**************************************************************************** File name: 2lx1.pdb no. of DNA/RNA chains: 2 [A=11,B=11] no. of nucleotides: 22 no. of atoms: 712 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 8 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.G1 B.C21 G-C WC 19-XIX cWW cW-W 2 A.A2 B.U20 A-U WC 20-XX cWW cW-W 3 A.C3 B.G19 C-G WC 19-XIX cWW cW-W 4 A.G4 B.G17 G-G -- 07-VII tHW tM-W 5 A.G6 B.G15 G-G -- 07-VII tWH tW-M 6 A.G8 B.C14 G-C WC 19-XIX cWW cW-W 7 A.U9 B.A13 U-A WC 20-XX cWW cW-W 8 A.C10 B.G12 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 2 helices 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=4 strand-1 5'-GACG-3' bp-type |||. strand-2 3'-CUGG-5' helix-form AAx 1 A.G1 B.C21 G-C WC 19-XIX cWW cW-W 2 A.A2 B.U20 A-U WC 20-XX cWW cW-W 3 A.C3 B.G19 C-G WC 19-XIX cWW cW-W 4 A.G4 B.G17 G-G -- 07-VII tHW tM-W -------------------------------------------------------------------------- helix#2[1] bps=4 strand-1 5'-GGUC-3' bp-type .||| strand-2 3'-GCAG-5' helix-form xAA 1 A.G6 B.G15 G-G -- 07-VII tWH tW-M 2 A.G8 B.C14 G-C WC 19-XIX cWW cW-W 3 A.U9 B.A13 U-A WC 20-XX cWW cW-W 4 A.C10 B.G12 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=3 strand-1 5'-GAC-3' bp-type ||| strand-2 3'-CUG-5' helix-form AA 1 A.G1 B.C21 G-C WC 19-XIX cWW cW-W 2 A.A2 B.U20 A-U WC 20-XX cWW cW-W 3 A.C3 B.G19 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=3 strand-1 5'-GUC-3' bp-type ||| strand-2 3'-CAG-5' helix-form AA 1 A.G8 B.C14 G-C WC 19-XIX cWW cW-W 2 A.U9 B.A13 U-A WC 20-XX cWW cW-W 3 A.C10 B.G12 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 5 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 GG A.G6,A.G8 2 nts=2 CA A.C10,A.A11 3 nts=2 GG B.G17,B.G19 4 nts=2 CA B.C21,B.A22 5 nts=6 CGAAGC A.C3,A.G4,B.A16,A.A5,B.G15,B.C14 **************************************************************************** Nucleotides not involved in stacking interactions nts=2 UU A.U7,B.U18 **************************************************************************** List of 2 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 sugar O4'@A.A5 A.G6 2.91 2 sugar O4'@B.A16 B.G17 3.01 **************************************************************************** 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=12; [4,4]; linked by [#1,#2] summary: [2] 4 4 [A.3 B.19 A.8 B.14] 3 3 nts=12 CGAGUGCGAGUG A.C3,A.G4,A.A5,A.G6,A.U7,A.G8,B.C14,B.G15,B.A16,B.G17,B.U18,B.G19 nts=4 GAGU A.G4,A.A5,A.G6,A.U7 nts=4 GAGU B.G15,B.A16,B.G17,B.U18 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=1 A A.A11 2 nts=1 A B.A22 **************************************************************************** List of 4 splayed-apart dinucleotides 1 A.G6 A.U7 angle=100 distance=15.0 ratio=0.77 2 A.U7 A.G8 angle=118 distance=17.2 ratio=0.86 3 B.G17 B.U18 angle=99 distance=14.9 ratio=0.76 4 B.U18 B.G19 angle=115 distance=17.0 ratio=0.84 ---------------------------------------------------------------- Summary of 2 splayed-apart units 1 nts=3 GUG A.G6,A.U7,A.G8 2 nts=3 GUG B.G17,B.U18,B.G19 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >2lx1 nts=22 [whole] GACGAGUGUCA&GACGAGUGUCA (((....(((.&)))....))). >2lx1-A #1 nts=11 3.46(1.39) [chain] RNA GACGAGUGUCA (((....(((. >2lx1-B #2 nts=11 3.64(1.52) [chain] RNA GACGAGUGUCA )))....))). **************************************************************************** Summary of structural features of 22 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 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 A ( A.A2 0.033 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 3 C ( A.C3 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 4 G . A.G4 0.027 syn,~C2'-endo,non-canonical,non-pair-contact,helix-end,internal-loop,phosphate 5 A . A.A5 0.032 anti,~C2'-endo,non-pair-contact,internal-loop,cap-donor 6 G . A.G6 0.028 syn,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,internal-loop,cap-acceptor,splayed-apart 7 U . A.U7 0.025 turn,anti,~C2'-endo,non-stack,internal-loop,splayed-apart 8 G ( A.G8 0.029 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop,splayed-apart 9 U ( A.U9 0.026 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 10 C ( A.C10 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 11 A . A.A11 0.034 anti,~C3'-endo,non-pair-contact,ss-non-loop 12 G ) B.G12 0.023 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 13 A ) B.A13 0.030 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 14 C ) B.C14 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 15 G . B.G15 0.029 syn,~C2'-endo,non-canonical,non-pair-contact,helix-end,internal-loop,phosphate 16 A . B.A16 0.034 anti,~C2'-endo,non-pair-contact,internal-loop,cap-donor 17 G . B.G17 0.031 syn,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,internal-loop,cap-acceptor,splayed-apart 18 U . B.U18 0.026 turn,anti,~C2'-endo,non-stack,internal-loop,splayed-apart 19 G ) B.G19 0.028 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop,splayed-apart 20 U ) B.U20 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 21 C ) B.C21 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 22 A . B.A22 0.033 anti,~C3'-endo,non-pair-contact,ss-non-loop **************************************************************************** List of 15 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-splays.pdb -- an ensemble of splayed-apart units 10 dssr-stacks.pdb -- an ensemble of base stacks 11 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions 12 dssr-rotmat.txt -- position vector and rotation matrix 13 dssr-viewV.pdb -- vertical view of the principal moment of inertia 14 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 15 dssr-viewT.pdb -- top view of the principal moment of inertia