W 32 I.DT-27 J.DA27 T-A WC 20-XX cWW cW-W 33 I.DG-26 J.DC26 G-C WC 19-XIX cWW cW-W 34 I.DG-25 J.DC25 G-C WC 19-XIX cWW cW-W 35 I.DG-24 J.DC24 G-C WC 19-XIX cWW cW-W 36 I.DC-23 J.DG23 C-G WC 19-XIX cWW cW-W 37 I.DC-22 J.DG22 C-G WC 19-XIX cWW cW-W 38 I.DC-21 J.DG21 C-G WC 19-XIX cWW cW-W 39 I.DC-20 J.DG20 C-G WC 19-XIX cWW cW-W 40 I.DC-19 J.DG19 C-G WC 19-XIX cWW cW-W 41 I.DC-18 J.DG18 C-G WC 19-XIX cWW cW-W 42 I.DC-17 J.DG17 C-G WC 19-XIX cWW cW-W 43 I.DC-16 J.DG16 C-G WC 19-XIX cWW cW-W 44 I.DA-15 J.DT15 A-T WC 20-XX cWW cW-W 45 I.DG-14 J.DC14 G-C WC 19-XIX cWW cW-W 46 I.DA-13 J.DT13 A-T WC 20-XX cWW cW-W 47 I.DA-12 J.DT12 A-T WC 20-XX cWW cW-W 48 I.DG-11 J.DC11 G-C WC 19-XIX cWW cW-W 49 I.DG-10 J.DC10 G-C WC 19-XIX cWW cW-W 50 I.DC-9 J.DG9 C-G WC 19-XIX cWW cW-W 51 I.DA-8 J.DT8 A-T WC 20-XX cWW cW-W 52 I.DG-7 J.DC7 G-C WC 19-XIX cWW cW-W 53 I.DC-6 J.DG6 C-G WC 19-XIX cWW cW-W 54 I.DA-5 J.DT5 A-T WC 20-XX cWW cW-W 55 I.DC-4 J.DG4 C-G WC 19-XIX cWW cW-W 56 I.DA-3 J.DT3 A-T WC 20-XX cWW cW-W 57 I.DA-2 J.DT2 A-T WC 20-XX cWW cW-W 58 I.DG-1 J.DC1 G-C WC 19-XIX cWW cW-W 59 I.DG0 J.DC0 G-C WC 19-XIX cWW cW-W 60 I.DG1 J.DC-1 G-C WC 19-XIX cWW cW-W 61 I.DG2 J.DC-2 G-C WC 19-XIX cWW cW-W 62 I.DA3 J.DT-3 A-T WC 20-XX cWW cW-W 63 I.DG4 J.DC-4 G-C WC 19-XIX cWW cW-W 64 I.DG5 J.DC-5 G-C WC 19-XIX cWW cW-W 65 I.DA6 J.DT-6 A-T WC 20-XX cWW cW-W 66 I.DA7 J.DT-7 A-T WC 20-XX cWW cW-W 67 I.DA8 J.DT-8 A-T WC 20-XX cWW cW-W 68 I.DA9 J.DT-9 A-T WC 20-XX cWW cW-W 69 I.DG10 J.DC-10 G-C WC 19-XIX cWW cW-W 70 I.DT11 J.DA-11 T-A WC 20-XX cWW cW-W 71 I.DC12 J.DG-12 C-G WC 19-XIX cWW cW-W 72 I.DA13 J.DT-13 A-T WC 20-XX cWW cW-W 73 I.DG14 J.DC-14 G-C WC 19-XIX cWW cW-W 74 I.DC15 J.DG-15 C-G WC 19-XIX cWW cW-W 75 I.DC16 J.DG-16 C-G WC 19-XIX cWW cW-W 76 I.DT17 J.DA-17 T-A WC 20-XX cWW cW-W 77 I.DT18 J.DA-18 T-A WC 20-XX cWW cW-W 78 I.DG19 J.DC-19 G-C WC 19-XIX cWW cW-W 79 I.DT20 J.DA-20 T-A WC 20-XX cWW cW-W 80 I.DG21 J.DC-21 G-C WC 19-XIX cWW cW-W 81 I.DC22 J.DG-22 C-G WC 19-XIX cWW cW-W 82 I.DT23 J.DA-23 T-A WC 20-XX cWW cW-W 83 I.DC24 J.DG-24 C-G WC 19-XIX cWW cW-W 84 I.DG25 J.DC-25 G-C WC 19-XIX cWW cW-W 85 I.DC26 J.DG-26 C-G WC 19-XIX cWW cW-W 86 I.DC27 J.DG-27 C-G WC 19-XIX cWW cW-W 87 I.DT28 J.DA-28 T-A WC 20-XX cWW cW-W 88 I.DA29 J.DT-29 A-T WC 20-XX cWW cW-W 89 I.DC30 J.DG-30 C-G WC 19-XIX cWW cW-W 90 I.DG31 J.DC-31 G-C WC 19-XIX cWW cW-W 91 I.DG32 J.DC-32 G-C WC 19-XIX cWW cW-W 92 I.DC33 J.DG-33 C-G WC 19-XIX cWW cW-W 93 I.DC34 J.DG-34 C-G WC 19-XIX cWW cW-W 94 I.DA35 J.DT-35 A-T WC 20-XX cWW cW-W 95 I.DT36 J.DA-36 T-A WC 20-XX cWW cW-W 96 I.DA37 J.DT-37 A-T WC 20-XX cWW cW-W 97 I.DC38 J.DG-38 C-G WC 19-XIX cWW cW-W 98 I.DC39 J.DG-39 C-G WC 19-XIX cWW cW-W 99 I.DA40 J.DT-40 A-T WC 20-XX cWW cW-W 100 I.DC41 J.DG-41 C-G WC 19-XIX cWW cW-W 101 I.DC42 J.DG-42 C-G WC 19-XIX cWW cW-W 102 I.DC43 J.DG-43 C-G WC 19-XIX cWW cW-W 103 I.DT44 J.DA-44 T-A WC 20-XX cWW cW-W 104 I.DG45 J.DC-45 G-C WC 19-XIX cWW cW-W 105 I.DA46 J.DT-46 A-T WC 20-XX cWW cW-W 106 I.DA47 J.DT-47 A-T WC 20-XX cWW cW-W 107 I.DA48 J.DT-48 A-T WC 20-XX cWW cW-W 108 I.DG49 J.DC-49 G-C WC 19-XIX cWW cW-W 109 I.DT50 J.DA-50 T-A WC 20-XX cWW cW-W **************************************************************************** List of 2 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=21 strand-1 5'-TGGGGGAAAAGACCCTGGCAT-3' bp-type ||||||||||||||||||||| strand-2 3'-ACCCCCTTTTCTGGGACCGTA-5' helix-form BBB.....BBBBBBBBBBBB 1 I.DT-58 J.DA58 T-A WC 20-XX cWW cW-W 2 I.DG-57 J.DC57 G-C WC 19-XIX cWW cW-W 3 I.DG-56 J.DC56 G-C WC 19-XIX cWW cW-W 4 I.DG-55 J.DC55 G-C WC 19-XIX cWW cW-W 5 I.DG-54 J.DC54 G-C WC 19-XIX cWW cW-W 6 I.DG-53 J.DC53 G-C WC 19-XIX cWW cW-W 7 I.DA-52 J.DT52 A-T WC 20-XX cWW cW-W 8 I.DA-51 J.DT51 A-T WC 20-XX cWW cW-W 9 I.DA-50 J.DT50 A-T WC 20-XX cWW cW-W 10 I.DA-49 J.DT49 A-T WC 20-XX cWW cW-W 11 I.DG-48 J.DC48 G-C WC 19-XIX cWW cW-W 12 I.DA-47 J.DT47 A-T WC 20-XX cWW cW-W 13 I.DC-46 J.DG46 C-G WC 19-XIX cWW cW-W 14 I.DC-45 J.DG45 C-G WC 19-XIX cWW cW-W 15 I.DC-44 J.DG44 C-G WC 19-XIX cWW cW-W 16 I.DT-43 J.DA43 T-A WC 20-XX cWW cW-W 17 I.DG-42 J.DC42 G-C WC 19-XIX cWW cW-W 18 I.DG-41 J.DC41 G-C WC 19-XIX cWW cW-W 19 I.DC-40 J.DG40 C-G WC 19-XIX cWW cW-W 20 I.DA-39 J.DT39 A-T WC 20-XX cWW cW-W 21 I.DT-38 J.DA38 T-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=87 strand-1 5'-GGGAGGAGCTGGGCCCCCCCCAGAAGGCAGCACAAGGGGAGGAAAAGTCAGCCTTGTGCTCGCCTACGGCCATACCACCCTGAAAGT-3' bp-type ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| strand-2 3'-CCCTCCTCGACCCGGGGGGGGTCTTCCGTCGTGTTCCCCTCCTTTTCAGTCGGAACACGAGCGGATGCCGGTATGGTGGGACTTTCA-5' helix-form BB..BBBBBBBBB.BBBBBB.B...BBBBBBBBBBBBBBBBB....BBBBBB.BB.BBBBBBBBBBBBBBBB.BBBBBBBBB.... 1 I.DG-36 J.DC36 G-C WC 19-XIX cWW cW-W 2 I.DG-35 J.DC35 G-C WC 19-XIX cWW cW-W 3 I.DG-34 J.DC34 G-C WC 19-XIX cWW cW-W 4 I.DA-33 J.DT33 A-T WC 20-XX cWW cW-W 5 I.DG-32 J.DC32 G-C WC 19-XIX cWW cW-W 6 I.DG-31 J.DC31 G-C WC 19-XIX cWW cW-W 7 I.DA-30 J.DT30 A-T WC 20-XX cWW cW-W 8 I.DG-29 J.DC29 G-C WC 19-XIX cWW cW-W 9 I.DC-28 J.DG28 C-G WC 19-XIX cWW cW-W 10 I.DT-27 J.DA27 T-A WC 20-XX cWW cW-W 11 I.DG-26 J.DC26 G-C WC 19-XIX cWW cW-W 12 I.DG-25 J.DC25 G-C WC 19-XIX cWW cW-W 13 I.DG-24 J.DC24 G-C WC 19-XIX cWW cW-W 14 I.DC-23 J.DG23 C-G WC 19-XIX cWW cW-W 15 I.DC-22 J.DG22 C-G WC 19-XIX cWW cW-W 16 I.DC-21 J.DG21 C-G WC 19-XIX cWW cW-W 17 I.DC-20 J.DG20 C-G WC 19-XIX cWW cW-W 18 I.DC-19 J.DG19 C-G WC 19-XIX cWW cW-W 19 I.DC-18 J.DG18 C-G WC 19-XIX cWW cW-W 20 I.DC-17 J.DG17 C-G WC 19-XIX cWW cW-W 21 I.DC-16 J.DG16 C-G WC 19-XIX cWW cW-W 22 I.DA-15 J.DT15 A-T WC 20-XX cWW cW-W 23 I.DG-14 J.DC14 G-C WC 19-XIX cWW cW-W 24 I.DA-13 J.DT13 A-T WC 20-XX cWW cW-W 25 I.DA-12 J.DT12 A-T WC 20-XX cWW cW-W 26 I.DG-11 J.DC11 G-C WC 19-XIX cWW cW-W 27 I.DG-10 J.DC10 G-C WC 19-XIX cWW cW-W 28 I.DC-9 J.DG9 C-G WC 19-XIX cWW cW-W 29 I.DA-8 J.DT8 A-T WC 20-XX cWW cW-W 30 I.DG-7 J.DC7 G-C WC 19-XIX cWW cW-W 31 I.DC-6 J.DG6 C-G WC 19-XIX cWW cW-W 32 I.DA-5 J.DT5 A-T WC 20-XX cWW cW-W 33 I.DC-4 J.DG4 C-G WC 19-XIX cWW cW-W 34 I.DA-3 J.DT3 A-T WC 20-XX cWW cW-W 35 I.DA-2 J.DT2 A-T WC 20-XX cWW cW-W 36 I.DG-1 J.DC1 G-C WC 19-XIX cWW cW-W 37 I.DG0 J.DC0 G-C WC 19-XIX cWW cW-W 38 I.DG1 J.DC-1 G-C WC 19-XIX cWW cW-W 39 I.DG2 J.DC-2 G-C WC 19-XIX cWW cW-W 40 I.DA3 J.DT-3 A-T WC 20-XX cWW cW-W 41 I.DG4 J.DC-4 G-C WC 19-XIX cWW cW-W 42 I.DG5 J.DC-5 G-C WC 19-XIX cWW cW-W 43 I.DA6 J.DT-6 A-T WC 20-XX cWW cW-W 44 I.DA7 J.DT-7 A-T WC 20-XX cWW cW-W 45 I.DA8 J.DT-8 A-T WC 20-XX cWW cW-W 46 I.DA9 J.DT-9 A-T WC 20-XX cWW cW-W 47 I.DG10 J.DC-10 G-C WC 19-XIX cWW cW-W 48 I.DT11 J.DA-11 T-A WC 20-XX cWW cW-W 49 I.DC12 J.DG-12 C-G WC 19-XIX cWW cW-W 50 I.DA13 J.DT-13 A-T WC 20-XX cWW cW-W 51 I.DG14 J.DC-14 G-C WC 19-XIX cWW cW-W 52 I.DC15 J.DG-15 C-G WC 19-XIX cWW cW-W 53 I.DC16 J.DG-16 C-G WC 19-XIX cWW cW-W 54 I.DT17 J.DA-17 T-A WC 20-XX cWW cW-W 55 I.DT18 J.DA-18 T-A WC 20-XX cWW cW-W 56 I.DG19 J.DC-19 G-C WC 19-XIX cWW cW-W 57 I.DT20 J.DA-20 T-A WC 20-XX cWW cW-W 58 I.DG21 J.DC-21 G-C WC 19-XIX cWW cW-W 59 I.DC22 J.DG-22 C-G WC 19-XIX cWW cW-W 60 I.DT23 J.DA-23 T-A WC 20-XX cWW cW-W 61 I.DC24 J.DG-24 C-G WC 19-XIX cWW cW-W 62 I.DG25 J.DC-25 G-C WC 19-XIX cWW cW-W 63 I.DC26 J.DG-26 C-G WC 19-XIX cWW cW-W 64 I.DC27 J.DG-27 C-G WC 19-XIX cWW cW-W 65 I.DT28 J.DA-28 T-A WC 20-XX cWW cW-W 66 I.DA29 J.DT-29 A-T WC 20-XX cWW cW-W 67 I.DC30 J.DG-30 C-G WC 19-XIX cWW cW-W 68 I.DG31 J.DC-31 G-C WC 19-XIX cWW cW-W 69 I.DG32 J.DC-32 G-C WC 19-XIX cWW cW-W 70 I.DC33 J.DG-33 C-G WC 19-XIX cWW cW-W 71 I.DC34 J.DG-34 C-G WC 19-XIX cWW cW-W 72 I.DA35 J.DT-35 A-T WC 20-XX cWW cW-W 73 I.DT36 J.DA-36 T-A WC 20-XX cWW cW-W 74 I.DA37 J.DT-37 A-T WC 20-XX cWW cW-W 75 I.DC38 J.DG-38 C-G WC 19-XIX cWW cW-W 76 I.DC39 J.DG-39 C-G WC 19-XIX cWW cW-W 77 I.DA40 J.DT-40 A-T WC 20-XX cWW cW-W 78 I.DC41 J.DG-41 C-G WC 19-XIX cWW cW-W 79 I.DC42 J.DG-42 C-G WC 19-XIX cWW cW-W 80 I.DC43 J.DG-43 C-G WC 19-XIX cWW cW-W 81 I.DT44 J.DA-44 T-A WC 20-XX cWW cW-W 82 I.DG45 J.DC-45 G-C WC 19-XIX cWW cW-W 83 I.DA46 J.DT-46 A-T WC 20-XX cWW cW-W 84 I.DA47 J.DT-47 A-T WC 20-XX cWW cW-W 85 I.DA48 J.DT-48 A-T WC 20-XX cWW cW-W 86 I.DG49 J.DC-49 G-C WC 19-XIX cWW cW-W 87 I.DT50 J.DA-50 T-A WC 20-XX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#1 contains 2 stems: [#1,#2] **************************************************************************** List of 2 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=3 TGG I.DT-38,I.DG-37,I.DG-36 2 nts=3 CCA J.DC36,J.DC37,J.DA38 **************************************************************************** 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 1 internal loop 1 symmetric internal loop: nts=6; [1,1]; linked by [#1,#2] summary: [2] 1 1 [I.-38 J.38 I.-36 J.36] 21 87 nts=6 TGGCCA I.DT-38,I.DG-37,I.DG-36,J.DC36,J.DC37,J.DA38 nts=1 G I.DG-37 nts=1 C J.DC37 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >9d3q nts=218 [whole] TGGGGGAAAAGACCCTGGCATGGGGAGGAGCTGGGCCCCCCCCAGAAGGCAGCACAAGGGGAGGAAAAGTCAGCCTTGTGCTCGCCTACGGCCATACCACCCTGAAAGT&ACTTTCAGGGTGGTATGGCCGTAGGCGAGCACAAGGCTGACTTTTCCTCCCCTTGTGCTGCCTTCTGGGGGGGGCCCAGCTCCTCCCCATGCCAGGGTCTTTTCCCCCA (((((((((((((((((((((.(((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((&))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))).))))))))))))))))))))) >9d3q-I #1 nts=109 0.31(2.32) [chain] DNA TGGGGGAAAAGACCCTGGCATGGGGAGGAGCTGGGCCCCCCCCAGAAGGCAGCACAAGGGGAGGAAAAGTCAGCCTTGTGCTCGCCTACGGCCATACCACCCTGAAAGT (((((((((((((((((((((.((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((( >9d3q-J #2 nts=109 0.32(2.34) [chain] DNA ACTTTCAGGGTGGTATGGCCGTAGGCGAGCACAAGGCTGACTTTTCCTCCCCTTGTGCTGCCTTCTGGGGGGGGCCCAGCTCCTCCCCATGCCAGGGTCTTTTCCCCCA ))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))).))))))))))))))))))))) **************************************************************************** Summary of structural features of 218 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 ( I.DT-58 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 2 G ( I.DG-57 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 3 G ( I.DG-56 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 4 G ( I.DG-55 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 5 G ( I.DG-54 0.005 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 6 G ( I.DG-53 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 7 A ( I.DA-52 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 8 A ( I.DA-51 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 9 A ( I.DA-50 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 10 A ( I.DA-49 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 11 G ( I.DG-48 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 12 A ( I.DA-47 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 13 C ( I.DC-46 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 14 C ( I.DC-45 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 15 C ( I.DC-44 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 16 T ( I.DT-43 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 17 G ( I.DG-42 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 18 G ( I.DG-41 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 19 C ( I.DC-40 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 20 A ( I.DA-39 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 21 T ( I.DT-38 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 22 G . I.DG-37 0.004 anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop 23 G ( I.DG-36 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 24 G ( I.DG-35 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 25 G ( I.DG-34 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 26 A ( I.DA-33 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 27 G ( I.DG-32 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 28 G ( I.DG-31 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 29 A ( I.DA-30 0.004 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 30 G ( I.DG-29 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 31 C ( I.DC-28 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 32 T ( I.DT-27 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 33 G ( I.DG-26 0.005 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 34 G ( I.DG-25 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 35 G ( I.DG-24 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 36 C ( I.DC-23 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 37 C ( I.DC-22 0.003 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 38 C ( I.DC-21 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 39 C ( I.DC-20 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 40 C ( I.DC-19 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 41 C ( I.DC-18 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 42 C ( I.DC-17 0.006 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 43 C ( I.DC-16 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 44 A ( I.DA-15 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 45 G ( I.DG-14 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 46 A ( I.DA-13 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 47 A ( I.DA-12 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 48 G ( I.DG-11 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 49 G ( I.DG-10 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 50 C ( I.DC-9 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 51 A ( I.DA-8 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 52 G ( I.DG-7 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 53 C ( I.DC-6 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 54 A ( I.DA-5 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 55 C ( I.DC-4 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 56 A ( I.DA-3 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 57 A ( I.DA-2 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 58 G ( I.DG-1 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 59 G ( I.DG0 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 60 G ( I.DG1 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 61 G ( I.DG2 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 62 A ( I.DA3 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 63 G ( I.DG4 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 64 G ( I.DG5 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 65 A ( I.DA6 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 66 A ( I.DA7 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 67 A ( I.DA8 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 68 A ( I.DA9 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 69 G ( I.DG10 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 70 T ( I.DT11 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 71 C ( I.DC12 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 72 A ( I.DA13 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 73 G ( I.DG14 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 74 C ( I.DC15 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 75 C ( I.DC16 0.004 ~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 76 T ( I.DT17 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 77 T ( I.DT18 0.002 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 78 G ( I.DG19 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 79 T ( I.DT20 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 80 G ( I.DG21 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 81 C ( I.DC22 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 82 T ( I.DT23 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 83 C ( I.DC24 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 84 G ( I.DG25 0.005 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 85 C ( I.DC26 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 86 C ( I.DC27 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 87 T ( I.DT28 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 88 A ( I.DA29 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 89 C ( I.DC30 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 90 G ( I.DG31 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 91 G ( I.DG32 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 92 C ( I.DC33 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 93 C ( I.DC34 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 94 A ( I.DA35 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 95 T ( I.DT36 0.002 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 96 A ( I.DA37 0.004 BI,canonical,non-pair-contact,helix,stem,coaxial-stack 97 C ( I.DC38 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 98 C ( I.DC39 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 99 A ( I.DA40 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 100 C ( I.DC41 0.002 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 101 C ( I.DC42 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 102 C ( I.DC43 0.003 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 103 T ( I.DT44 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 104 G ( I.DG45 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 105 A ( I.DA46 0.005 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 106 A ( I.DA47 0.005 ~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 107 A ( I.DA48 0.005 ~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 108 G ( I.DG49 0.005 anti,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 109 T ( I.DT50 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 110 A ) J.DA-50 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 111 C ) J.DC-49 0.005 BI,canonical,non-pair-contact,helix,stem,coaxial-stack 112 T ) J.DT-48 0.005 anti,~C2'-endo,BII,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 113 T ) J.DT-47 0.004 ~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 114 T ) J.DT-46 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 115 C ) J.DC-45 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 116 A ) J.DA-44 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 117 G ) J.DG-43 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 118 G ) J.DG-42 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 119 G ) J.DG-41 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 120 T ) J.DT-40 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 121 G ) J.DG-39 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 122 G ) J.DG-38 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 123 T ) J.DT-37 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 124 A ) J.DA-36 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 125 T ) J.DT-35 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 126 G ) J.DG-34 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 127 G ) J.DG-33 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 128 C ) J.DC-32 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 129 C ) J.DC-31 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 130 G ) J.DG-30 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 131 T ) J.DT-29 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 132 A ) J.DA-28 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 133 G ) J.DG-27 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 134 G ) J.DG-26 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 135 C ) J.DC-25 0.005 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 136 G ) J.DG-24 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 137 A ) J.DA-23 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 138 G ) J.DG-22 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 139 C ) J.DC-21 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 140 A ) J.DA-20 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 141 C ) J.DC-19 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 142 A ) J.DA-18 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 143 A ) J.DA-17 0.004 canonical,non-pair-contact,helix,stem,coaxial-stack 144 G ) J.DG-16 0.004 ~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 145 G ) J.DG-15 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 146 C ) J.DC-14 0.003 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 147 T ) J.DT-13 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 148 G ) J.DG-12 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 149 A ) J.DA-11 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 150 C ) J.DC-10 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 151 T ) J.DT-9 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 152 T ) J.DT-8 0.004 ~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 153 T ) J.DT-7 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 154 T ) J.DT-6 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 155 C ) J.DC-5 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 156 C ) J.DC-4 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 157 T ) J.DT-3 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 158 C ) J.DC-2 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 159 C ) J.DC-1 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 160 C ) J.DC0 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 161 C ) J.DC1 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 162 T ) J.DT2 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 163 T ) J.DT3 0.002 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 164 G ) J.DG4 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 165 T ) J.DT5 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 166 G ) J.DG6 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 167 C ) J.DC7 0.004 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 168 T ) J.DT8 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 169 G ) J.DG9 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 170 C ) J.DC10 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 171 C ) J.DC11 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 172 T ) J.DT12 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 173 T ) J.DT13 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 174 C ) J.DC14 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 175 T ) J.DT15 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 176 G ) J.DG16 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 177 G ) J.DG17 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 178 G ) J.DG18 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 179 G ) J.DG19 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 180 G ) J.DG20 0.008 anti,canonical,non-pair-contact,helix,stem,coaxial-stack 181 G ) J.DG21 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 182 G ) J.DG22 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 183 G ) J.DG23 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 184 C ) J.DC24 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 185 C ) J.DC25 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 186 C ) J.DC26 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 187 A ) J.DA27 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 188 G ) J.DG28 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 189 C ) J.DC29 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 190 T ) J.DT30 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 191 C ) J.DC31 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 192 C ) J.DC32 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 193 T ) J.DT33 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 194 C ) J.DC34 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 195 C ) J.DC35 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 196 C ) J.DC36 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 197 C . J.DC37 0.003 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 198 A ) J.DA38 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 199 T ) J.DT39 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 200 G ) J.DG40 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 201 C ) J.DC41 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 202 C ) J.DC42 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 203 A ) J.DA43 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 204 G ) J.DG44 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 205 G ) J.DG45 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 206 G ) J.DG46 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 207 T ) J.DT47 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 208 C ) J.DC48 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 209 T ) J.DT49 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 210 T ) J.DT50 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 211 T ) J.DT51 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 212 T ) J.DT52 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 213 C ) J.DC53 0.005 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 214 C ) J.DC54 0.003 ~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 215 C ) J.DC55 0.002 ~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 216 C ) J.DC56 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 217 C ) J.DC57 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 218 A ) J.DA58 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,phosphate **************************************************************************** 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-iloops.pdb -- an ensemble of internal loops 5 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 6 dssr-2ndstrs.ct -- secondary structure in connectivity table format 7 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 8 dssr-torsions.txt -- backbone torsion angles and suite names 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