**************************************************************************** Note: By default, each nucleotide is identified by chainId.name#. So a common case would be B.A1689, meaning adenosine #1689 on chain B. One-letter base names for modified nucleotides are put in lower case (e.g., 'c' for 5MC). For further information about the output notation, please refer to the DSSR User Manual. Questions and suggestions are *always* welcome on the 3DNA Forum. Command: x3dna-dssr -i=2xro.pdb -o=2xro.out File name: 2xro.pdb no. of DNA/RNA chains: 2 [X=42,Y=43] no. of nucleotides: 85 no. of atoms: 8840 no. of waters: 0 no. of metals: 2 [Os=2] **************************************************************************** List of 44 base pairs nt1 nt2 bp name Saenger LW DSSR 1 X.DG1 Y.DC42 G-C WC 19-XIX cWW cW-W 2 X.DA2 Y.DT41 A-T WC 20-XX cWW cW-W 3 X.DG3 Y.DC40 G-C WC 19-XIX cWW cW-W 4 X.DT4 Y.DA39 T-A WC 20-XX cWW cW-W 5 X.DA5 Y.DT38 A-T WC 20-XX cWW cW-W 6 X.DT6 Y.DA37 T-A WC 20-XX cWW cW-W 7 X.DC7 Y.DG36 C-G WC 19-XIX cWW cW-W 8 X.DA8 Y.DT35 A-T WC 20-XX cWW cW-W 9 X.DC9 Y.DG34 C-G WC 19-XIX cWW cW-W 10 X.DA10 Y.DT33 A-T WC 20-XX cWW cW-W 11 X.DT11 Y.DA32 T-A WC 20-XX cWW cW-W 12 X.DA12 Y.DT30 A-T -- -- cWW cW-W 13 X.DA12 Y.DT31 A-T WC 20-XX cWW cW-W 14 X.DA13 Y.DT30 A-T WC 20-XX cWW cW-W 15 X.DT14 Y.DA29 T-A WC 20-XX cWW cW-W 16 X.DG15 Y.DC28 G-C WC 19-XIX cWW cW-W 17 X.DC16 Y.DG27 C-G WC 19-XIX cWW cW-W 18 X.DT17 Y.DA26 T-A WC 20-XX cWW cW-W 19 X.DA18 Y.DT25 A-T WC 20-XX cWW cW-W 20 X.DC19 Y.DG24 C-G WC 19-XIX cWW cW-W 21 X.DA20 Y.DT23 A-T WC 20-XX cWW cW-W 22 X.DC21 Y.DG22 C-G WC 19-XIX cWW cW-W 23 X.DT22 Y.DA21 T-A WC 20-XX cWW cW-W 24 X.DC23 Y.DG20 C-G WC 19-XIX cWW cW-W 25 X.DT24 Y.DA19 T-A WC 20-XX cWW cW-W 26 X.DA25 Y.DT18 A-T WC 20-XX cWW cW-W 27 X.DC26 Y.DG17 C-G WC 19-XIX cWW cW-W 28 X.DC27 Y.DG16 C-G WC 19-XIX cWW cW-W 29 X.DG28 Y.DC15 G-C WC 19-XIX cWW cW-W 30 X.DC29 Y.DT13 C-T -- -- cWW cW-W 31 X.DC29 Y.DG14 C-G WC 19-XIX cWW cW-W 32 X.DA30 Y.DT13 A-T WC 20-XX cWW cW-W 33 X.DT31 Y.DA12 T-A WC 20-XX cWW cW-W 34 X.DT32 Y.DA11 T-A WC 20-XX cWW cW-W 35 X.DA33 Y.DT10 A-T WC 20-XX cWW cW-W 36 X.DC34 Y.DG9 C-G WC 19-XIX cWW cW-W 37 X.DG35 Y.DC8 G-C WC 19-XIX cWW cW-W 38 X.DA36 Y.DT7 A-T WC 20-XX cWW cW-W 39 X.DT37 Y.DA6 T-A WC 20-XX cWW cW-W 40 X.DT38 Y.DA5 T-A WC 20-XX cWW cW-W 41 X.DC39 Y.DG4 C-G WC 19-XIX cWW cW-W 42 X.DA40 Y.DT3 A-T WC 20-XX cWW cW-W 43 X.DG41 Y.DC2 G-C WC 19-XIX cWW cW-W 44 X.DC42 Y.DG1 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 1 helix Note: a helix is defined by base-stacking interactions, regardless of bp 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=42 strand-1 5'-GAGTATCACATAATGCTACACTCTACCGCATTACGATTCAGC-3' bp-type |||||||||||||||||||||||||||||||||||||||||| strand-2 3'-CTCATAGTGTATTACGATGTGAGATGGCGTAATGCTAAGTCG-5' helix-form ........B.......B..............BBB....... 1 X.DG1 Y.DC42 G-C WC 19-XIX cWW cW-W 2 X.DA2 Y.DT41 A-T WC 20-XX cWW cW-W 3 X.DG3 Y.DC40 G-C WC 19-XIX cWW cW-W 4 X.DT4 Y.DA39 T-A WC 20-XX cWW cW-W 5 X.DA5 Y.DT38 A-T WC 20-XX cWW cW-W 6 X.DT6 Y.DA37 T-A WC 20-XX cWW cW-W 7 X.DC7 Y.DG36 C-G WC 19-XIX cWW cW-W 8 X.DA8 Y.DT35 A-T WC 20-XX cWW cW-W 9 X.DC9 Y.DG34 C-G WC 19-XIX cWW cW-W 10 X.DA10 Y.DT33 A-T WC 20-XX cWW cW-W 11 X.DT11 Y.DA32 T-A WC 20-XX cWW cW-W 12 X.DA12 Y.DT31 A-T WC 20-XX cWW cW-W 13 X.DA13 Y.DT30 A-T WC 20-XX cWW cW-W 14 X.DT14 Y.DA29 T-A WC 20-XX cWW cW-W 15 X.DG15 Y.DC28 G-C WC 19-XIX cWW cW-W 16 X.DC16 Y.DG27 C-G WC 19-XIX cWW cW-W 17 X.DT17 Y.DA26 T-A WC 20-XX cWW cW-W 18 X.DA18 Y.DT25 A-T WC 20-XX cWW cW-W 19 X.DC19 Y.DG24 C-G WC 19-XIX cWW cW-W 20 X.DA20 Y.DT23 A-T WC 20-XX cWW cW-W 21 X.DC21 Y.DG22 C-G WC 19-XIX cWW cW-W 22 X.DT22 Y.DA21 T-A WC 20-XX cWW cW-W 23 X.DC23 Y.DG20 C-G WC 19-XIX cWW cW-W 24 X.DT24 Y.DA19 T-A WC 20-XX cWW cW-W 25 X.DA25 Y.DT18 A-T WC 20-XX cWW cW-W 26 X.DC26 Y.DG17 C-G WC 19-XIX cWW cW-W 27 X.DC27 Y.DG16 C-G WC 19-XIX cWW cW-W 28 X.DG28 Y.DC15 G-C WC 19-XIX cWW cW-W 29 X.DC29 Y.DG14 C-G WC 19-XIX cWW cW-W 30 X.DA30 Y.DT13 A-T WC 20-XX cWW cW-W 31 X.DT31 Y.DA12 T-A WC 20-XX cWW cW-W 32 X.DT32 Y.DA11 T-A WC 20-XX cWW cW-W 33 X.DA33 Y.DT10 A-T WC 20-XX cWW cW-W 34 X.DC34 Y.DG9 C-G WC 19-XIX cWW cW-W 35 X.DG35 Y.DC8 G-C WC 19-XIX cWW cW-W 36 X.DA36 Y.DT7 A-T WC 20-XX cWW cW-W 37 X.DT37 Y.DA6 T-A WC 20-XX cWW cW-W 38 X.DT38 Y.DA5 T-A WC 20-XX cWW cW-W 39 X.DC39 Y.DG4 C-G WC 19-XIX cWW cW-W 40 X.DA40 Y.DT3 A-T WC 20-XX cWW cW-W 41 X.DG41 Y.DC2 G-C WC 19-XIX cWW cW-W 42 X.DC42 Y.DG1 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 1 stem Note: a stem is defined as a helix consisting of only 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=42 strand-1 5'-GAGTATCACATAATGCTACACTCTACCGCATTACGATTCAGC-3' bp-type |||||||||||||||||||||||||||||||||||||||||| strand-2 3'-CTCATAGTGTATTACGATGTGAGATGGCGTAATGCTAAGTCG-5' helix-form ........B.......B..............BBB....... 1 X.DG1 Y.DC42 G-C WC 19-XIX cWW cW-W 2 X.DA2 Y.DT41 A-T WC 20-XX cWW cW-W 3 X.DG3 Y.DC40 G-C WC 19-XIX cWW cW-W 4 X.DT4 Y.DA39 T-A WC 20-XX cWW cW-W 5 X.DA5 Y.DT38 A-T WC 20-XX cWW cW-W 6 X.DT6 Y.DA37 T-A WC 20-XX cWW cW-W 7 X.DC7 Y.DG36 C-G WC 19-XIX cWW cW-W 8 X.DA8 Y.DT35 A-T WC 20-XX cWW cW-W 9 X.DC9 Y.DG34 C-G WC 19-XIX cWW cW-W 10 X.DA10 Y.DT33 A-T WC 20-XX cWW cW-W 11 X.DT11 Y.DA32 T-A WC 20-XX cWW cW-W 12 X.DA12 Y.DT31 A-T WC 20-XX cWW cW-W 13 X.DA13 Y.DT30 A-T WC 20-XX cWW cW-W 14 X.DT14 Y.DA29 T-A WC 20-XX cWW cW-W 15 X.DG15 Y.DC28 G-C WC 19-XIX cWW cW-W 16 X.DC16 Y.DG27 C-G WC 19-XIX cWW cW-W 17 X.DT17 Y.DA26 T-A WC 20-XX cWW cW-W 18 X.DA18 Y.DT25 A-T WC 20-XX cWW cW-W 19 X.DC19 Y.DG24 C-G WC 19-XIX cWW cW-W 20 X.DA20 Y.DT23 A-T WC 20-XX cWW cW-W 21 X.DC21 Y.DG22 C-G WC 19-XIX cWW cW-W 22 X.DT22 Y.DA21 T-A WC 20-XX cWW cW-W 23 X.DC23 Y.DG20 C-G WC 19-XIX cWW cW-W 24 X.DT24 Y.DA19 T-A WC 20-XX cWW cW-W 25 X.DA25 Y.DT18 A-T WC 20-XX cWW cW-W 26 X.DC26 Y.DG17 C-G WC 19-XIX cWW cW-W 27 X.DC27 Y.DG16 C-G WC 19-XIX cWW cW-W 28 X.DG28 Y.DC15 G-C WC 19-XIX cWW cW-W 29 X.DC29 Y.DG14 C-G WC 19-XIX cWW cW-W 30 X.DA30 Y.DT13 A-T WC 20-XX cWW cW-W 31 X.DT31 Y.DA12 T-A WC 20-XX cWW cW-W 32 X.DT32 Y.DA11 T-A WC 20-XX cWW cW-W 33 X.DA33 Y.DT10 A-T WC 20-XX cWW cW-W 34 X.DC34 Y.DG9 C-G WC 19-XIX cWW cW-W 35 X.DG35 Y.DC8 G-C WC 19-XIX cWW cW-W 36 X.DA36 Y.DT7 A-T WC 20-XX cWW cW-W 37 X.DT37 Y.DA6 T-A WC 20-XX cWW cW-W 38 X.DT38 Y.DA5 T-A WC 20-XX cWW cW-W 39 X.DC39 Y.DG4 C-G WC 19-XIX cWW cW-W 40 X.DA40 Y.DT3 A-T WC 20-XX cWW cW-W 41 X.DG41 Y.DC2 G-C WC 19-XIX cWW cW-W 42 X.DC42 Y.DG1 C-G WC 19-XIX cWW cW-W **************************************************************************** Nucleotides not involved in stacking interactions nts=1 T Y.DT43 **************************************************************************** List of 1 non-loop single-stranded segment 1 nts=1 T Y.DT43 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >2xro nts=85 [whole] GAGTATCACATAATGCTACACTCTACCGCATTACGATTCAGC&GCTGAATCGTAATGCGGTAGAGTGTAGCATTATGTGATACTCT ((((((((((((((((((((((((((((((((((((((((((&)))))))))))))))))))))))))))))))))))))))))). >2xro-X #1 nts=42 2.77(1.24) [chain] DNA GAGTATCACATAATGCTACACTCTACCGCATTACGATTCAGC (((((((((((((((((((((((((((((((((((((((((( >2xro-Y #2 nts=43 2.76(1.28) [chain] DNA GCTGAATCGTAATGCGGTAGAGTGTAGCATTATGTGATACTCT )))))))))))))))))))))))))))))))))))))))))). **************************************************************************** Summary of structural features of 85 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 ( X.DG1 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 A ( X.DA2 0.034 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,phosphate 3 G ( X.DG3 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 4 T ( X.DT4 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 5 A ( X.DA5 0.014 anti,BI,canonical,non-pair-contact,helix,stem 6 T ( X.DT6 0.025 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 7 C ( X.DC7 0.016 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 8 A ( X.DA8 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 9 C ( X.DC9 0.019 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 10 A ( X.DA10 0.015 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 11 T ( X.DT11 0.018 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 12 A ( X.DA12 0.016 anti,~C2'-endo,canonical,non-canonical,non-pair-contact,helix,stem 13 A ( X.DA13 0.025 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 14 T ( X.DT14 0.016 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 15 G ( X.DG15 0.024 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,phosphate 16 C ( X.DC16 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 17 T ( X.DT17 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 18 A ( X.DA18 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 19 C ( X.DC19 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 20 A ( X.DA20 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 21 C ( X.DC21 0.028 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 22 T ( X.DT22 0.022 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 23 C ( X.DC23 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 24 T ( X.DT24 0.022 anti,BI,canonical,non-pair-contact,helix,stem 25 A ( X.DA25 0.013 anti,BI,canonical,non-pair-contact,helix,stem 26 C ( X.DC26 0.022 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 27 C ( X.DC27 0.018 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 28 G ( X.DG28 0.023 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 29 C ( X.DC29 0.023 anti,~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem 30 A ( X.DA30 0.016 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 31 T ( X.DT31 0.028 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 32 T ( X.DT32 0.026 anti,BI,canonical,non-pair-contact,helix,stem 33 A ( X.DA33 0.020 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 34 C ( X.DC34 0.011 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 35 G ( X.DG35 0.031 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 36 A ( X.DA36 0.024 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 37 T ( X.DT37 0.023 anti,BI,canonical,non-pair-contact,helix,stem 38 T ( X.DT38 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 39 C ( X.DC39 0.039 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 40 A ( X.DA40 0.020 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 41 G ( X.DG41 0.027 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 42 C ( X.DC42 0.018 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end 43 G ) Y.DG1 0.028 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 44 C ) Y.DC2 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 45 T ) Y.DT3 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 46 G ) Y.DG4 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 47 A ) Y.DA5 0.039 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 48 A ) Y.DA6 0.017 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 49 T ) Y.DT7 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 50 C ) Y.DC8 0.025 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 51 G ) Y.DG9 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 52 T ) Y.DT10 0.015 anti,BI,canonical,non-pair-contact,helix,stem 53 A ) Y.DA11 0.021 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 54 A ) Y.DA12 0.024 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 55 T ) Y.DT13 0.019 anti,BI,canonical,non-canonical,non-pair-contact,helix,stem 56 G ) Y.DG14 0.024 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 57 C ) Y.DC15 0.023 anti,canonical,non-pair-contact,helix,stem,phosphate 58 G ) Y.DG16 0.033 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,phosphate 59 G ) Y.DG17 0.023 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 60 T ) Y.DT18 0.021 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 61 A ) Y.DA19 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 62 G ) Y.DG20 0.020 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 63 A ) Y.DA21 0.019 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 64 G ) Y.DG22 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 65 T ) Y.DT23 0.020 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 66 G ) Y.DG24 0.026 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 67 T ) Y.DT25 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 68 A ) Y.DA26 0.019 anti,BI,canonical,non-pair-contact,helix,stem 69 G ) Y.DG27 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 70 C ) Y.DC28 0.020 ~C2'-endo,canonical,non-pair-contact,helix,stem 71 A ) Y.DA29 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 72 T ) Y.DT30 0.008 anti,~C2'-endo,canonical,non-canonical,non-pair-contact,helix,stem 73 T ) Y.DT31 0.025 anti,canonical,non-pair-contact,helix,stem 74 A ) Y.DA32 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 75 T ) Y.DT33 0.019 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 76 G ) Y.DG34 0.014 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 77 T ) Y.DT35 0.014 anti,canonical,non-pair-contact,helix,stem,phosphate 78 G ) Y.DG36 0.025 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 79 A ) Y.DA37 0.020 anti,BI,canonical,non-pair-contact,helix,stem 80 T ) Y.DT38 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 81 A ) Y.DA39 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 82 C ) Y.DC40 0.027 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 83 T ) Y.DT41 0.014 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 84 C ) Y.DC42 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 85 T . Y.DT43 0.011 syn,~C3'-endo,non-stack,non-pair-contact,ss-non-loop **************************************************************************** List of 7 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