**************************************************************************** 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=8icx.pdb -o=8icx.out File name: 8icx.pdb no. of DNA/RNA chains: 2 [P=7,T=7] no. of nucleotides: 15 no. of atoms: 3070 no. of waters: 134 no. of metals: 4 [Na=2,Mn=2] **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 TTP-? 1 A.TTP338 **************************************************************************** List of 7 base pairs nt1 nt2 bp name Saenger LW DSSR 1 T.DC1 P.DG7 C-G WC 19-XIX cWW cW-W 2 T.DA2 P.DT6 A-T WC 20-XX cWW cW-W 3 T.DT3 P.DA5 T-A WC 20-XX cWW cW-W 4 T.DT4 P.DA4 T-A WC 20-XX cWW cW-W 5 T.DA5 P.DT3 A-T WC 20-XX cWW cW-W 6 T.DG6 P.DC2 G-C WC 19-XIX cWW cW-W 7 T.DA7 P.DT1 A-T 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=7 strand-1 5'-CATTAGA-3' bp-type ||||||| strand-2 3'-GTAATCT-5' helix-form BBBBBB 1 T.DC1 P.DG7 C-G WC 19-XIX cWW cW-W 2 T.DA2 P.DT6 A-T WC 20-XX cWW cW-W 3 T.DT3 P.DA5 T-A WC 20-XX cWW cW-W 4 T.DT4 P.DA4 T-A WC 20-XX cWW cW-W 5 T.DA5 P.DT3 A-T WC 20-XX cWW cW-W 6 T.DG6 P.DC2 G-C WC 19-XIX cWW cW-W 7 T.DA7 P.DT1 A-T 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=7 strand-1 5'-CATTAGA-3' bp-type ||||||| strand-2 3'-GTAATCT-5' helix-form BBBBBB 1 T.DC1 P.DG7 C-G WC 19-XIX cWW cW-W 2 T.DA2 P.DT6 A-T WC 20-XX cWW cW-W 3 T.DT3 P.DA5 T-A WC 20-XX cWW cW-W 4 T.DT4 P.DA4 T-A WC 20-XX cWW cW-W 5 T.DA5 P.DT3 A-T WC 20-XX cWW cW-W 6 T.DG6 P.DC2 G-C WC 19-XIX cWW cW-W 7 T.DA7 P.DT1 A-T WC 20-XX cWW cW-W **************************************************************************** List of 1 non-loop single-stranded segment 1 nts=1 ? A.TTP338 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >8icx nts=15 [whole] CATTAGA&TCTAATG&? (((((((&)))))))&. >8icx-T #1 nts=7 3.26(0.15) [chain] DNA CATTAGA ((((((( >8icx-P #2 nts=7 3.67(0.22) [chain] DNA TCTAATG ))))))) **************************************************************************** Summary of structural features of 15 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 ( T.DC1 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 A ( T.DA2 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 3 T ( T.DT3 0.021 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 4 T ( T.DT4 0.035 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 5 A ( T.DA5 0.034 anti,BI,canonical,non-pair-contact,helix,stem 6 G ( T.DG6 0.037 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 7 A ( T.DA7 0.023 anti,canonical,non-pair-contact,helix-end,stem-end 8 T ) P.DT1 0.029 anti,BI,canonical,non-pair-contact,helix-end,stem-end 9 C ) P.DC2 0.022 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 10 T ) P.DT3 0.047 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 11 A ) P.DA4 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 12 A ) P.DA5 0.026 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 13 T ) P.DT6 0.013 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 14 G ) P.DG7 0.017 anti,canonical,non-pair-contact,helix-end,stem-end,phosphate 15 ? . A.TTP338 --- modified,~C2'-endo,non-stack,ss-non-loop **************************************************************************** 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