**************************************************************************** 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=2c9n.pdb -o=2c9n.out File name: 2c9n.pdb no. of DNA/RNA chains: 2 [A=11,B=11] no. of nucleotides: 22 no. of atoms: 1414 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 10 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DA5 B.DT116 A-T WC 20-XX cWW cW-W 2 A.DC6 B.DG115 C-G WC 19-XIX cWW cW-W 3 A.DT7 B.DA114 T-A WC 20-XX cWW cW-W 4 A.DG8 B.DC113 G-C WC 19-XIX cWW cW-W 5 A.DA9 B.DT112 A-T WC 20-XX cWW cW-W 6 A.DC10 B.DG111 C-G WC 19-XIX cWW cW-W 7 A.DT11 B.DA110 T-A WC 20-XX cWW cW-W 8 A.DC12 B.DG109 C-G WC 19-XIX cWW cW-W 9 A.DA13 B.DT108 A-T WC 20-XX cWW cW-W 10 A.DT14 B.DA107 T-A WC 20-XX 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=10 strand-1 5'-ACTGACTCAT-3' bp-type |||||||||| strand-2 3'-TGACTGAGTA-5' helix-form .BBBBBBBB 1 A.DA5 B.DT116 A-T WC 20-XX cWW cW-W 2 A.DC6 B.DG115 C-G WC 19-XIX cWW cW-W 3 A.DT7 B.DA114 T-A WC 20-XX cWW cW-W 4 A.DG8 B.DC113 G-C WC 19-XIX cWW cW-W 5 A.DA9 B.DT112 A-T WC 20-XX cWW cW-W 6 A.DC10 B.DG111 C-G WC 19-XIX cWW cW-W 7 A.DT11 B.DA110 T-A WC 20-XX cWW cW-W 8 A.DC12 B.DG109 C-G WC 19-XIX cWW cW-W 9 A.DA13 B.DT108 A-T WC 20-XX cWW cW-W 10 A.DT14 B.DA107 T-A WC 20-XX 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=10 strand-1 5'-ACTGACTCAT-3' bp-type |||||||||| strand-2 3'-TGACTGAGTA-5' helix-form .BBBBBBBB 1 A.DA5 B.DT116 A-T WC 20-XX cWW cW-W 2 A.DC6 B.DG115 C-G WC 19-XIX cWW cW-W 3 A.DT7 B.DA114 T-A WC 20-XX cWW cW-W 4 A.DG8 B.DC113 G-C WC 19-XIX cWW cW-W 5 A.DA9 B.DT112 A-T WC 20-XX cWW cW-W 6 A.DC10 B.DG111 C-G WC 19-XIX cWW cW-W 7 A.DT11 B.DA110 T-A WC 20-XX cWW cW-W 8 A.DC12 B.DG109 C-G WC 19-XIX cWW cW-W 9 A.DA13 B.DT108 A-T WC 20-XX cWW cW-W 10 A.DT14 B.DA107 T-A WC 20-XX cWW cW-W **************************************************************************** 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=2 CA A.DC4,A.DA5 2 nts=2 CA B.DC106,B.DA107 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=1 C A.DC4 2 nts=1 C B.DC106 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >2c9n nts=22 [whole] CACTGACTCAT&CATGAGTCAGT .((((((((((&.)))))))))) >2c9n-A #1 nts=11 3.25(0.28) [chain] DNA CACTGACTCAT .(((((((((( >2c9n-B #2 nts=11 3.11(0.30) [chain] DNA CATGAGTCAGT .)))))))))) **************************************************************************** Summary of structural features of 22 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 C . A.DC4 0.003 anti,~C2'-endo,non-pair-contact,ss-non-loop 2 A ( A.DA5 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 3 C ( A.DC6 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 4 T ( A.DT7 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 5 G ( A.DG8 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 6 A ( A.DA9 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 7 C ( A.DC10 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 8 T ( A.DT11 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 9 C ( A.DC12 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 10 A ( A.DA13 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 11 T ( A.DT14 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 12 C . B.DC106 0.011 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 13 A ) B.DA107 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 14 T ) B.DT108 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,phosphate 15 G ) B.DG109 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 16 A ) B.DA110 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 17 G ) B.DG111 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 18 T ) B.DT112 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 19 C ) B.DC113 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 20 A ) B.DA114 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 21 G ) B.DG115 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 22 T ) B.DT116 0.009 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** List of 8 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-stacks.pdb -- an ensemble of base stacks