**************************************************************************** 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=4qqz.pdb -o=4qqz.out File name: 4qqz.pdb no. of DNA/RNA chains: 4 [B=9,D=9,F=9,H=9] no. of nucleotides: 40 no. of atoms: 28851 no. of waters: 0 no. of metals: 8 [Fe=8] **************************************************************************** List of 1 type of 4 modified nucleotides nt count list 1 ANP-a 4 A.ANP1003,C.ANP1003,E.ANP1003,G.ANP1003 **************************************************************************** List of 8 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=3 AAA B.DA9,B.DA10,B.DA11 2 nts=3 AAA D.DA9,D.DA10,D.DA11 3 nts=3 AAA F.DA9,F.DA10,F.DA11 4 nts=3 AAA H.DA9,H.DA10,H.DA11 5 nts=5 AAAAA B.DA2,B.DA3,B.DA4,B.DA5,B.DA6 6 nts=5 AAAAA D.DA2,D.DA3,D.DA4,D.DA5,D.DA6 7 nts=5 AAAAA F.DA2,F.DA3,F.DA4,F.DA5,F.DA6 8 nts=5 AAAAA H.DA2,H.DA3,H.DA4,H.DA5,H.DA6 **************************************************************************** Nucleotides not involved in stacking interactions nts=4 aaaa A.ANP1003,C.ANP1003,E.ANP1003,G.ANP1003 **************************************************************************** List of 8 non-loop single-stranded segments 1 nts=9* AAAAAAAAA B.DA1,B.DA2,B.DA3,B.DA4,B.DA5,B.DA6,B.DA9,B.DA10,B.DA11 2 nts=9* AAAAAAAAA D.DA1,D.DA2,D.DA3,D.DA4,D.DA5,D.DA6,D.DA9,D.DA10,D.DA11 3 nts=9* AAAAAAAAA F.DA1,F.DA2,F.DA3,F.DA4,F.DA5,F.DA6,F.DA9,F.DA10,F.DA11 4 nts=9* AAAAAAAAA H.DA1,H.DA2,H.DA3,H.DA4,H.DA5,H.DA6,H.DA9,H.DA10,H.DA11 5 nts=1 a A.ANP1003 6 nts=1 a C.ANP1003 7 nts=1 a E.ANP1003 8 nts=1 a G.ANP1003 **************************************************************************** List of 4 splayed-apart dinucleotides 1 B.DA1 B.DA2 angle=102 distance=16.0 ratio=0.78 2 D.DA1 D.DA2 angle=103 distance=15.8 ratio=0.78 3 F.DA1 F.DA2 angle=109 distance=16.6 ratio=0.82 4 H.DA1 H.DA2 angle=103 distance=16.1 ratio=0.78 ---------------------------------------------------------------- Summary of 4 splayed-apart units 1 nts=2 AA B.DA1,B.DA2 2 nts=2 AA D.DA1,D.DA2 3 nts=2 AA F.DA1,F.DA2 4 nts=2 AA H.DA1,H.DA2 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >4qqz nts=40 [whole] AAAAAA&AAA&AAAAAA&AAA&AAAAAA&AAA&AAAAAA&AAA&a&a&a&a ......&...&......&...&......&...&......&...&.&.&.&. >4qqz-B #1 nts=9 1.56(0.97) [chain] DNA* AAAAAA&AAA ......&... >4qqz-D #2 nts=9 1.49(0.83) [chain] DNA* AAAAAA&AAA ......&... >4qqz-F #3 nts=9 1.46(0.78) [chain] DNA* AAAAAA&AAA ......&... >4qqz-H #4 nts=9 1.50(0.85) [chain] DNA* AAAAAA&AAA ......&... **************************************************************************** Summary of structural features of 40 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 . B.DA1 0.022 anti,~C2'-endo,ss-non-loop,phosphate,splayed-apart 2 A . B.DA2 0.021 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 3 A . B.DA3 0.007 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 4 A . B.DA4 0.015 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 5 A . B.DA5 0.020 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 6 A . B.DA6 0.014 break,anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate 7 A . B.DA9 0.015 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 8 A . B.DA10 0.023 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 9 A . B.DA11 0.012 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate 10 A . D.DA1 0.008 anti,~C2'-endo,ss-non-loop,splayed-apart 11 A . D.DA2 0.019 anti,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 12 A . D.DA3 0.017 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 13 A . D.DA4 0.016 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 14 A . D.DA5 0.018 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 15 A . D.DA6 0.014 break,anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate 16 A . D.DA9 0.011 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 17 A . D.DA10 0.024 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 18 A . D.DA11 0.017 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate 19 A . F.DA1 0.009 anti,~C2'-endo,ss-non-loop,phosphate,splayed-apart 20 A . F.DA2 0.022 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 21 A . F.DA3 0.015 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 22 A . F.DA4 0.019 anti,BI,non-pair-contact,ss-non-loop,phosphate 23 A . F.DA5 0.019 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 24 A . F.DA6 0.013 break,anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate 25 A . F.DA9 0.015 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 26 A . F.DA10 0.013 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 27 A . F.DA11 0.014 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate 28 A . H.DA1 0.008 anti,~C2'-endo,ss-non-loop,splayed-apart 29 A . H.DA2 0.014 anti,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 30 A . H.DA3 0.007 anti,BI,non-pair-contact,ss-non-loop,phosphate 31 A . H.DA4 0.009 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 32 A . H.DA5 0.012 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 33 A . H.DA6 0.006 break,anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate 34 A . H.DA9 0.014 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 35 A . H.DA10 0.032 anti,~C2'-endo,non-pair-contact,ss-non-loop 36 A . H.DA11 0.016 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate 37 a . A.ANP1003 0.004 modified,syn,~C2'-endo,non-stack,ss-non-loop 38 a . C.ANP1003 0.061 modified,anti,non-stack,ss-non-loop 39 a . E.ANP1003 0.054 modified,syn,~C2'-endo,non-stack,ss-non-loop 40 a . G.ANP1003 0.063 modified,syn,~C2'-endo,non-stack,ss-non-loop **************************************************************************** List of 6 additional files 1 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 2 dssr-2ndstrs.ct -- secondary structure in connectivity table format 3 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 4 dssr-torsions.txt -- backbone torsion angles and suite names 5 dssr-splays.pdb -- an ensemble of splayed-apart units 6 dssr-stacks.pdb -- an ensemble of base stacks