**************************************************************************** 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=2n0q.pdb -o=2n0q.out File name: 2n0q.pdb no. of DNA/RNA chains: 2 [A=12,B=12] no. of nucleotides: 24 no. of atoms: 780 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 IQG-g 1 A.IQG4 **************************************************************************** List of 11 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DC1 B.DG24 C-G WC 19-XIX cWW cW-W 2 A.DT2 B.DA23 T-A WC 20-XX cWW cW-W 3 A.DC3 B.DG22 C-G WC 19-XIX cWW cW-W 4 A.DG5 B.DC20 G-C WC 19-XIX cWW cW-W 5 A.DC6 B.DG19 C-G WC 19-XIX cWW cW-W 6 A.DG7 B.DC18 G-C WC 19-XIX cWW cW-W 7 A.DC8 B.DG17 C-G WC 19-XIX cWW cW-W 8 A.DC9 B.DG16 C-G WC 19-XIX cWW cW-W 9 A.DA10 B.DT15 A-T WC 20-XX cWW cW-W 10 A.DT11 B.DA14 T-A WC 20-XX cWW cW-W 11 A.DC12 B.DG13 C-G WC 19-XIX 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=11 strand-1 5'-CTCGCGCCATC-3' bp-type ||||||||||| strand-2 3'-GAGCGCGGTAG-5' helix-form ..xBBBB..B 1 A.DC1 B.DG24 C-G WC 19-XIX cWW cW-W 2 A.DT2 B.DA23 T-A WC 20-XX cWW cW-W 3 A.DC3 B.DG22 C-G WC 19-XIX cWW cW-W 4 A.DG5 B.DC20 G-C WC 19-XIX cWW cW-W 5 A.DC6 B.DG19 C-G WC 19-XIX cWW cW-W 6 A.DG7 B.DC18 G-C WC 19-XIX cWW cW-W 7 A.DC8 B.DG17 C-G WC 19-XIX cWW cW-W 8 A.DC9 B.DG16 C-G WC 19-XIX cWW cW-W 9 A.DA10 B.DT15 A-T WC 20-XX cWW cW-W 10 A.DT11 B.DA14 T-A WC 20-XX cWW cW-W 11 A.DC12 B.DG13 C-G WC 19-XIX 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=3 strand-1 5'-CTC-3' bp-type ||| strand-2 3'-GAG-5' helix-form .. 1 A.DC1 B.DG24 C-G WC 19-XIX cWW cW-W 2 A.DT2 B.DA23 T-A WC 20-XX cWW cW-W 3 A.DC3 B.DG22 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=8 strand-1 5'-GCGCCATC-3' bp-type |||||||| strand-2 3'-CGCGGTAG-5' helix-form BBBB..B 1 A.DG5 B.DC20 G-C WC 19-XIX cWW cW-W 2 A.DC6 B.DG19 C-G WC 19-XIX cWW cW-W 3 A.DG7 B.DC18 G-C WC 19-XIX cWW cW-W 4 A.DC8 B.DG17 C-G WC 19-XIX cWW cW-W 5 A.DC9 B.DG16 C-G WC 19-XIX cWW cW-W 6 A.DA10 B.DT15 A-T WC 20-XX cWW cW-W 7 A.DT11 B.DA14 T-A WC 20-XX cWW cW-W 8 A.DC12 B.DG13 C-G WC 19-XIX 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 Cg A.DC3,A.IQG4 **************************************************************************** Nucleotides not involved in stacking interactions nts=1 C B.DC21 **************************************************************************** List of 1 atom-base capping interaction dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 other N7@A.IQG4 A.DC3 3.44 **************************************************************************** Note: for the various types of loops listed below, numbers within the first set of brackets are the number of loop nts, and numbers in the second set of brackets are the identities of the stems (positive number) or isolated WC/wobble pairs (negative numbers) to which they are linked. **************************************************************************** List of 1 internal loop 1 symmetric internal loop: nts=6; [1,1]; linked by [#1,#2] summary: [2] 1 1 [A.3 B.22 A.5 B.20] 3 8 nts=6 CgGCCG A.DC3,A.IQG4,A.DG5,B.DC20,B.DC21,B.DG22 nts=1 g A.IQG4 nts=1 C B.DC21 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >2n0q nts=24 [whole] CTCgGCGCCATC&GATGGCGCCGAG (((.((((((((&)))))))).))) >2n0q-A #1 nts=12 3.02(0.49) [chain] DNA CTCgGCGCCATC (((.(((((((( >2n0q-B #2 nts=12 2.96(1.02) [chain] DNA GATGGCGCCGAG )))))))).))) **************************************************************************** Summary of structural features of 24 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 ( A.DC1 0.022 anti,~C2'-endo,BII,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 2 T ( A.DT2 0.032 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 3 C ( A.DC3 0.024 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,cap-acceptor 4 g . A.IQG4 0.028 modified,anti,~C2'-endo,BII,non-pair-contact,internal-loop,cap-donor 5 G ( A.DG5 0.025 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 6 C ( A.DC6 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 7 G ( A.DG7 0.039 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 8 C ( A.DC8 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 9 C ( A.DC9 0.020 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 10 A ( A.DA10 0.032 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 11 T ( A.DT11 0.030 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 12 C ( A.DC12 0.028 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 13 G ) B.DG13 0.028 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 14 A ) B.DA14 0.031 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 15 T ) B.DT15 0.030 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 16 G ) B.DG16 0.027 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 17 G ) B.DG17 0.030 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 18 C ) B.DC18 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 19 G ) B.DG19 0.030 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 20 C ) B.DC20 0.018 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 21 C . B.DC21 0.034 turn,anti,~C2'-endo,non-stack,non-pair-contact,internal-loop 22 G ) B.DG22 0.025 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 23 A ) B.DA23 0.030 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 24 G ) B.DG24 0.026 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack **************************************************************************** List of 10 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-iloops.pdb -- an ensemble of internal loops 5 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 6 dssr-2ndstrs.ct -- secondary structure in connectivity table format 7 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 8 dssr-torsions.txt -- backbone torsion angles and suite names 9 dssr-stacks.pdb -- an ensemble of base stacks 10 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions