**************************************************************************** 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=6rid.pdb -o=6rid.out File name: 6rid.pdb no. of DNA/RNA chains: 3 [N=7,P=9,T=18] no. of nucleotides: 34 no. of atoms: 26705 no. of waters: 0 no. of metals: 5 [Mg=1,Zn=4] **************************************************************************** List of 16 base pairs nt1 nt2 bp name Saenger LW DSSR 1 N.DG23 T.DC23 G-C WC 19-XIX cWW cW-W 2 N.DG24 T.DC22 G-C WC 19-XIX cWW cW-W 3 N.DA25 T.DT21 A-T WC 20-XX cWW cW-W 4 N.DC26 T.DG20 C-G WC 19-XIX cWW cW-W 5 N.DT27 T.DA19 T-A WC 20-XX cWW cW-W 6 N.DC28 T.DG18 C-G WC 19-XIX cWW cW-W 7 N.DT29 T.DA17 T-A WC 20-XX cWW cW-W 8 T.DC26 P.G30 C-G WC 19-XIX cWW cW-W 9 T.DC27 P.G29 C-G WC 19-XIX cWW cW-W 10 T.DA28 P.U28 A-U WC 20-XX cWW cW-W 11 T.DA29 P.U27 A-U WC 20-XX cWW cW-W 12 T.DT30 P.A26 T-A WC 20-XX cWW cW-W 13 T.DG31 P.C25 G-C WC 19-XIX cWW cW-W 14 T.DA32 P.U24 A-U WC 20-XX cWW cW-W 15 T.DC33 P.G23 C-G WC 19-XIX cWW cW-W 16 T.DA34 P.U22 A-U WC 20-XX cWW cW-W **************************************************************************** List of 2 helices 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=7 strand-1 5'-GGACTCT-3' bp-type ||||||| strand-2 3'-CCTGAGA-5' helix-form B..... 1 N.DG23 T.DC23 G-C WC 19-XIX cWW cW-W 2 N.DG24 T.DC22 G-C WC 19-XIX cWW cW-W 3 N.DA25 T.DT21 A-T WC 20-XX cWW cW-W 4 N.DC26 T.DG20 C-G WC 19-XIX cWW cW-W 5 N.DT27 T.DA19 T-A WC 20-XX cWW cW-W 6 N.DC28 T.DG18 C-G WC 19-XIX cWW cW-W 7 N.DT29 T.DA17 T-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=9 strand-1 5'-CCAATGACA-3' bp-type ||||||||| strand-2 3'-GGUUACUGU-5' helix-form A.AA.... 1 T.DC26 P.G30 C-G WC 19-XIX cWW cW-W 2 T.DC27 P.G29 C-G WC 19-XIX cWW cW-W 3 T.DA28 P.U28 A-U WC 20-XX cWW cW-W 4 T.DA29 P.U27 A-U WC 20-XX cWW cW-W 5 T.DT30 P.A26 T-A WC 20-XX cWW cW-W 6 T.DG31 P.C25 G-C WC 19-XIX cWW cW-W 7 T.DA32 P.U24 A-U WC 20-XX cWW cW-W 8 T.DC33 P.G23 C-G WC 19-XIX cWW cW-W 9 T.DA34 P.U22 A-U WC 20-XX cWW cW-W **************************************************************************** List of 2 stems 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=7 strand-1 5'-GGACTCT-3' bp-type ||||||| strand-2 3'-CCTGAGA-5' helix-form B..... 1 N.DG23 T.DC23 G-C WC 19-XIX cWW cW-W 2 N.DG24 T.DC22 G-C WC 19-XIX cWW cW-W 3 N.DA25 T.DT21 A-T WC 20-XX cWW cW-W 4 N.DC26 T.DG20 C-G WC 19-XIX cWW cW-W 5 N.DT27 T.DA19 T-A WC 20-XX cWW cW-W 6 N.DC28 T.DG18 C-G WC 19-XIX cWW cW-W 7 N.DT29 T.DA17 T-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=9 strand-1 5'-CCAATGACA-3' bp-type ||||||||| strand-2 3'-GGUUACUGU-5' helix-form A.AA.... 1 T.DC26 P.G30 C-G WC 19-XIX cWW cW-W 2 T.DC27 P.G29 C-G WC 19-XIX cWW cW-W 3 T.DA28 P.U28 A-U WC 20-XX cWW cW-W 4 T.DA29 P.U27 A-U WC 20-XX cWW cW-W 5 T.DT30 P.A26 T-A WC 20-XX cWW cW-W 6 T.DG31 P.C25 G-C WC 19-XIX cWW cW-W 7 T.DA32 P.U24 A-U WC 20-XX cWW cW-W 8 T.DC33 P.G23 C-G WC 19-XIX cWW cW-W 9 T.DA34 P.U22 A-U WC 20-XX cWW cW-W **************************************************************************** List of 3 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.PHE208,P.U22 2 nts=2 CA T.DC23,T.DA24 3 nts=2 GC T.DG25,T.DC26 **************************************************************************** List of 1 non-loop single-stranded segment 1 nts=2 AG T.DA24,T.DG25 **************************************************************************** List of 1 splayed-apart dinucleotide 1 T.DA24 T.DG25 angle=136 distance=18.0 ratio=0.93 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=2 AG T.DA24,T.DG25 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >6rid nts=34 [whole] GGACTCT&AGAGTCCAGCCAATGACA&UGUCAUUGG (((((((&)))))))..(((((((((&))))))))) >6rid-N #1 nts=7 3.01(0.14) [chain] DNA GGACTCT ((((((( >6rid-T #2 nts=18 2.49(1.63) [chain] DNA AGAGTCCAGCCAATGACA )))))))..((((((((( >6rid-P #3 nts=9 3.33(0.28) [chain] RNA UGUCAUUGG ))))))))) **************************************************************************** Summary of structural features of 34 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 ( N.DG23 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 G ( N.DG24 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 3 A ( N.DA25 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 4 C ( N.DC26 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 5 T ( N.DT27 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 6 C ( N.DC28 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 7 T ( N.DT29 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 8 A ) T.DA17 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,phosphate 9 G ) T.DG18 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 10 A ) T.DA19 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 11 G ) T.DG20 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 12 T ) T.DT21 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 13 C ) T.DC22 0.005 anti,BI,canonical,non-pair-contact,helix,stem 14 C ) T.DC23 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 15 A . T.DA24 0.004 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 16 G . T.DG25 0.006 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 17 C ( T.DC26 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 18 C ( T.DC27 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,phosphate 19 A ( T.DA28 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,phosphate 20 A ( T.DA29 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 21 T ( T.DT30 0.005 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 22 G ( T.DG31 0.007 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 23 A ( T.DA32 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 24 C ( T.DC33 0.004 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 25 A ( T.DA34 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end 26 U ) P.U22 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 27 G ) P.G23 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 28 U ) P.U24 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 29 C ) P.C25 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 30 A ) P.A26 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 31 U ) P.U27 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 32 U ) P.U28 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 33 G ) P.G29 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 34 G ) P.G30 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,phosphate **************************************************************************** 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