**************************************************************************** File name: 2h1m.pdb no. of DNA/RNA chains: 2 [A=16,B=16] no. of nucleotides: 32 no. of atoms: 695 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 1 type of 2 modified nucleotides nt count list 1 XUG-g 2 A.XUG4,B.XUG20 **************************************************************************** List of 16 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.G1 B.C32 G-C WC 19-XIX cWW cW-W 2 A.C2 B.G31 C-G WC 19-XIX cWW cW-W 3 A.A3 B.U30 A-U WC 20-XX cWW cW-W 4 A.XUG4 B.C29 g-C WC 19-XIX cWW cW-W 5 A.A5 B.U28 A-U WC 20-XX cWW cW-W 6 A.G6 B.A27 G+A -- 09-IX cHW cM+W 7 A.U7 B.A26 U-A WC 20-XX cWW cW-W 8 A.U8 B.A25 U-A WC 20-XX cWW cW-W 9 A.A9 B.U24 A-U WC 20-XX cWW cW-W 10 A.A10 B.U23 A-U WC 20-XX cWW cW-W 11 A.A11 B.G22 A+G -- -- cWH cW+M 12 A.U12 B.A21 U-A WC 20-XX cWW cW-W 13 A.C13 B.XUG20 C-g WC 19-XIX cWW cW-W 14 A.U14 B.A19 U-A WC 20-XX cWW cW-W 15 A.G15 B.C18 G-C WC 19-XIX cWW cW-W 16 A.C16 B.G17 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[3] bps=16 strand-1 5'-GCAgAGUUAAAUCUGC-3' bp-type |||||.||||.||||| strand-2 3'-CGUCUAAAUUGAgACG-5' helix-form AAAA....A..AAAA 1 A.G1 B.C32 G-C WC 19-XIX cWW cW-W 2 A.C2 B.G31 C-G WC 19-XIX cWW cW-W 3 A.A3 B.U30 A-U WC 20-XX cWW cW-W 4 A.XUG4 B.C29 g-C WC 19-XIX cWW cW-W 5 A.A5 B.U28 A-U WC 20-XX cWW cW-W 6 A.G6 B.A27 G+A -- 09-IX cHW cM+W 7 A.U7 B.A26 U-A WC 20-XX cWW cW-W 8 A.U8 B.A25 U-A WC 20-XX cWW cW-W 9 A.A9 B.U24 A-U WC 20-XX cWW cW-W 10 A.A10 B.U23 A-U WC 20-XX cWW cW-W 11 A.A11 B.G22 A+G -- -- cWH cW+M 12 A.U12 B.A21 U-A WC 20-XX cWW cW-W 13 A.C13 B.XUG20 C-g WC 19-XIX cWW cW-W 14 A.U14 B.A19 U-A WC 20-XX cWW cW-W 15 A.G15 B.C18 G-C WC 19-XIX cWW cW-W 16 A.C16 B.G17 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 3 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'-GCAgA-3' bp-type ||||| strand-2 3'-CGUCU-5' helix-form AAAA 1 A.G1 B.C32 G-C WC 19-XIX cWW cW-W 2 A.C2 B.G31 C-G WC 19-XIX cWW cW-W 3 A.A3 B.U30 A-U WC 20-XX cWW cW-W 4 A.XUG4 B.C29 g-C WC 19-XIX cWW cW-W 5 A.A5 B.U28 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=4 strand-1 5'-UUAA-3' bp-type |||| strand-2 3'-AAUU-5' helix-form ..A 1 A.U7 B.A26 U-A WC 20-XX cWW cW-W 2 A.U8 B.A25 U-A WC 20-XX cWW cW-W 3 A.A9 B.U24 A-U WC 20-XX cWW cW-W 4 A.A10 B.U23 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#3[#1] bps=5 strand-1 5'-UCUGC-3' bp-type ||||| strand-2 3'-AgACG-5' helix-form AAAA 1 A.U12 B.A21 U-A WC 20-XX cWW cW-W 2 A.C13 B.XUG20 C-g WC 19-XIX cWW cW-W 3 A.U14 B.A19 U-A WC 20-XX cWW cW-W 4 A.G15 B.C18 G-C WC 19-XIX cWW cW-W 5 A.C16 B.G17 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#1 contains 3 stems: [#1,#2,#3] **************************************************************************** List of 4 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 AGU A.A5,A.G6,A.U7 2 nts=3 AAU A.A10,A.A11,A.U12 3 nts=3 AGU B.A21,B.G22,B.U23 4 nts=3 AAU B.A26,B.A27,B.U28 **************************************************************************** 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 2 internal loops 1 symmetric internal loop: nts=6; [1,1]; linked by [#1,#2] summary: [2] 1 1 [A.5 B.28 A.7 B.26] 5 4 nts=6 AGUAAU A.A5,A.G6,A.U7,B.A26,B.A27,B.U28 nts=1 G A.G6 nts=1 A B.A27 2 symmetric internal loop: nts=6; [1,1]; linked by [#2,#3] summary: [2] 1 1 [A.10 B.23 A.12 B.21] 4 5 nts=6 AAUAGU A.A10,A.A11,A.U12,B.A21,B.G22,B.U23 nts=1 A A.A11 nts=1 G B.G22 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >2h1m nts=32 [whole] GCAgAGUUAAAUCUGC&GCAgAGUUAAAUCUGC (((((.((((.(((((&))))).)))).))))) >2h1m-A #1 nts=16 2.69(0.38) [chain] RNA GCAgAGUUAAAUCUGC (((((.((((.((((( >2h1m-B #2 nts=16 2.69(0.34) [chain] RNA GCAgAGUUAAAUCUGC ))))).)))).))))) **************************************************************************** Summary of structural features of 32 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 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 2 C ( A.C2 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 3 A ( A.A3 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 4 g ( A.XUG4 0.065 modified,anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 5 A ( A.A5 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 6 G . A.G6 0.013 syn,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 7 U ( A.U7 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 8 U ( A.U8 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 9 A ( A.A9 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 10 A ( A.A10 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 11 A . A.A11 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 12 U ( A.U12 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 13 C ( A.C13 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 14 U ( A.U14 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 15 G ( A.G15 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 16 C ( A.C16 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 17 G ) B.G17 0.012 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 18 C ) B.C18 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 19 A ) B.A19 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 20 g ) B.XUG20 0.064 modified,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 21 A ) B.A21 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 22 G . B.G22 0.013 syn,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 23 U ) B.U23 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 24 U ) B.U24 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 25 A ) B.A25 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 26 A ) B.A26 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 27 A . B.A27 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 28 U ) B.U28 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 29 C ) B.C29 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 30 U ) B.U30 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 31 G ) B.G31 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 32 C ) B.C32 0.005 anti,~C3'-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