**************************************************************************** File name: 1da4.pdb no. of DNA/RNA chains: 2 [A=13,B=13] no. of nucleotides: 26 no. of atoms: 834 no. of waters: 0 no. of metals: 1 [Pt=1] **************************************************************************** List of 11 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DC1 B.DG26 C-G WC 19-XIX cWW cW-W 2 A.DT2 B.DA25 T-A WC 20-XX cWW cW-W 3 A.DC3 B.DG24 C-G WC 19-XIX cWW cW-W 4 A.DT4 B.DA23 T-A WC 20-XX cWW cW-W 5 A.DA5 B.DT22 A-T WC 20-XX cWW cW-W 6 A.DG8 B.DC19 G-C WC 19-XIX cWW cW-W 7 A.DC9 B.DG18 C-G WC 19-XIX cWW cW-W 8 A.DT10 B.DA17 T-A WC 20-XX cWW cW-W 9 A.DC11 B.DG16 C-G WC 19-XIX cWW cW-W 10 A.DA12 B.DT15 A-T WC 20-XX cWW cW-W 11 A.DC13 B.DG14 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 1 helix Note: A helix is defined by base-stacking interactions, regardless of pair 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'-CTCTAGCTCAC-3' bp-type ||||||||||| strand-2 3'-GAGATCGAGTG-5' helix-form B..Bx..B.B 1 A.DC1 B.DG26 C-G WC 19-XIX cWW cW-W 2 A.DT2 B.DA25 T-A WC 20-XX cWW cW-W 3 A.DC3 B.DG24 C-G WC 19-XIX cWW cW-W 4 A.DT4 B.DA23 T-A WC 20-XX cWW cW-W 5 A.DA5 B.DT22 A-T WC 20-XX cWW cW-W 6 A.DG8 B.DC19 G-C WC 19-XIX cWW cW-W 7 A.DC9 B.DG18 C-G WC 19-XIX cWW cW-W 8 A.DT10 B.DA17 T-A WC 20-XX cWW cW-W 9 A.DC11 B.DG16 C-G WC 19-XIX cWW cW-W 10 A.DA12 B.DT15 A-T WC 20-XX cWW cW-W 11 A.DC13 B.DG14 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 2 stems Note: A stem is defined as a helix consisting strictly of 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'-CTCTA-3' bp-type ||||| strand-2 3'-GAGAT-5' helix-form B..B 1 A.DC1 B.DG26 C-G WC 19-XIX cWW cW-W 2 A.DT2 B.DA25 T-A WC 20-XX cWW cW-W 3 A.DC3 B.DG24 C-G WC 19-XIX cWW cW-W 4 A.DT4 B.DA23 T-A WC 20-XX cWW cW-W 5 A.DA5 B.DT22 A-T WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=6 strand-1 5'-GCTCAC-3' bp-type |||||| strand-2 3'-CGAGTG-5' helix-form ..B.B 1 A.DG8 B.DC19 G-C WC 19-XIX cWW cW-W 2 A.DC9 B.DG18 C-G WC 19-XIX cWW cW-W 3 A.DT10 B.DA17 T-A WC 20-XX cWW cW-W 4 A.DC11 B.DG16 C-G WC 19-XIX cWW cW-W 5 A.DA12 B.DT15 A-T WC 20-XX cWW cW-W 6 A.DC13 B.DG14 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#1 contains 2 stems: [#1,#2] **************************************************************************** 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=2 GT A.DG6,A.DT7 2 nts=4 GACT A.DG8,B.DA20,B.DC21,B.DT22 **************************************************************************** Note: For the various types of loops listed below, numbers within the first set of brackets are the number of loop nts. Numbers in the second set of brackets are the identities of the stems (positive) or isolated WC/wobble pairs (negative) to which they are linked. **************************************************************************** List of 1 internal loop 1 symmetric internal loop: nts=8; [2,2]; linked by [#1,#2] summary: [2] 2 2 [A.5 B.22 A.8 B.19] 5 6 nts=8 AGTGCACT A.DA5,A.DG6,A.DT7,A.DG8,B.DC19,B.DA20,B.DC21,B.DT22 nts=2 GT A.DG6,A.DT7 nts=2 AC B.DA20,B.DC21 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >1da4 nts=26 [whole] CTCTAGTGCTCAC>GAGCACTAGAG (((((..((((((&))))))..))))) >1da4-A #1 nts=13 3.29(0.96) [chain] DNA CTCTAGTGCTCAC (((((..(((((( >1da4-B #2 nts=13 3.28(0.32) [chain] DNA GTGAGCACTAGAG ))))))..))))) **************************************************************************** Summary of structural features of 26 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 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 2 T ( A.DT2 0.026 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 3 C ( A.DC3 0.018 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 4 T ( A.DT4 0.027 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 5 A ( A.DA5 0.024 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 6 G . A.DG6 0.064 ~C3'-endo,BI,non-pair-contact,internal-loop 7 T . A.DT7 0.033 ~C2'-endo,BI,non-pair-contact,internal-loop 8 G ( A.DG8 0.029 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 9 C ( A.DC9 0.039 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 10 T ( A.DT10 0.030 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 11 C ( A.DC11 0.021 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 12 A ( A.DA12 0.028 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 13 C ( A.DC13 0.015 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 14 G ) B.DG14 0.022 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 15 T ) B.DT15 0.023 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 16 G ) B.DG16 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 17 A ) B.DA17 0.021 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 18 G ) B.DG18 0.018 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 19 C ) B.DC19 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 20 A . B.DA20 0.020 anti,~C2'-endo,BI,non-pair-contact,internal-loop 21 C . B.DC21 0.016 anti,BI,non-pair-contact,internal-loop 22 T ) B.DT22 0.024 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 23 A ) B.DA23 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 24 G ) B.DG24 0.020 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 25 A ) B.DA25 0.021 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 26 G ) B.DG26 0.017 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack **************************************************************************** List of 13 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-rotmat.txt -- position vector and rotation matrix 11 dssr-viewV.pdb -- vertical view of the principal moment of inertia 12 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 13 dssr-viewT.pdb -- top view of the principal moment of inertia