**************************************************************************** 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=6wan.pdb -o=6wan.out File name: 6wan.pdb no. of DNA/RNA chains: 6 [G=3,H=3,I=3,J=3,K=3,L=3] no. of nucleotides: 18 no. of atoms: 21812 no. of waters: 492 no. of metals: 0 **************************************************************************** List of 12 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 RA A.ARG301,G.A1 2 nts=2 WA A.TRP449,G.A3 3 nts=2 RA B.ARG301,H.A3 4 nts=2 WA B.TRP449,H.A2 5 nts=2 RA C.ARG301,I.A3 6 nts=2 WA C.TRP449,I.A2 7 nts=2 RA D.ARG301,J.A3 8 nts=2 WA D.TRP449,J.A2 9 nts=2 RA E.ARG301,K.A3 10 nts=2 WA E.TRP449,K.A2 11 nts=2 RA F.ARG301,L.A3 12 nts=2 WA F.TRP449,L.A2 **************************************************************************** Nucleotides not involved in stacking interactions nts=6 AAAAAA G.A2,H.A1,I.A1,J.A1,K.A1,L.A1 **************************************************************************** List of 6 non-loop single-stranded segments 1 nts=3 AAA G.A1,G.A2,G.A3 2 nts=3 AAA H.A1,H.A2,H.A3 3 nts=3 AAA I.A1,I.A2,I.A3 4 nts=3 AAA J.A1,J.A2,J.A3 5 nts=3 AAA K.A1,K.A2,K.A3 6 nts=3 AAA L.A1,L.A2,L.A3 **************************************************************************** List of 12 splayed-apart dinucleotides 1 G.A1 G.A2 angle=164 distance=19.0 ratio=0.99 2 G.A2 G.A3 angle=124 distance=16.5 ratio=0.88 3 H.A1 H.A2 angle=134 distance=17.0 ratio=0.92 4 H.A2 H.A3 angle=152 distance=18.5 ratio=0.97 5 I.A1 I.A2 angle=131 distance=17.0 ratio=0.91 6 I.A2 I.A3 angle=153 distance=18.6 ratio=0.97 7 J.A1 J.A2 angle=134 distance=16.9 ratio=0.92 8 J.A2 J.A3 angle=149 distance=18.5 ratio=0.96 9 K.A1 K.A2 angle=133 distance=16.9 ratio=0.92 10 K.A2 K.A3 angle=148 distance=18.1 ratio=0.96 11 L.A1 L.A2 angle=131 distance=16.7 ratio=0.91 12 L.A2 L.A3 angle=151 distance=19.0 ratio=0.97 ---------------------------------------------------------------- Summary of 6 splayed-apart units 1 nts=3 AAA G.A1,G.A2,G.A3 2 nts=3 AAA H.A1,H.A2,H.A3 3 nts=3 AAA I.A1,I.A2,I.A3 4 nts=3 AAA J.A1,J.A2,J.A3 5 nts=3 AAA K.A1,K.A2,K.A3 6 nts=3 AAA L.A1,L.A2,L.A3 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >6wan nts=18 [whole] AAA&AAA&AAA&AAA&AAA&AAA ...&...&...&...&...&... >6wan-G #1 nts=3 2.62(0.53) [chain] RNAo AAA ... >6wan-H #2 nts=3 3.09(0.29) [chain] RNAo AAA ... >6wan-I #3 nts=3 3.34(0.25) [chain] RNAo AAA ... >6wan-J #4 nts=3 3.06(0.23) [chain] RNAo AAA ... >6wan-K #5 nts=3 3.24(0.23) [chain] RNAo AAA ... >6wan-L #6 nts=3 2.84(0.28) [chain] RNAo AAA ... **************************************************************************** Summary of structural features of 18 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 . G.A1 0.065 anti,non-pair-contact,ss-non-loop,phosphate,splayed-apart 2 A . G.A2 0.087 turn,anti,~C2'-endo,non-stack,non-pair-contact,ss-non-loop,phosphate,splayed-apart 3 A . G.A3 0.081 syn,~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart 4 A . H.A1 0.090 anti,~C2'-endo,non-stack,ss-non-loop,phosphate,splayed-apart 5 A . H.A2 0.077 turn,syn,~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart 6 A . H.A3 0.067 anti,non-pair-contact,ss-non-loop,phosphate,splayed-apart 7 A . I.A1 0.093 anti,~C2'-endo,non-stack,ss-non-loop,phosphate,splayed-apart 8 A . I.A2 0.077 turn,syn,~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart 9 A . I.A3 0.065 anti,non-pair-contact,ss-non-loop,phosphate,splayed-apart 10 A . J.A1 0.092 anti,~C2'-endo,non-stack,ss-non-loop,phosphate,splayed-apart 11 A . J.A2 0.078 turn,syn,~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart 12 A . J.A3 0.065 anti,non-pair-contact,ss-non-loop,phosphate,splayed-apart 13 A . K.A1 0.089 anti,~C2'-endo,non-stack,ss-non-loop,phosphate,splayed-apart 14 A . K.A2 0.075 turn,syn,~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart 15 A . K.A3 0.067 anti,non-pair-contact,ss-non-loop,phosphate,splayed-apart 16 A . L.A1 0.095 anti,~C2'-endo,non-stack,ss-non-loop,phosphate,splayed-apart 17 A . L.A2 0.078 turn,syn,~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart 18 A . L.A3 0.063 anti,non-pair-contact,ss-non-loop,phosphate,splayed-apart **************************************************************************** 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