**************************************************************************** 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=5j2f.pdb -o=5j2f.out File name: 5j2f.pdb no. of DNA/RNA chains: 3 [D=5,P=10,T=16] no. of nucleotides: 32 no. of atoms: 3649 no. of waters: 365 no. of metals: 4 [Na=2,Mg=2] **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 DUP-u 1 A.DUP401 **************************************************************************** List of 16 base pairs nt1 nt2 bp name Saenger LW DSSR 1 T.DC1 D.DG5 C-G WC 19-XIX cWW cW-W 2 T.DC2 D.DG4 C-G WC 19-XIX cWW cW-W 3 T.DG3 D.DC3 G-C WC 19-XIX cWW cW-W 4 T.DA4 D.DT2 A-T WC 20-XX cWW cW-W 5 T.DC5 D.DG1 C-G WC 19-XIX cWW cW-W 6 T.DA6 A.DUP401 A-u WC 20-XX cWW cW-W 7 T.DG7 P.DA10 G+A -- 09-IX cWH cW+M 8 T.DC8 P.DG9 C-G WC 19-XIX cWW cW-W 9 T.DG9 P.DC8 G-C WC 19-XIX cWW cW-W 10 T.DC10 P.DG7 C-G WC 19-XIX cWW cW-W 11 T.DA11 P.DT6 A-T WC 20-XX cWW cW-W 12 T.DT12 P.DA5 T-A WC 20-XX cWW cW-W 13 T.DC13 P.DG4 C-G WC 19-XIX cWW cW-W 14 T.DA14 P.DT3 A-T WC 20-XX cWW cW-W 15 T.DG15 P.DC2 G-C WC 19-XIX cWW cW-W 16 T.DC16 P.DG1 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 2 helices 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=5 strand-1 5'-CCGAC-3' bp-type ||||| strand-2 3'-GGCTG-5' helix-form BBBB 1 T.DC1 D.DG5 C-G WC 19-XIX cWW cW-W 2 T.DC2 D.DG4 C-G WC 19-XIX cWW cW-W 3 T.DG3 D.DC3 G-C WC 19-XIX cWW cW-W 4 T.DA4 D.DT2 A-T WC 20-XX cWW cW-W 5 T.DC5 D.DG1 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=11 strand-1 5'-AGCGCATCAGC-3' bp-type |.||||||||| strand-2 3'-uAGCGTAGTCG-5' helix-form x..BBBBBBB 1 T.DA6 A.DUP401 A-u WC 20-XX cWW cW-W 2 T.DG7 P.DA10 G+A -- 09-IX cWH cW+M 3 T.DC8 P.DG9 C-G WC 19-XIX cWW cW-W 4 T.DG9 P.DC8 G-C WC 19-XIX cWW cW-W 5 T.DC10 P.DG7 C-G WC 19-XIX cWW cW-W 6 T.DA11 P.DT6 A-T WC 20-XX cWW cW-W 7 T.DT12 P.DA5 T-A WC 20-XX cWW cW-W 8 T.DC13 P.DG4 C-G WC 19-XIX cWW cW-W 9 T.DA14 P.DT3 A-T WC 20-XX cWW cW-W 10 T.DG15 P.DC2 G-C WC 19-XIX cWW cW-W 11 T.DC16 P.DG1 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 2 stems 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=5 strand-1 5'-CCGAC-3' bp-type ||||| strand-2 3'-GGCTG-5' helix-form BBBB 1 T.DC1 D.DG5 C-G WC 19-XIX cWW cW-W 2 T.DC2 D.DG4 C-G WC 19-XIX cWW cW-W 3 T.DG3 D.DC3 G-C WC 19-XIX cWW cW-W 4 T.DA4 D.DT2 A-T WC 20-XX cWW cW-W 5 T.DC5 D.DG1 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=9 strand-1 5'-CGCATCAGC-3' bp-type ||||||||| strand-2 3'-GCGTAGTCG-5' helix-form .BBBBBBB 1 T.DC8 P.DG9 C-G WC 19-XIX cWW cW-W 2 T.DG9 P.DC8 G-C WC 19-XIX cWW cW-W 3 T.DC10 P.DG7 C-G WC 19-XIX cWW cW-W 4 T.DA11 P.DT6 A-T WC 20-XX cWW cW-W 5 T.DT12 P.DA5 T-A WC 20-XX cWW cW-W 6 T.DC13 P.DG4 C-G WC 19-XIX cWW cW-W 7 T.DA14 P.DT3 A-T WC 20-XX cWW cW-W 8 T.DG15 P.DC2 G-C WC 19-XIX cWW cW-W 9 T.DC16 P.DG1 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 1 isolated WC/wobble pair Note: isolated WC/wobble pairs are assigned negative indices to differentiate them from the stem numbers, which are positive. -------------------------------------------------------------------- [#2] -1 T.DA6 A.DUP401 A-u WC 20-XX cWW cW-W **************************************************************************** List of 3 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 HC A.HIS34,T.DC5 2 nts=3 AGC T.DA6,T.DG7,T.DC8 3 nts=3 GAu P.DG9,P.DA10,A.DUP401 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=1 G T.DG7 2 nts=1 A P.DA10 **************************************************************************** List of 1 splayed-apart dinucleotide 1 T.DC5 T.DA6 angle=132 distance=16.1 ratio=0.91 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=2 CA T.DC5,T.DA6 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >5j2f nts=32 [whole] CCGACAGCGCATCAGC&GCTGATGCGA>CGG&u (((((..(((((((((&))))))))).&)))))&. >5j2f-T #1 nts=16 2.77(1.21) [chain] DNA CCGACAGCGCATCAGC (((((..((((((((( >5j2f-P #2 nts=10 3.24(0.31) [chain] DNA GCTGATGCGA ))))))))). >5j2f-D #3 nts=5 3.17(0.34) [chain] DNA GTCGG ))))) **************************************************************************** Summary of structural features of 32 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 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 C ( T.DC2 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 3 G ( T.DG3 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 4 A ( T.DA4 0.003 anti,BI,canonical,non-pair-contact,helix,stem 5 C ( T.DC5 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,splayed-apart 6 A . T.DA6 0.016 anti,~C2'-endo,BI,isolated-canonical,non-pair-contact,helix-end,phosphate,splayed-apart 7 G . T.DG7 0.004 anti,BI,non-canonical,non-pair-contact,helix,ss-non-loop,phosphate 8 C ( T.DC8 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,phosphate 9 G ( T.DG9 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 10 C ( T.DC10 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 11 A ( T.DA11 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 12 T ( T.DT12 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 13 C ( T.DC13 0.007 anti,BI,canonical,non-pair-contact,helix,stem 14 A ( T.DA14 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 15 G ( T.DG15 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 16 C ( T.DC16 0.005 anti,canonical,non-pair-contact,helix-end,stem-end 17 G ) P.DG1 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 18 C ) P.DC2 0.005 anti,BI,canonical,non-pair-contact,helix,stem 19 T ) P.DT3 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 20 G ) P.DG4 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 21 A ) P.DA5 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 22 T ) P.DT6 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 23 G ) P.DG7 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 24 C ) P.DC8 0.005 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 25 G ) P.DG9 0.009 anti,BI,canonical,non-pair-contact,helix,stem-end,phosphate 26 A . P.DA10 0.005 syn,non-canonical,non-pair-contact,helix,ss-non-loop,phosphate 27 G ) D.DG1 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 28 T ) D.DT2 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 29 C ) D.DC3 0.007 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 30 G ) D.DG4 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 31 G ) D.DG5 0.010 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 32 u . A.DUP401 0.010 modified,anti,~C3'-endo,isolated-canonical,non-pair-contact,helix-end **************************************************************************** List of 9 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-splays.pdb -- an ensemble of splayed-apart units 9 dssr-stacks.pdb -- an ensemble of base stacks