**************************************************************************** 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=2n6x.pdb -o=2n6x.out File name: 2n6x.pdb no. of DNA/RNA chains: 1 [A=43] no. of nucleotides: 43 no. of atoms: 1368 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 16 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.G1 A.C43 G-C WC 19-XIX cWW cW-W 2 A.G2 A.C42 G-C WC 19-XIX cWW cW-W 3 A.U3 A.A41 U-A WC 20-XX cWW cW-W 4 A.G4 A.U40 G-U Wobble 28-XXVIII cWW cW-W 5 A.A5 A.U39 A-U WC 20-XX cWW cW-W 6 A.G6 A.C38 G-C WC 19-XIX cWW cW-W 7 A.U7 A.A37 U-A WC 20-XX cWW cW-W 8 A.A8 A.U36 A-U WC 20-XX cWW cW-W 9 A.A14 A.U31 A-U WC 20-XX cWW cW-W 10 A.G15 A.C30 G-C WC 19-XIX cWW cW-W 11 A.U16 A.A29 U-A WC 20-XX cWW cW-W 12 A.A17 A.U28 A-U WC 20-XX cWW cW-W 13 A.U18 A.A27 U-A WC 20-XX cWW cW-W 14 A.A19 A.U26 A-U WC 20-XX cWW cW-W 15 A.C20 A.G25 C-G WC 19-XIX cWW cW-W 16 A.U21 A.G24 U+G -- -- tSW tm+W **************************************************************************** List of 2 helices 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=8 strand-1 5'-GGUGAGUA-3' bp-type |||||||| strand-2 3'-CCAUUCAU-5' helix-form ....... 1 A.G1 A.C43 G-C WC 19-XIX cWW cW-W 2 A.G2 A.C42 G-C WC 19-XIX cWW cW-W 3 A.U3 A.A41 U-A WC 20-XX cWW cW-W 4 A.G4 A.U40 G-U Wobble 28-XXVIII cWW cW-W 5 A.A5 A.U39 A-U WC 20-XX cWW cW-W 6 A.G6 A.C38 G-C WC 19-XIX cWW cW-W 7 A.U7 A.A37 U-A WC 20-XX cWW cW-W 8 A.A8 A.U36 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=8 strand-1 5'-AGUAUACU-3' bp-type |||||||. strand-2 3'-UCAUAUGG-5' helix-form ....... 1 A.A14 A.U31 A-U WC 20-XX cWW cW-W 2 A.G15 A.C30 G-C WC 19-XIX cWW cW-W 3 A.U16 A.A29 U-A WC 20-XX cWW cW-W 4 A.A17 A.U28 A-U WC 20-XX cWW cW-W 5 A.U18 A.A27 U-A WC 20-XX cWW cW-W 6 A.A19 A.U26 A-U WC 20-XX cWW cW-W 7 A.C20 A.G25 C-G WC 19-XIX cWW cW-W 8 A.U21 A.G24 U+G -- -- tSW tm+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=8 strand-1 5'-GGUGAGUA-3' bp-type |||||||| strand-2 3'-CCAUUCAU-5' helix-form ....... 1 A.G1 A.C43 G-C WC 19-XIX cWW cW-W 2 A.G2 A.C42 G-C WC 19-XIX cWW cW-W 3 A.U3 A.A41 U-A WC 20-XX cWW cW-W 4 A.G4 A.U40 G-U Wobble 28-XXVIII cWW cW-W 5 A.A5 A.U39 A-U WC 20-XX cWW cW-W 6 A.G6 A.C38 G-C WC 19-XIX cWW cW-W 7 A.U7 A.A37 U-A WC 20-XX cWW cW-W 8 A.A8 A.U36 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=7 strand-1 5'-AGUAUAC-3' bp-type ||||||| strand-2 3'-UCAUAUG-5' helix-form ...... 1 A.A14 A.U31 A-U WC 20-XX cWW cW-W 2 A.G15 A.C30 G-C WC 19-XIX cWW cW-W 3 A.U16 A.A29 U-A WC 20-XX cWW cW-W 4 A.A17 A.U28 A-U WC 20-XX cWW cW-W 5 A.U18 A.A27 U-A WC 20-XX cWW cW-W 6 A.A19 A.U26 A-U WC 20-XX cWW cW-W 7 A.C20 A.G25 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 7 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 AC A.A8,A.C9 2 nts=2 GG A.G24,A.G25 3 nts=2 UU A.U31,A.U32 4 nts=2 AU A.A33,A.U34 5 nts=2 AU A.A35,A.U36 6 nts=3 GUA A.G10,A.U11,A.A12 7 nts=3 CUC A.C20,A.U21,A.C23 **************************************************************************** Nucleotides not involved in stacking interactions nts=3 GUC A.G13,A.U22,A.C43 **************************************************************************** List of 2 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 phosphate OP2@A.G10 A.G10 3.50 2 sugar O2'@A.A12 A.G13 2.91 **************************************************************************** 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=6; [4]; linked by [#2] summary: [1] 4 [A.20 A.25] 7 nts=6 CUUCGG A.C20,A.U21,A.U22,A.C23,A.G24,A.G25 nts=4 UUCG A.U21,A.U22,A.C23,A.G24 **************************************************************************** List of 1 internal loop 1 asymmetric internal loop: nts=13; [5,4]; linked by [#1,#2] summary: [2] 5 4 [A.8 A.36 A.14 A.31] 8 7 nts=13 ACGUAGAUUAUAU A.A8,A.C9,A.G10,A.U11,A.A12,A.G13,A.A14,A.U31,A.U32,A.A33,A.U34,A.A35,A.U36 nts=5 CGUAG A.C9,A.G10,A.U11,A.A12,A.G13 nts=4 UAUA A.U32,A.A33,A.U34,A.A35 **************************************************************************** List of 2 splayed-apart dinucleotides 1 A.U21 A.U22 angle=93 distance=13.3 ratio=0.73 2 A.U22 A.C23 angle=85 distance=13.6 ratio=0.68 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=3 UUC A.U21,A.U22,A.C23 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >2n6x nts=43 [whole] GGUGAGUACGUAGAGUAUACUUCGGUAUACUUAUAUACUUACC ((((((((.....(((((((....)))))))....)))))))) >2n6x-A #1 nts=43 0.13(1.96) [chain] RNA GGUGAGUACGUAGAGUAUACUUCGGUAUACUUAUAUACUUACC ((((((((.....(((((((....)))))))....)))))))) **************************************************************************** Summary of structural features of 43 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 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 G ( A.G2 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 3 U ( A.U3 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 4 G ( A.G4 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 5 A ( A.A5 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 6 G ( A.G6 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 7 U ( A.U7 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 8 A ( A.A8 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop 9 C . A.C9 0.009 syn,~C3'-endo,BI,non-pair-contact,internal-loop 10 G . A.G10 0.008 syn,~C3'-endo,BI,non-pair-contact,internal-loop,cap-donor,cap-acceptor,phosphate 11 U . A.U11 0.016 syn,~C3'-endo,BI,non-pair-contact,internal-loop 12 A . A.A12 0.009 anti,~C3'-endo,BI,non-pair-contact,internal-loop,cap-donor 13 G . A.G13 0.007 syn,~C3'-endo,BI,non-stack,non-pair-contact,internal-loop,cap-acceptor 14 A ( A.A14 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop 15 G ( A.G15 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 16 U ( A.U16 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 17 A ( A.A17 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 18 U ( A.U18 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 19 A ( A.A19 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 20 C ( A.C20 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 21 U . A.U21 0.016 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,splayed-apart 22 U . A.U22 0.017 turn,anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,splayed-apart 23 C . A.C23 0.009 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,splayed-apart 24 G . A.G24 0.008 syn,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop 25 G ) A.G25 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 26 U ) A.U26 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 27 A ) A.A27 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 28 U ) A.U28 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 29 A ) A.A29 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 30 C ) A.C30 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 31 U ) A.U31 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop 32 U . A.U32 0.016 anti,~C3'-endo,BI,non-pair-contact,internal-loop 33 A . A.A33 0.008 anti,~C3'-endo,BI,non-pair-contact,internal-loop 34 U . A.U34 0.017 anti,~C3'-endo,BI,non-pair-contact,internal-loop 35 A . A.A35 0.011 anti,~C3'-endo,BI,non-pair-contact,internal-loop 36 U ) A.U36 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop 37 A ) A.A37 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 38 C ) A.C38 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 39 U ) A.U39 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 40 U ) A.U40 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 41 A ) A.A41 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 42 C ) A.C42 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 43 C ) A.C43 0.008 anti,~C3'-endo,non-stack,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** List of 12 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-iloops.pdb -- an ensemble of internal loops 6 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 7 dssr-2ndstrs.ct -- secondary structure in connectivity table format 8 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 9 dssr-torsions.txt -- backbone torsion angles and suite names 10 dssr-splays.pdb -- an ensemble of splayed-apart units 11 dssr-stacks.pdb -- an ensemble of base stacks 12 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions