**************************************************************************** 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=5wty.pdb -o=5wty.out File name: 5wty.pdb no. of DNA/RNA chains: 2 [C=11,D=11] no. of nucleotides: 22 no. of atoms: 9520 no. of waters: 104 no. of metals: 0 **************************************************************************** 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=2 RA B.ARG485,D.A1143 2 nts=2 QG B.GLN604,D.G1140 3 nts=4 HGHG B.HIS204,D.G1149,B.HIS144,D.G1150 4 nts=4 HGHA B.HIS566,D.G1141,B.HIS528,D.A1142 5 nts=4 HGHG A.HIS204,C.G1149,A.HIS144,C.G1150 6 nts=5 FGHAC B.PHE388,D.G1146,B.HIS350,D.A1147,D.C1148 7 nts=5 FGHAC A.PHE388,C.G1146,A.HIS350,C.A1147,C.C1148 8 nts=6 HGHARA A.HIS566,C.G1141,A.HIS528,C.A1142,A.ARG485,C.A1143 **************************************************************************** Nucleotides not involved in stacking interactions nts=4 UUUU C.U1144,C.U1145,D.U1144,D.U1145 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=11 GGAAUUGACGG C.G1140,C.G1141,C.A1142,C.A1143,C.U1144,C.U1145,C.G1146,C.A1147,C.C1148,C.G1149,C.G1150 2 nts=11 GGAAUUGACGG D.G1140,D.G1141,D.A1142,D.A1143,D.U1144,D.U1145,D.G1146,D.A1147,D.C1148,D.G1149,D.G1150 **************************************************************************** List of 4 splayed-apart dinucleotides 1 C.A1143 C.U1144 angle=101 distance=16.4 ratio=0.77 2 C.U1144 C.U1145 angle=86 distance=13.7 ratio=0.68 3 D.A1143 D.U1144 angle=134 distance=18.2 ratio=0.92 4 D.U1144 D.U1145 angle=159 distance=18.1 ratio=0.98 ---------------------------------------------------------------- Summary of 2 splayed-apart units 1 nts=3 AUU C.A1143,C.U1144,C.U1145 2 nts=3 AUU D.A1143,D.U1144,D.U1145 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >5wty nts=22 [whole] GGAAUUGACGG&GGAAUUGACGG ...........&........... >5wty-C #1 nts=11 0.46(2.36) [chain] RNA GGAAUUGACGG ........... >5wty-D #2 nts=11 1.49(2.31) [chain] RNA GGAAUUGACGG ........... **************************************************************************** Summary of structural features of 22 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 G . C.G1140 0.006 anti,~C2'-endo,BII,ss-non-loop 2 G . C.G1141 0.009 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 3 A . C.A1142 0.010 anti,~C2'-endo,BII,non-pair-contact,ss-non-loop,phosphate 4 A . C.A1143 0.010 anti,~C2'-endo,ss-non-loop,splayed-apart 5 U . C.U1144 0.008 turn,anti,~C2'-endo,non-stack,ss-non-loop,splayed-apart 6 U . C.U1145 0.022 anti,~C2'-endo,non-stack,non-pair-contact,ss-non-loop,splayed-apart 7 G . C.G1146 0.009 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate 8 A . C.A1147 0.015 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 9 C . C.C1148 0.010 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 10 G . C.G1149 0.009 anti,~C3'-endo,BI,ss-non-loop 11 G . C.G1150 0.021 anti,~C3'-endo,ss-non-loop 12 G . D.G1140 0.017 anti,~C2'-endo,non-pair-contact,ss-non-loop 13 G . D.G1141 0.010 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate 14 A . D.A1142 0.016 anti,~C2'-endo,BII,ss-non-loop,phosphate 15 A . D.A1143 0.010 anti,~C2'-endo,ss-non-loop,splayed-apart 16 U . D.U1144 0.005 turn,anti,~C2'-endo,non-stack,non-pair-contact,ss-non-loop,phosphate,splayed-apart 17 U . D.U1145 0.018 anti,~C2'-endo,non-stack,non-pair-contact,ss-non-loop,phosphate,splayed-apart 18 G . D.G1146 0.011 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 19 A . D.A1147 0.021 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 20 C . D.C1148 0.007 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 21 G . D.G1149 0.007 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 22 G . D.G1150 0.013 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate **************************************************************************** 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