**************************************************************************** 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=1gtc.pdb -o=1gtc.out File name: 1gtc.pdb no. of DNA/RNA chains: 2 [A=8,B=8] no. of nucleotides: 16 no. of atoms: 508 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 8 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DG1 B.DC8 G-C WC 19-XIX cWW cW-W 2 A.DC2 B.DG7 C-G WC 19-XIX cWW cW-W 3 A.DA3 B.DT6 A-T WC 20-XX cWW cW-W 4 A.DG4 B.DC5 G-C WC 19-XIX cWW cW-W 5 A.DT5 B.A4 T-A WC 20-XX cWW cW-W 6 A.DG6 B.C3 G-C WC 19-XIX cWW cW-W 7 A.DG7 B.C2 G-C WC 19-XIX cWW cW-W 8 A.DC8 B.G1 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=8 strand-1 5'-GCAGTGGC-3' bp-type |||||||| strand-2 3'-CGTCACCG-5' helix-form ....... 1 A.DG1 B.DC8 G-C WC 19-XIX cWW cW-W 2 A.DC2 B.DG7 C-G WC 19-XIX cWW cW-W 3 A.DA3 B.DT6 A-T WC 20-XX cWW cW-W 4 A.DG4 B.DC5 G-C WC 19-XIX cWW cW-W 5 A.DT5 B.A4 T-A WC 20-XX cWW cW-W 6 A.DG6 B.C3 G-C WC 19-XIX cWW cW-W 7 A.DG7 B.C2 G-C WC 19-XIX cWW cW-W 8 A.DC8 B.G1 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=8 strand-1 5'-GCAGTGGC-3' bp-type |||||||| strand-2 3'-CGTCACCG-5' helix-form ....... 1 A.DG1 B.DC8 G-C WC 19-XIX cWW cW-W 2 A.DC2 B.DG7 C-G WC 19-XIX cWW cW-W 3 A.DA3 B.DT6 A-T WC 20-XX cWW cW-W 4 A.DG4 B.DC5 G-C WC 19-XIX cWW cW-W 5 A.DT5 B.A4 T-A WC 20-XX cWW cW-W 6 A.DG6 B.C3 G-C WC 19-XIX cWW cW-W 7 A.DG7 B.C2 G-C WC 19-XIX cWW cW-W 8 A.DC8 B.G1 C-G WC 19-XIX cWW cW-W **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >1gtc nts=16 [whole] GCAGTGGC&GCCACTGC ((((((((&)))))))) >1gtc-A #1 nts=8 2.53(0.20) [chain] DNA GCAGTGGC (((((((( >1gtc-B #2 nts=8 1.73(0.27) [chain] DNA[4]/RNA[4] GCCACTGC )))))))) **************************************************************************** Summary of structural features of 16 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 ( A.DG1 0.020 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 C ( A.DC2 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 3 A ( A.DA3 0.020 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 4 G ( A.DG4 0.022 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 5 T ( A.DT5 0.025 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 6 G ( A.DG6 0.023 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 7 G ( A.DG7 0.031 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 8 C ( A.DC8 0.014 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 9 G ) B.G1 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 10 C ) B.C2 0.030 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 11 C ) B.C3 0.021 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 12 A ) B.A4 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 13 C ) B.DC5 0.014 anti,BI,canonical,non-pair-contact,helix,stem 14 T ) B.DT6 0.026 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 15 G ) B.DG7 0.029 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 16 C ) B.DC8 0.017 anti,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