**************************************************************************** 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=6gc5.pdb -o=6gc5.out File name: 6gc5.pdb no. of DNA/RNA chains: 4 [E=5,F=3,G=4,H=3] no. of nucleotides: 15 no. of atoms: 2815 no. of waters: 191 no. of metals: 0 **************************************************************************** List of 11 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 FU A.PHE247,E.U3 2 nts=2 YU A.TYR249,E.U2 3 nts=2 FU B.PHE247,F.U3 4 nts=2 YU B.TYR249,F.U2 5 nts=2 FU B.PHE289,F.U4 6 nts=2 FU C.PHE247,G.U3 7 nts=2 YU C.TYR249,G.U2 8 nts=2 FA C.PHE289,G.A4 9 nts=2 FU D.PHE247,H.U3 10 nts=2 YU D.TYR249,H.U2 11 nts=2 FU D.PHE289,H.U4 **************************************************************************** Nucleotides not involved in stacking interactions nts=2 AU E.A1,E.U5 **************************************************************************** List of 4 non-loop single-stranded segments 1 nts=5 AUUUU E.A1,E.U2,E.U3,E.U4,E.U5 2 nts=3 UUU F.U2,F.U3,F.U4 3 nts=4 UUUA G.U1,G.U2,G.U3,G.A4 4 nts=3 UUU H.U2,H.U3,H.U4 **************************************************************************** List of 6 splayed-apart dinucleotides 1 E.A1 E.U2 angle=114 distance=16.2 ratio=0.84 2 E.U3 E.U4 angle=108 distance=15.8 ratio=0.81 3 F.U3 F.U4 angle=96 distance=14.8 ratio=0.74 4 G.U1 G.U2 angle=88 distance=13.7 ratio=0.69 5 G.U3 G.A4 angle=91 distance=13.7 ratio=0.71 6 H.U3 H.U4 angle=93 distance=14.5 ratio=0.73 ---------------------------------------------------------------- Summary of 6 splayed-apart units 1 nts=2 AU E.A1,E.U2 2 nts=2 UU E.U3,E.U4 3 nts=2 UU F.U3,F.U4 4 nts=2 UU G.U1,G.U2 5 nts=2 UA G.U3,G.A4 6 nts=2 UU H.U3,H.U4 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >6gc5 nts=15 [whole] AUUUU&UUU&UUUA&UUU .....&...&....&... >6gc5-E #1 nts=5 0.11(0.54) [chain] RNA AUUUU ..... >6gc5-F #2 nts=3 2.82(0.16) [chain] RNA UUU ... >6gc5-G #3 nts=4 1.36(0.32) [chain] RNA UUUA .... >6gc5-H #4 nts=3 2.43(0.14) [chain] RNA UUU ... **************************************************************************** Summary of structural features of 15 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 . E.A1 0.009 anti,~C2'-endo,non-stack,ss-non-loop,splayed-apart 2 U . E.U2 0.018 anti,~C2'-endo,BII,ss-non-loop,splayed-apart 3 U . E.U3 0.008 anti,~C2'-endo,ss-non-loop,splayed-apart 4 U . E.U4 0.009 anti,~C2'-endo,BII,ss-non-loop,phosphate,splayed-apart 5 U . E.U5 0.009 anti,~C3'-endo,non-stack,ss-non-loop 6 U . F.U2 0.008 anti,~C2'-endo,BII,ss-non-loop 7 U . F.U3 0.011 anti,~C2'-endo,ss-non-loop,splayed-apart 8 U . F.U4 0.009 anti,~C2'-endo,ss-non-loop,phosphate,splayed-apart 9 U . G.U1 0.009 syn,~C2'-endo,ss-non-loop,splayed-apart 10 U . G.U2 0.010 anti,~C2'-endo,BII,ss-non-loop,splayed-apart 11 U . G.U3 0.007 anti,~C2'-endo,ss-non-loop,splayed-apart 12 A . G.A4 0.006 anti,~C3'-endo,ss-non-loop,phosphate,splayed-apart 13 U . H.U2 0.007 anti,~C2'-endo,BII,ss-non-loop 14 U . H.U3 0.015 anti,~C2'-endo,ss-non-loop,splayed-apart 15 U . H.U4 0.013 anti,~C2'-endo,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