**************************************************************************** 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=1bjd.pdb -o=1bjd.out File name: 1bjd.pdb no. of DNA/RNA chains: 2 [A=12,B=12] no. of nucleotides: 24 no. of atoms: 762 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 12 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DC1 B.DG12 C-G WC 19-XIX cWW cW-W 2 A.DG2 B.DC11 G-C WC 19-XIX cWW cW-W 3 A.DT3 B.DA10 T-A WC 20-XX cWW cW-W 4 A.DG4 B.DT9 G-T Wobble 28-XXVIII cWW cW-W 5 A.DA5 B.DT8 A-T WC 20-XX cWW cW-W 6 A.DC6 B.DG7 C-G WC 19-XIX cWW cW-W 7 A.DG7 B.DC6 G-C WC 19-XIX cWW cW-W 8 A.DT8 B.DA5 T-A WC 20-XX cWW cW-W 9 A.DT9 B.DG4 T-G Wobble 28-XXVIII cWW cW-W 10 A.DA10 B.DT3 A-T WC 20-XX cWW cW-W 11 A.DC11 B.DG2 C-G WC 19-XIX cWW cW-W 12 A.DG12 B.DC1 G-C 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'-CGTGACGTTACG-3' bp-type |||||||||||| strand-2 3'-GCATTGCAGTGC-5' helix-form .B..BBB..B. 1 A.DC1 B.DG12 C-G WC 19-XIX cWW cW-W 2 A.DG2 B.DC11 G-C WC 19-XIX cWW cW-W 3 A.DT3 B.DA10 T-A WC 20-XX cWW cW-W 4 A.DG4 B.DT9 G-T Wobble 28-XXVIII cWW cW-W 5 A.DA5 B.DT8 A-T WC 20-XX cWW cW-W 6 A.DC6 B.DG7 C-G WC 19-XIX cWW cW-W 7 A.DG7 B.DC6 G-C WC 19-XIX cWW cW-W 8 A.DT8 B.DA5 T-A WC 20-XX cWW cW-W 9 A.DT9 B.DG4 T-G Wobble 28-XXVIII cWW cW-W 10 A.DA10 B.DT3 A-T WC 20-XX cWW cW-W 11 A.DC11 B.DG2 C-G WC 19-XIX cWW cW-W 12 A.DG12 B.DC1 G-C 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'-CGTGACGTTACG-3' bp-type |||||||||||| strand-2 3'-GCATTGCAGTGC-5' helix-form .B..BBB..B. 1 A.DC1 B.DG12 C-G WC 19-XIX cWW cW-W 2 A.DG2 B.DC11 G-C WC 19-XIX cWW cW-W 3 A.DT3 B.DA10 T-A WC 20-XX cWW cW-W 4 A.DG4 B.DT9 G-T Wobble 28-XXVIII cWW cW-W 5 A.DA5 B.DT8 A-T WC 20-XX cWW cW-W 6 A.DC6 B.DG7 C-G WC 19-XIX cWW cW-W 7 A.DG7 B.DC6 G-C WC 19-XIX cWW cW-W 8 A.DT8 B.DA5 T-A WC 20-XX cWW cW-W 9 A.DT9 B.DG4 T-G Wobble 28-XXVIII cWW cW-W 10 A.DA10 B.DT3 A-T WC 20-XX cWW cW-W 11 A.DC11 B.DG2 C-G WC 19-XIX cWW cW-W 12 A.DG12 B.DC1 G-C WC 19-XIX cWW cW-W **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >1bjd nts=24 [whole] CGTGACGTTACG&CGTGACGTTACG ((((((((((((&)))))))))))) >1bjd-A #1 nts=12 3.13(0.18) [chain] DNA CGTGACGTTACG (((((((((((( >1bjd-B #2 nts=12 3.13(0.18) [chain] DNA CGTGACGTTACG )))))))))))) **************************************************************************** Summary of structural features of 24 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.DC1 0.007 anti,BI,canonical,non-pair-contact,helix-end,stem-end 2 G ( A.DG2 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 3 T ( A.DT3 0.021 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 4 G ( A.DG4 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 5 A ( A.DA5 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 6 C ( A.DC6 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 7 G ( A.DG7 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 8 T ( A.DT8 0.021 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 9 T ( A.DT9 0.021 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 10 A ( A.DA10 0.009 anti,BI,canonical,non-pair-contact,helix,stem 11 C ( A.DC11 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 12 G ( A.DG12 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 13 C ) B.DC1 0.007 anti,BI,canonical,non-pair-contact,helix-end,stem-end 14 G ) B.DG2 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 15 T ) B.DT3 0.021 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 16 G ) B.DG4 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 17 A ) B.DA5 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 18 C ) B.DC6 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 19 G ) B.DG7 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 20 T ) B.DT8 0.021 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 21 T ) B.DT9 0.021 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 22 A ) B.DA10 0.009 anti,BI,canonical,non-pair-contact,helix,stem 23 C ) B.DC11 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 24 G ) B.DG12 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** 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