**************************************************************************** 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=4glx.pdb -o=4glx.out File name: 4glx.pdb no. of DNA/RNA chains: 3 [B=26,C=13,D=13] no. of nucleotides: 52 no. of atoms: 5598 no. of waters: 204 no. of metals: 1 [Zn=1] **************************************************************************** List of 26 base pairs nt1 nt2 bp name Saenger LW DSSR 1 B.DC1 D.DG52 C-G WC 19-XIX cWW cW-W 2 B.DA2 D.DT51 A-T WC 20-XX cWW cW-W 3 B.DT3 D.DA50 T-A WC 20-XX cWW cW-W 4 B.DT4 D.DA49 T-A WC 20-XX cWW cW-W 5 B.DC5 D.DG48 C-G WC 19-XIX cWW cW-W 6 B.DC6 D.DG47 C-G WC 19-XIX cWW cW-W 7 B.DG7 D.DC46 G-C WC 19-XIX cWW cW-W 8 B.DA8 D.DT45 A-T WC 20-XX cWW cW-W 9 B.DT9 D.DA44 T-A WC 20-XX cWW cW-W 10 B.DA10 D.DT43 A-T WC 20-XX cWW cW-W 11 B.DG11 D.DC42 G-C WC 19-XIX cWW cW-W 12 B.DT12 D.DA41 T-A WC 20-XX cWW cW-W 13 B.DG13 D.DC40 G-C WC 19-XIX cWW cW-W 14 B.DG14 C.DC39 G-C WC 19-XIX cWW cW-W 15 B.DG15 C.DC38 G-C WC 19-XIX cWW cW-W 16 B.DG16 C.DC37 G-C WC 19-XIX cWW cW-W 17 B.DT17 C.DA36 T-A WC 20-XX cWW cW-W 18 B.DC18 C.DG35 C-G WC 19-XIX cWW cW-W 19 B.DG19 C.DC34 G-C WC 19-XIX cWW cW-W 20 B.DC20 C.DG33 C-G WC 19-XIX cWW cW-W 21 B.DA21 C.DT32 A-T WC 20-XX cWW cW-W 22 B.DA22 C.DT31 A-T WC 20-XX cWW cW-W 23 B.DT23 C.DA30 T-A WC 20-XX cWW cW-W 24 B.DT24 C.DA29 T-A WC 20-XX cWW cW-W 25 B.DG25 C.DC28 G-C WC 19-XIX cWW cW-W 26 B.DT26 C.DA27 T-A WC 20-XX 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[2] bps=26 strand-1 5'-CATTCCGATAGTGGGGTCGCAATTGT-3' bp-type |||||||||||||||||||||||||| strand-2 3'-GTAAGGCTATCACCCCAGCGTTAACA-5' helix-form BBBBBBBB.BB.x.BBBBBBBBB.. 1 B.DC1 D.DG52 C-G WC 19-XIX cWW cW-W 2 B.DA2 D.DT51 A-T WC 20-XX cWW cW-W 3 B.DT3 D.DA50 T-A WC 20-XX cWW cW-W 4 B.DT4 D.DA49 T-A WC 20-XX cWW cW-W 5 B.DC5 D.DG48 C-G WC 19-XIX cWW cW-W 6 B.DC6 D.DG47 C-G WC 19-XIX cWW cW-W 7 B.DG7 D.DC46 G-C WC 19-XIX cWW cW-W 8 B.DA8 D.DT45 A-T WC 20-XX cWW cW-W 9 B.DT9 D.DA44 T-A WC 20-XX cWW cW-W 10 B.DA10 D.DT43 A-T WC 20-XX cWW cW-W 11 B.DG11 D.DC42 G-C WC 19-XIX cWW cW-W 12 B.DT12 D.DA41 T-A WC 20-XX cWW cW-W 13 B.DG13 D.DC40 G-C WC 19-XIX cWW cW-W 14 B.DG14 C.DC39 G-C WC 19-XIX cWW cW-W 15 B.DG15 C.DC38 G-C WC 19-XIX cWW cW-W 16 B.DG16 C.DC37 G-C WC 19-XIX cWW cW-W 17 B.DT17 C.DA36 T-A WC 20-XX cWW cW-W 18 B.DC18 C.DG35 C-G WC 19-XIX cWW cW-W 19 B.DG19 C.DC34 G-C WC 19-XIX cWW cW-W 20 B.DC20 C.DG33 C-G WC 19-XIX cWW cW-W 21 B.DA21 C.DT32 A-T WC 20-XX cWW cW-W 22 B.DA22 C.DT31 A-T WC 20-XX cWW cW-W 23 B.DT23 C.DA30 T-A WC 20-XX cWW cW-W 24 B.DT24 C.DA29 T-A WC 20-XX cWW cW-W 25 B.DG25 C.DC28 G-C WC 19-XIX cWW cW-W 26 B.DT26 C.DA27 T-A 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=13 strand-1 5'-CATTCCGATAGTG-3' bp-type ||||||||||||| strand-2 3'-GTAAGGCTATCAC-5' helix-form BBBBBBBB.BB. 1 B.DC1 D.DG52 C-G WC 19-XIX cWW cW-W 2 B.DA2 D.DT51 A-T WC 20-XX cWW cW-W 3 B.DT3 D.DA50 T-A WC 20-XX cWW cW-W 4 B.DT4 D.DA49 T-A WC 20-XX cWW cW-W 5 B.DC5 D.DG48 C-G WC 19-XIX cWW cW-W 6 B.DC6 D.DG47 C-G WC 19-XIX cWW cW-W 7 B.DG7 D.DC46 G-C WC 19-XIX cWW cW-W 8 B.DA8 D.DT45 A-T WC 20-XX cWW cW-W 9 B.DT9 D.DA44 T-A WC 20-XX cWW cW-W 10 B.DA10 D.DT43 A-T WC 20-XX cWW cW-W 11 B.DG11 D.DC42 G-C WC 19-XIX cWW cW-W 12 B.DT12 D.DA41 T-A WC 20-XX cWW cW-W 13 B.DG13 D.DC40 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=13 strand-1 5'-GGGTCGCAATTGT-3' bp-type ||||||||||||| strand-2 3'-CCCAGCGTTAACA-5' helix-form .BBBBBBBBB.. 1 B.DG14 C.DC39 G-C WC 19-XIX cWW cW-W 2 B.DG15 C.DC38 G-C WC 19-XIX cWW cW-W 3 B.DG16 C.DC37 G-C WC 19-XIX cWW cW-W 4 B.DT17 C.DA36 T-A WC 20-XX cWW cW-W 5 B.DC18 C.DG35 C-G WC 19-XIX cWW cW-W 6 B.DG19 C.DC34 G-C WC 19-XIX cWW cW-W 7 B.DC20 C.DG33 C-G WC 19-XIX cWW cW-W 8 B.DA21 C.DT32 A-T WC 20-XX cWW cW-W 9 B.DA22 C.DT31 A-T WC 20-XX cWW cW-W 10 B.DT23 C.DA30 T-A WC 20-XX cWW cW-W 11 B.DT24 C.DA29 T-A WC 20-XX cWW cW-W 12 B.DG25 C.DC28 G-C WC 19-XIX cWW cW-W 13 B.DT26 C.DA27 T-A WC 20-XX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#1 contains 2 stems: [#1,#2] **************************************************************************** List of 1 base stack 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 GC B.DG14,D.DC40 **************************************************************************** List of 1 atom-base capping interaction dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 sugar O4'@D.DC40 C.DC39 3.17 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >4glx nts=52 [whole] CATTCCGATAGTGGGGTCGCAATTGT&ACAATTGCGACCC&CACTATCGGAATG ((((((((((((((((((((((((((&)))))))))))))&))))))))))))) >4glx-B #1 nts=26 3.24(0.55) [chain] DNA CATTCCGATAGTGGGGTCGCAATTGT (((((((((((((((((((((((((( >4glx-C #2 nts=13 3.43(0.37) [chain] DNA ACAATTGCGACCC ))))))))))))) >4glx-D #3 nts=13 3.27(0.61) [chain] DNA CACTATCGGAATG ))))))))))))) **************************************************************************** Summary of structural features of 52 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 C ( B.DC1 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 2 A ( B.DA2 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 3 T ( B.DT3 0.007 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 4 T ( B.DT4 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 5 C ( B.DC5 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 6 C ( B.DC6 0.007 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 7 G ( B.DG7 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 8 A ( B.DA8 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 9 T ( B.DT9 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 10 A ( B.DA10 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 11 G ( B.DG11 0.026 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 12 T ( B.DT12 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 13 G ( B.DG13 0.025 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,phosphate 14 G ( B.DG14 0.019 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 15 G ( B.DG15 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 16 G ( B.DG16 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 17 T ( B.DT17 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 18 C ( B.DC18 0.012 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 19 G ( B.DG19 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 20 C ( B.DC20 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 21 A ( B.DA21 0.009 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 22 A ( B.DA22 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 23 T ( B.DT23 0.005 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 24 T ( B.DT24 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 25 G ( B.DG25 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 26 T ( B.DT26 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 27 A ) C.DA27 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 28 C ) C.DC28 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 29 A ) C.DA29 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 30 A ) C.DA30 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 31 T ) C.DT31 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 32 T ) C.DT32 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 33 G ) C.DG33 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 34 C ) C.DC34 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 35 G ) C.DG35 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 36 A ) C.DA36 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 37 C ) C.DC37 0.024 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 38 C ) C.DC38 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 39 C ) C.DC39 0.014 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,cap-acceptor,phosphate 40 C ) D.DC40 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,cap-donor,phosphate 41 A ) D.DA41 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 42 C ) D.DC42 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 43 T ) D.DT43 0.006 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 44 A ) D.DA44 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 45 T ) D.DT45 0.016 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 46 C ) D.DC46 0.009 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 47 G ) D.DG47 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 48 G ) D.DG48 0.014 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 49 A ) D.DA49 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 50 A ) D.DA50 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 51 T ) D.DT51 0.014 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 52 G ) D.DG52 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack **************************************************************************** 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-stacks.pdb -- an ensemble of base stacks 9 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions