**************************************************************************** DSSR: an Integrated Software Tool for Dissecting the Spatial Structure of RNA v2.4.2-2023may01 by xiangjun@x3dna.org **************************************************************************** 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=AATAAA_dna.pdb -o=AATAAA_dna.out Date and time: Fri Feb 2 12:05:29 2024 File name: AATAAA_dna.pdb no. of DNA/RNA chains: 1 [_=16] no. of nucleotides: 16 no. of atoms: 504 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 8 base pairs nt1 nt2 bp name Saenger LW DSSR 1 DG1 DC16 G-C WC 19-XIX cWW cW-W 2 DC2 DG15 C-G WC 19-XIX cWW cW-W 3 DG3 DC14 G-C WC 19-XIX cWW cW-W 4 DC4 DG13 C-G WC 19-XIX cWW cW-W 5 DG5 DC12 G-C WC 19-XIX cWW cW-W 6 DA7 DA9 A+A -- -- tSH tm+M 7 DA7 DA10 A-A -- -- cWW cW-W 8 DT8 DA11 T+A -- -- cWH cW+M **************************************************************************** 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[1] bps=7 strand-1 5'-GCGCGTA-3' bp-type |||||.. strand-2 3'-CGCGCAA-5' helix-form AAAAx. 1 DG1 DC16 G-C WC 19-XIX cWW cW-W 2 DC2 DG15 C-G WC 19-XIX cWW cW-W 3 DG3 DC14 G-C WC 19-XIX cWW cW-W 4 DC4 DG13 C-G WC 19-XIX cWW cW-W 5 DG5 DC12 G-C WC 19-XIX cWW cW-W 6 DT8 DA11 T+A -- -- cWH cW+M 7 DA7 DA10 A-A -- -- cWW cW-W **************************************************************************** List of 1 stem 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=5 strand-1 5'-GCGCG-3' bp-type ||||| strand-2 3'-CGCGC-5' helix-form AAAA 1 DG1 DC16 G-C WC 19-XIX cWW cW-W 2 DC2 DG15 C-G WC 19-XIX cWW cW-W 3 DG3 DC14 G-C WC 19-XIX cWW cW-W 4 DC4 DG13 C-G WC 19-XIX cWW cW-W 5 DG5 DC12 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 2 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=3 AAT DA6,DA7,DT8 2 nts=4 AAAC DA9,DA10,DA11,DC12 **************************************************************************** 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 hairpin loop 1 hairpin loop: nts=8; [6]; linked by [#1] summary: [1] 6 [ .5 .12] 5 nts=8 GAATAAAC DG5,DA6,DA7,DT8,DA9,DA10,DA11,DC12 nts=6 AATAAA DA6,DA7,DT8,DA9,DA10,DA11 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >AATAAA_dna nts=16 [whole] GCGCGAATAAACGCGC (((((......))))) >AATAAA_dna-_ #1 nts=16 0.07(2.18) [chain] DNA GCGCGAATAAACGCGC (((((......))))) **************************************************************************** Summary of structural features of 16 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 ( DG1 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 C ( DC2 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 3 G ( DG3 0.042 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 4 C ( DC4 0.025 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 5 G ( DG5 0.024 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,hairpin-loop 6 A . DA6 0.025 anti,~C3'-endo,non-pair-contact,hairpin-loop 7 A . DA7 0.030 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop 8 T . DT8 0.029 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix,hairpin-loop 9 A . DA9 0.024 anti,non-canonical,non-pair-contact,hairpin-loop 10 A . DA10 0.023 ~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop 11 A . DA11 0.020 anti,BI,non-canonical,non-pair-contact,helix,hairpin-loop 12 C ) DC12 0.030 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 13 G ) DG13 0.024 anti,BI,canonical,non-pair-contact,helix,stem 14 C ) DC14 0.025 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 15 G ) DG15 0.044 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 16 C ) DC16 0.021 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** 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-hairpins.pdb -- an ensemble of hairpin 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 **************************************************************************** Time used: 00:00:00:00