**************************************************************************** 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=4qzd.pdb -o=4qzd.out File name: 4qzd.pdb no. of DNA/RNA chains: 3 [D=5,T=7,U=4] no. of nucleotides: 17 no. of atoms: 3064 no. of waters: 63 no. of metals: 3 [Na=1,Mg=2] **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 DCT-c 1 A.DCT604 **************************************************************************** List of 6 base pairs nt1 nt2 bp name Saenger LW DSSR 1 D.DA1 T.DT5 A-T WC 20-XX cWW cW-W 2 D.DA2 T.DT4 A-T WC 20-XX cWW cW-W 3 D.DA3 T.DT3 A-T WC 20-XX cWW cW-W 4 D.DA4 T.DT2 A-T WC 20-XX cWW cW-W 5 D.DA5 T.DT1 A-T WC 20-XX cWW cW-W 6 T.DG6 A.DCT604 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=5 strand-1 5'-AAAAA-3' bp-type ||||| strand-2 3'-TTTTT-5' helix-form BBBB 1 D.DA1 T.DT5 A-T WC 20-XX cWW cW-W 2 D.DA2 T.DT4 A-T WC 20-XX cWW cW-W 3 D.DA3 T.DT3 A-T WC 20-XX cWW cW-W 4 D.DA4 T.DT2 A-T WC 20-XX cWW cW-W 5 D.DA5 T.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=5 strand-1 5'-AAAAA-3' bp-type ||||| strand-2 3'-TTTTT-5' helix-form BBBB 1 D.DA1 T.DT5 A-T WC 20-XX cWW cW-W 2 D.DA2 T.DT4 A-T WC 20-XX cWW cW-W 3 D.DA3 T.DT3 A-T WC 20-XX cWW cW-W 4 D.DA4 T.DT2 A-T WC 20-XX cWW cW-W 5 D.DA5 T.DT1 A-T WC 20-XX 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. -------------------------------------------------------------------- -- -1 T.DG6 A.DCT604 G-c 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=3 RGC A.ARG458,T.DG6,T.DC7 2 nts=4 AAAA U.DA1,U.DA2,U.DA3,U.DA4 **************************************************************************** Nucleotides not involved in stacking interactions nts=1 c A.DCT604 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=1 C T.DC7 2 nts=4 AAAA U.DA1,U.DA2,U.DA3,U.DA4 **************************************************************************** List of 1 splayed-apart dinucleotide 1 T.DT5 T.DG6 angle=136 distance=16.8 ratio=0.93 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=2 TG T.DT5,T.DG6 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >4qzd nts=17 [whole] AAAAA&TTTTTGC&AAAA&c (((((&)))))..&....&. >4qzd-D #1 nts=5 3.47(0.20) [chain] DNA AAAAA ((((( >4qzd-T #2 nts=7 1.58(0.59) [chain] DNA TTTTTGC ))))).. >4qzd-U #3 nts=4 2.63(0.24) [chain] DNA AAAA .... **************************************************************************** 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 ( D.DA1 0.029 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 A ( D.DA2 0.025 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 3 A ( D.DA3 0.022 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 4 A ( D.DA4 0.019 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 5 A ( D.DA5 0.016 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 6 T ) T.DT1 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 7 T ) T.DT2 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 8 T ) T.DT3 0.019 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 9 T ) T.DT4 0.019 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 10 T ) T.DT5 0.015 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,phosphate,splayed-apart 11 G . T.DG6 0.024 anti,~C2'-endo,isolated-canonical,non-pair-contact,phosphate,splayed-apart 12 C . T.DC7 0.027 anti,non-pair-contact,ss-non-loop,phosphate 13 A . U.DA1 0.014 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 14 A . U.DA2 0.015 anti,BI,non-pair-contact,ss-non-loop 15 A . U.DA3 0.014 syn,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 16 A . U.DA4 0.014 syn,non-pair-contact,ss-non-loop,phosphate 17 c . A.DCT604 0.036 modified,anti,~C3'-endo,non-stack,isolated-canonical **************************************************************************** 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