**************************************************************************** File name: 9sy8.pdb no. of DNA/RNA chains: 1 [A=14] no. of nucleotides: 14 no. of atoms: 460 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 6 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.G1 A.C14 G-C WC 19-XIX cWW cW-W 2 A.G2 A.C13 G-C WC 19-XIX cWW cW-W 3 A.C3 A.G12 C-G WC 19-XIX cWW cW-W 4 A.A4 A.U11 A-U WC 20-XX cWW cW-W 5 A.C5 A.G10 C-G WC 19-XIX cWW cW-W 6 A.G6 A.G9 G+G -- -- cWH cW+M **************************************************************************** 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[1] bps=6 strand-1 5'-GGCACG-3' bp-type |||||. strand-2 3'-CCGUGG-5' helix-form A..A. 1 A.G1 A.C14 G-C WC 19-XIX cWW cW-W 2 A.G2 A.C13 G-C WC 19-XIX cWW cW-W 3 A.C3 A.G12 C-G WC 19-XIX cWW cW-W 4 A.A4 A.U11 A-U WC 20-XX cWW cW-W 5 A.C5 A.G10 C-G WC 19-XIX cWW cW-W 6 A.G6 A.G9 G+G -- -- cWH cW+M **************************************************************************** List of 1 stem 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'-GGCAC-3' bp-type ||||| strand-2 3'-CCGUG-5' helix-form A..A 1 A.G1 A.C14 G-C WC 19-XIX cWW cW-W 2 A.G2 A.C13 G-C WC 19-XIX cWW cW-W 3 A.C3 A.G12 C-G WC 19-XIX cWW cW-W 4 A.A4 A.U11 A-U WC 20-XX cWW cW-W 5 A.C5 A.G10 C-G WC 19-XIX cWW cW-W **************************************************************************** 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=4 CGAA A.C5,A.G6,A.A8,A.A7 **************************************************************************** Nucleotides not involved in stacking interactions nts=1 G A.G9 **************************************************************************** List of 1 atom-base capping interaction dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 sugar O2'@A.G6 A.C5 2.92 **************************************************************************** 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 hairpin loop 1 hairpin loop: nts=6; [4]; linked by [#1] summary: [1] 4 [A.5 A.10] 5 nts=6 CGAAGG A.C5,A.G6,A.A7,A.A8,A.G9,A.G10 nts=4 GAAG A.G6,A.A7,A.A8,A.G9 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >9sy8 nts=14 [whole] GGCACGAAGGUGCC (((((....))))) >9sy8-A #1 nts=14 0.48(2.43) [chain] RNA GGCACGAAGGUGCC (((((....))))) **************************************************************************** Summary of structural features of 14 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 ( A.G1 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 G ( A.G2 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 3 C ( A.C3 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 4 A ( A.A4 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 5 C ( A.C5 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,hairpin-loop,cap-acceptor 6 G . A.G6 0.006 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-donor,phosphate 7 A . A.A7 0.011 turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 8 A . A.A8 0.004 anti,~C2'-endo,non-pair-contact,hairpin-loop,phosphate 9 G . A.G9 0.005 turn,anti,~C3'-endo,non-stack,non-canonical,non-pair-contact,helix-end,hairpin-loop 10 G ) A.G10 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,phosphate 11 U ) A.U11 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 12 G ) A.G12 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 13 C ) A.C13 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 14 C ) A.C14 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** List of 14 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 10 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions 11 dssr-rotmat.txt -- position vector and rotation matrix 12 dssr-viewV.pdb -- vertical view of the principal moment of inertia 13 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 14 dssr-viewT.pdb -- top view of the principal moment of inertia