**************************************************************************** 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=4ebc.pdb -o=4ebc.out File name: 4ebc.pdb no. of DNA/RNA chains: 2 [P=7,T=9] no. of nucleotides: 17 no. of atoms: 3365 no. of waters: 78 no. of metals: 3 [Ca=3] **************************************************************************** List of 2 types of 2 modified nucleotides nt count list 1 0OH-a 1 A.0OH501 2 DOC-c 1 P.DOC7 **************************************************************************** List of 8 base pairs nt1 nt2 bp name Saenger LW DSSR 1 P.DA1 T.DT11 A-T WC 20-XX cWW cW-W 2 P.DG2 T.DC10 G-C WC 19-XIX cWW cW-W 3 P.DG3 T.DC9 G-C WC 19-XIX cWW cW-W 4 P.DA4 T.DT8 A-T WC 20-XX cWW cW-W 5 P.DC5 T.DG7 C-G WC 19-XIX cWW cW-W 6 P.DC6 T.DG6 C-G WC 19-XIX cWW cW-W 7 P.DOC7 T.DG5 c-G WC 19-XIX cWW cW-W 8 T.DT4 A.0OH501 T-a -- -- .WW .W-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'-AGGACCca-3' bp-type |||||||. strand-2 3'-TCCTGGGT-5' helix-form B.B...x 1 P.DA1 T.DT11 A-T WC 20-XX cWW cW-W 2 P.DG2 T.DC10 G-C WC 19-XIX cWW cW-W 3 P.DG3 T.DC9 G-C WC 19-XIX cWW cW-W 4 P.DA4 T.DT8 A-T WC 20-XX cWW cW-W 5 P.DC5 T.DG7 C-G WC 19-XIX cWW cW-W 6 P.DC6 T.DG6 C-G WC 19-XIX cWW cW-W 7 P.DOC7 T.DG5 c-G WC 19-XIX cWW cW-W 8 A.0OH501 T.DT4 a-T -- -- .WW .W-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'-AGGACCc-3' bp-type ||||||| strand-2 3'-TCCTGGG-5' helix-form B.B... 1 P.DA1 T.DT11 A-T WC 20-XX cWW cW-W 2 P.DG2 T.DC10 G-C WC 19-XIX cWW cW-W 3 P.DG3 T.DC9 G-C WC 19-XIX cWW cW-W 4 P.DA4 T.DT8 A-T WC 20-XX cWW cW-W 5 P.DC5 T.DG7 C-G WC 19-XIX cWW cW-W 6 P.DC6 T.DG6 C-G WC 19-XIX cWW cW-W 7 P.DOC7 T.DG5 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 ca P.DOC7,A.0OH501 2 nts=2 TG T.DT4,T.DG5 **************************************************************************** Nucleotides not involved in stacking interactions nts=1 C T.DC3 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=2 CT T.DC3,T.DT4 2 nts=1 a A.0OH501 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >4ebc nts=17 [whole] AGGACCc&CTGGGTCCT&a (((((((&..)))))))&. >4ebc-P #1 nts=7 3.61(0.20) [chain] DNA AGGACCc ((((((( >4ebc-T #2 nts=9 2.90(0.42) [chain] DNA CTGGGTCCT ..))))))) **************************************************************************** Summary of structural features of 17 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 A ( P.DA1 0.001 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 2 G ( P.DG2 0.015 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 3 G ( P.DG3 0.018 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 4 A ( P.DA4 0.008 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 5 C ( P.DC5 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 6 C ( P.DC6 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 7 c ( P.DOC7 0.010 modified,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,phosphate 8 C . T.DC3 0.012 anti,non-stack,non-pair-contact,ss-non-loop 9 T . T.DT4 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop,phosphate 10 G ) T.DG5 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,phosphate 11 G ) T.DG6 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 12 G ) T.DG7 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 13 T ) T.DT8 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 14 C ) T.DC9 0.016 anti,BI,canonical,non-pair-contact,helix,stem 15 C ) T.DC10 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 16 T ) T.DT11 0.012 anti,canonical,non-pair-contact,helix-end,stem-end 17 a . A.0OH501 0.057 modified,non-canonical,non-pair-contact,helix-end,ss-non-loop **************************************************************************** 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-stacks.pdb -- an ensemble of base stacks