**************************************************************************** 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=7owf.pdb -o=7owf.out File name: 7owf.pdb no. of DNA/RNA chains: 2 [B=12,C=16] no. of nucleotides: 28 no. of atoms: 9688 no. of waters: 102 no. of metals: 3 [Mg=3] **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 DOC-c 1 B.DOC112 **************************************************************************** List of 12 base pairs nt1 nt2 bp name Saenger LW DSSR 1 B.DG101 C.DC216 G-C WC 19-XIX cWW cW-W 2 B.DA102 C.DT215 A-T WC 20-XX cWW cW-W 3 B.DC103 C.DG214 C-G WC 19-XIX cWW cW-W 4 B.DC104 C.DG213 C-G WC 19-XIX cWW cW-W 5 B.DA105 C.DT212 A-T WC 20-XX cWW cW-W 6 B.DC106 C.DG211 C-G WC 19-XIX cWW cW-W 7 B.DG107 C.DC210 G-C WC 19-XIX cWW cW-W 8 B.DG108 C.DC209 G-C WC 19-XIX cWW cW-W 9 B.DC109 C.DG208 C-G WC 19-XIX cWW cW-W 10 B.DC110 C.DG207 C-G WC 19-XIX cWW cW-W 11 B.DA111 C.DT206 A-T WC 20-XX cWW cW-W 12 B.DOC112 C.DG205 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=12 strand-1 5'-GACCACGGCCAc-3' bp-type |||||||||||| strand-2 3'-CTGGTGCCGGTG-5' helix-form B.BBBBBB.A. 1 B.DG101 C.DC216 G-C WC 19-XIX cWW cW-W 2 B.DA102 C.DT215 A-T WC 20-XX cWW cW-W 3 B.DC103 C.DG214 C-G WC 19-XIX cWW cW-W 4 B.DC104 C.DG213 C-G WC 19-XIX cWW cW-W 5 B.DA105 C.DT212 A-T WC 20-XX cWW cW-W 6 B.DC106 C.DG211 C-G WC 19-XIX cWW cW-W 7 B.DG107 C.DC210 G-C WC 19-XIX cWW cW-W 8 B.DG108 C.DC209 G-C WC 19-XIX cWW cW-W 9 B.DC109 C.DG208 C-G WC 19-XIX cWW cW-W 10 B.DC110 C.DG207 C-G WC 19-XIX cWW cW-W 11 B.DA111 C.DT206 A-T WC 20-XX cWW cW-W 12 B.DOC112 C.DG205 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=12 strand-1 5'-GACCACGGCCAc-3' bp-type |||||||||||| strand-2 3'-CTGGTGCCGGTG-5' helix-form B.BBBBBB.A. 1 B.DG101 C.DC216 G-C WC 19-XIX cWW cW-W 2 B.DA102 C.DT215 A-T WC 20-XX cWW cW-W 3 B.DC103 C.DG214 C-G WC 19-XIX cWW cW-W 4 B.DC104 C.DG213 C-G WC 19-XIX cWW cW-W 5 B.DA105 C.DT212 A-T WC 20-XX cWW cW-W 6 B.DC106 C.DG211 C-G WC 19-XIX cWW cW-W 7 B.DG107 C.DC210 G-C WC 19-XIX cWW cW-W 8 B.DG108 C.DC209 G-C WC 19-XIX cWW cW-W 9 B.DC109 C.DG208 C-G WC 19-XIX cWW cW-W 10 B.DC110 C.DG207 C-G WC 19-XIX cWW cW-W 11 B.DA111 C.DT206 A-T WC 20-XX cWW cW-W 12 B.DOC112 C.DG205 c-G WC 19-XIX 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 AA C.DA201,C.DA202 2 nts=2 AG C.DA204,C.DG205 **************************************************************************** Nucleotides not involved in stacking interactions nts=1 C C.DC203 **************************************************************************** List of 1 non-loop single-stranded segment 1 nts=4 AACA C.DA201,C.DA202,C.DC203,C.DA204 **************************************************************************** List of 2 splayed-apart dinucleotides 1 C.DA202 C.DC203 angle=99 distance=14.2 ratio=0.76 2 C.DC203 C.DA204 angle=133 distance=18.2 ratio=0.92 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=3 ACA C.DA202,C.DC203,C.DA204 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >7owf nts=28 [whole] GACCACGGCCAc&AACAGTGGCCGTGGTC ((((((((((((&....)))))))))))) >7owf-B #1 nts=12 3.20(0.45) [chain] DNA GACCACGGCCAc (((((((((((( >7owf-C #2 nts=16 2.18(1.92) [chain] DNA AACAGTGGCCGTGGTC ....)))))))))))) **************************************************************************** Summary of structural features of 28 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 ( B.DG101 0.018 anti,BI,canonical,non-pair-contact,helix-end,stem-end 2 A ( B.DA102 0.010 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 3 C ( B.DC103 0.008 anti,BI,canonical,non-pair-contact,helix,stem 4 C ( B.DC104 0.015 anti,BI,canonical,non-pair-contact,helix,stem 5 A ( B.DA105 0.021 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 6 C ( B.DC106 0.021 anti,BI,canonical,non-pair-contact,helix,stem 7 G ( B.DG107 0.020 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 8 G ( B.DG108 0.013 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 9 C ( B.DC109 0.011 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 10 C ( B.DC110 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 11 A ( B.DA111 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 12 c ( B.DOC112 0.064 modified,anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end 13 A . C.DA201 0.005 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 14 A . C.DA202 0.008 anti,~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart 15 C . C.DC203 0.008 turn,syn,BI,non-stack,ss-non-loop,splayed-apart 16 A . C.DA204 0.017 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 17 G ) C.DG205 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 18 T ) C.DT206 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 19 G ) C.DG207 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 20 G ) C.DG208 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 21 C ) C.DC209 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 22 C ) C.DC210 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 23 G ) C.DG211 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 24 T ) C.DT212 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 25 G ) C.DG213 0.021 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 26 G ) C.DG214 0.017 anti,BI,canonical,non-pair-contact,helix,stem 27 T ) C.DT215 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 28 C ) C.DC216 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** List of 9 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