**************************************************************************** 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=2f8w.pdb -o=2f8w.out File name: 2f8w.pdb no. of DNA/RNA chains: 2 [A=6,B=6] no. of nucleotides: 12 no. of atoms: 330 no. of waters: 71 no. of metals: 0 **************************************************************************** List of 6 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DC1 B.DG12 C-G WC 19-XIX cWW cW-W 2 A.DA2 B.DT11 A-T WC 20-XX cWW cW-W 3 A.DC3 B.DG10 C-G WC 19-XIX cWW cW-W 4 A.DG4 B.DC9 G-C WC 19-XIX cWW cW-W 5 A.DT5 B.DA8 T-A WC 20-XX cWW cW-W 6 A.DG6 B.DC7 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=6 strand-1 5'-CACGTG-3' bp-type |||||| strand-2 3'-GTGCAC-5' helix-form ZZZZZ 1 A.DC1 B.DG12 C-G WC 19-XIX cWW cW-W 2 A.DA2 B.DT11 A-T WC 20-XX cWW cW-W 3 A.DC3 B.DG10 C-G WC 19-XIX cWW cW-W 4 A.DG4 B.DC9 G-C WC 19-XIX cWW cW-W 5 A.DT5 B.DA8 T-A WC 20-XX cWW cW-W 6 A.DG6 B.DC7 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=6 strand-1 5'-CACGTG-3' bp-type |||||| strand-2 3'-GTGCAC-5' helix-form ZZZZZ 1 A.DC1 B.DG12 C-G WC 19-XIX cWW cW-W 2 A.DA2 B.DT11 A-T WC 20-XX cWW cW-W 3 A.DC3 B.DG10 C-G WC 19-XIX cWW cW-W 4 A.DG4 B.DC9 G-C WC 19-XIX cWW cW-W 5 A.DT5 B.DA8 T-A WC 20-XX cWW cW-W 6 A.DG6 B.DC7 G-C WC 19-XIX cWW cW-W **************************************************************************** Nucleotides not involved in stacking interactions nts=2 GG A.DG6,B.DG12 **************************************************************************** List of 6 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 sugar O4'@A.DC1 A.DA2 2.98 2 sugar O4'@A.DC3 A.DG4 3.00 3 sugar O4'@A.DT5 A.DG6 2.89 4 sugar O4'@B.DC7 B.DA8 3.07 5 sugar O4'@B.DC9 B.DG10 2.91 6 sugar O4'@B.DT11 B.DG12 3.00 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >2f8w nts=12 [whole] CACGTG&CACGTG ((((((&)))))) >2f8w-A #1 nts=6 3.63(0.09) [chain] DNA CACGTG (((((( >2f8w-B #2 nts=6 3.61(0.14) [chain] DNA CACGTG )))))) **************************************************************************** Summary of structural features of 12 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 0.014 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,cap-donor 2 A ( A.DA2 0.028 syn,~C3'-endo,canonical,non-pair-contact,helix,stem,cap-acceptor 3 C ( A.DC3 0.017 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,cap-donor,phosphate 4 G ( A.DG4 0.017 turn,syn,~C3'-endo,canonical,non-pair-contact,helix,stem,cap-acceptor 5 T ( A.DT5 0.022 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,cap-donor 6 G ( A.DG6 0.038 syn,~C2'-endo,non-stack,canonical,helix-end,stem-end,cap-acceptor,phosphate 7 C ) B.DC7 0.028 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,cap-donor 8 A ) B.DA8 0.029 turn,syn,~C3'-endo,canonical,non-pair-contact,helix,stem,cap-acceptor 9 C ) B.DC9 0.015 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,cap-donor 10 G ) B.DG10 0.022 syn,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,cap-acceptor,phosphate 11 T ) B.DT11 0.016 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,cap-donor 12 G ) B.DG12 0.031 syn,~C2'-endo,non-stack,canonical,helix-end,stem-end,cap-acceptor **************************************************************************** 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-atom2bases.pdb -- an ensemble of atom-base stacking interactions