**************************************************************************** File name: 36ow.pdb no. of DNA/RNA chains: 2 [A=31,B=31] no. of nucleotides: 62 no. of atoms: 2908 no. of waters: 0 no. of metals: 1 [Mg=1] **************************************************************************** List of 4 types of 6 modified nucleotides nt count list 1 AS-a 1 A.AS20 2 GS-g 3 A.GS21,B.GS42,B.GS43 3 SC-c 1 A.SC19 4 PST-t 1 B.PST44 **************************************************************************** List of 30 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DG-4 B.DC48 G-C WC 19-XIX cWW cW-W 2 A.DA-3 B.DT47 A-T WC 20-XX cWW cW-W 3 A.DT-2 B.DA46 T-A WC 20-XX cWW cW-W 4 A.DA-1 B.DT45 A-T WC 20-XX cWW cW-W 5 A.DA0 B.PST44 A-t WC 20-XX cWW cW-W 6 A.DC1 B.GS43 C-g WC 19-XIX cWW cW-W 7 A.DC2 B.GS42 C-g WC 19-XIX cWW cW-W 8 A.DT3 B.DA41 T-A WC 20-XX cWW cW-W 9 A.DG4 B.DC40 G-C WC 19-XIX cWW cW-W 10 A.DT5 B.DA39 T-A WC 20-XX cWW cW-W 11 A.DG6 B.DC38 G-C WC 19-XIX cWW cW-W 12 A.DA7 B.DT37 A-T WC 20-XX cWW cW-W 13 A.DC8 B.DG36 C-G WC 19-XIX cWW cW-W 14 A.DA9 B.DT35 A-T WC 20-XX cWW cW-W 15 A.DA10 B.DT34 A-T WC 20-XX cWW cW-W 16 A.DA11 B.DT33 A-T WC 20-XX cWW cW-W 17 A.DT12 B.DA32 T-A WC 20-XX cWW cW-W 18 A.DT13 B.DA31 T-A WC 20-XX cWW cW-W 19 A.DG14 B.DC30 G-C WC 19-XIX cWW cW-W 20 A.DC15 B.DG29 C-G WC 19-XIX cWW cW-W 21 A.DC16 B.DG28 C-G WC 19-XIX cWW cW-W 22 A.DC17 B.DG27 C-G WC 19-XIX cWW cW-W 23 A.DT18 B.DA26 T-A WC 20-XX cWW cW-W 24 A.SC19 B.DG25 c-G WC 19-XIX cWW cW-W 25 A.AS20 B.DT24 a-T WC 20-XX cWW cW-W 26 A.GS21 B.DC23 g-C WC 19-XIX cWW cW-W 27 A.DC22 B.DG22 C-G WC 19-XIX cWW cW-W 28 A.DG23 B.DC21 G-C WC 19-XIX cWW cW-W 29 A.DC24 B.DG20 C-G WC 19-XIX cWW cW-W 30 A.DG25 B.DC19 G-C 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[1] bps=30 strand-1 5'-GATAACCTGTGACAAATTGCCCTcagCGCG-3' bp-type |||||||||||||||||||||||||||||| strand-2 3'-CTATtggACACTGTTTAACGGGAGTCGCGC-5' helix-form B.BB...BBBBBBBB.B....BBB..BBB 1 A.DG-4 B.DC48 G-C WC 19-XIX cWW cW-W 2 A.DA-3 B.DT47 A-T WC 20-XX cWW cW-W 3 A.DT-2 B.DA46 T-A WC 20-XX cWW cW-W 4 A.DA-1 B.DT45 A-T WC 20-XX cWW cW-W 5 A.DA0 B.PST44 A-t WC 20-XX cWW cW-W 6 A.DC1 B.GS43 C-g WC 19-XIX cWW cW-W 7 A.DC2 B.GS42 C-g WC 19-XIX cWW cW-W 8 A.DT3 B.DA41 T-A WC 20-XX cWW cW-W 9 A.DG4 B.DC40 G-C WC 19-XIX cWW cW-W 10 A.DT5 B.DA39 T-A WC 20-XX cWW cW-W 11 A.DG6 B.DC38 G-C WC 19-XIX cWW cW-W 12 A.DA7 B.DT37 A-T WC 20-XX cWW cW-W 13 A.DC8 B.DG36 C-G WC 19-XIX cWW cW-W 14 A.DA9 B.DT35 A-T WC 20-XX cWW cW-W 15 A.DA10 B.DT34 A-T WC 20-XX cWW cW-W 16 A.DA11 B.DT33 A-T WC 20-XX cWW cW-W 17 A.DT12 B.DA32 T-A WC 20-XX cWW cW-W 18 A.DT13 B.DA31 T-A WC 20-XX cWW cW-W 19 A.DG14 B.DC30 G-C WC 19-XIX cWW cW-W 20 A.DC15 B.DG29 C-G WC 19-XIX cWW cW-W 21 A.DC16 B.DG28 C-G WC 19-XIX cWW cW-W 22 A.DC17 B.DG27 C-G WC 19-XIX cWW cW-W 23 A.DT18 B.DA26 T-A WC 20-XX cWW cW-W 24 A.SC19 B.DG25 c-G WC 19-XIX cWW cW-W 25 A.AS20 B.DT24 a-T WC 20-XX cWW cW-W 26 A.GS21 B.DC23 g-C WC 19-XIX cWW cW-W 27 A.DC22 B.DG22 C-G WC 19-XIX cWW cW-W 28 A.DG23 B.DC21 G-C WC 19-XIX cWW cW-W 29 A.DC24 B.DG20 C-G WC 19-XIX cWW cW-W 30 A.DG25 B.DC19 G-C WC 19-XIX cWW cW-W **************************************************************************** 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=30 strand-1 5'-GATAACCTGTGACAAATTGCCCTcagCGCG-3' bp-type |||||||||||||||||||||||||||||| strand-2 3'-CTATtggACACTGTTTAACGGGAGTCGCGC-5' helix-form B.BB...BBBBBBBB.B....BBB..BBB 1 A.DG-4 B.DC48 G-C WC 19-XIX cWW cW-W 2 A.DA-3 B.DT47 A-T WC 20-XX cWW cW-W 3 A.DT-2 B.DA46 T-A WC 20-XX cWW cW-W 4 A.DA-1 B.DT45 A-T WC 20-XX cWW cW-W 5 A.DA0 B.PST44 A-t WC 20-XX cWW cW-W 6 A.DC1 B.GS43 C-g WC 19-XIX cWW cW-W 7 A.DC2 B.GS42 C-g WC 19-XIX cWW cW-W 8 A.DT3 B.DA41 T-A WC 20-XX cWW cW-W 9 A.DG4 B.DC40 G-C WC 19-XIX cWW cW-W 10 A.DT5 B.DA39 T-A WC 20-XX cWW cW-W 11 A.DG6 B.DC38 G-C WC 19-XIX cWW cW-W 12 A.DA7 B.DT37 A-T WC 20-XX cWW cW-W 13 A.DC8 B.DG36 C-G WC 19-XIX cWW cW-W 14 A.DA9 B.DT35 A-T WC 20-XX cWW cW-W 15 A.DA10 B.DT34 A-T WC 20-XX cWW cW-W 16 A.DA11 B.DT33 A-T WC 20-XX cWW cW-W 17 A.DT12 B.DA32 T-A WC 20-XX cWW cW-W 18 A.DT13 B.DA31 T-A WC 20-XX cWW cW-W 19 A.DG14 B.DC30 G-C WC 19-XIX cWW cW-W 20 A.DC15 B.DG29 C-G WC 19-XIX cWW cW-W 21 A.DC16 B.DG28 C-G WC 19-XIX cWW cW-W 22 A.DC17 B.DG27 C-G WC 19-XIX cWW cW-W 23 A.DT18 B.DA26 T-A WC 20-XX cWW cW-W 24 A.SC19 B.DG25 c-G WC 19-XIX cWW cW-W 25 A.AS20 B.DT24 a-T WC 20-XX cWW cW-W 26 A.GS21 B.DC23 g-C WC 19-XIX cWW cW-W 27 A.DC22 B.DG22 C-G WC 19-XIX cWW cW-W 28 A.DG23 B.DC21 G-C WC 19-XIX cWW cW-W 29 A.DC24 B.DG20 C-G WC 19-XIX cWW cW-W 30 A.DG25 B.DC19 G-C WC 19-XIX cWW cW-W **************************************************************************** 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 GG A.DG25,A.DG26 2 nts=2 CC B.DC48,B.DC49 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=1 G A.DG26 2 nts=1 C B.DC49 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >36ow nts=62 [whole] GATAACCTGTGACAAATTGCCCTcagCGCGG&CGCGCTGAGGGCAATTTGTCACAggtTATCC ((((((((((((((((((((((((((((((.&)))))))))))))))))))))))))))))). >36ow-A #1 nts=31 3.18(0.54) [chain] DNA GATAACCTGTGACAAATTGCCCTcagCGCGG ((((((((((((((((((((((((((((((. >36ow-B #2 nts=31 3.18(0.58) [chain] DNA CGCGCTGAGGGCAATTTGTCACAggtTATCC )))))))))))))))))))))))))))))). **************************************************************************** Summary of structural features of 62 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.DG-4 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 2 A ( A.DA-3 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 3 T ( A.DT-2 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 4 A ( A.DA-1 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 5 A ( A.DA0 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 6 C ( A.DC1 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 7 C ( A.DC2 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 8 T ( A.DT3 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 9 G ( A.DG4 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 10 T ( A.DT5 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 11 G ( A.DG6 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 12 A ( A.DA7 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 13 C ( A.DC8 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 14 A ( A.DA9 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 15 A ( A.DA10 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 16 A ( A.DA11 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 17 T ( A.DT12 0.002 anti,BI,canonical,non-pair-contact,helix,stem 18 T ( A.DT13 0.002 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 19 G ( A.DG14 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 20 C ( A.DC15 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 21 C ( A.DC16 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 22 C ( A.DC17 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 23 T ( A.DT18 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 24 c ( A.SC19 0.028 modified,anti,canonical,non-pair-contact,helix,stem 25 a ( A.AS20 0.057 modified,anti,~C2'-endo,canonical,non-pair-contact,helix,stem 26 g ( A.GS21 0.070 modified,anti,~C2'-endo,canonical,non-pair-contact,helix,stem 27 C ( A.DC22 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 28 G ( A.DG23 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 29 C ( A.DC24 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 30 G ( A.DG25 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix-end,stem-end 31 G . A.DG26 0.004 anti,~C2'-endo,non-pair-contact,ss-non-loop 32 C ) B.DC19 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 33 G ) B.DG20 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 34 C ) B.DC21 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 35 G ) B.DG22 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 36 C ) B.DC23 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 37 T ) B.DT24 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 38 G ) B.DG25 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 39 A ) B.DA26 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 40 G ) B.DG27 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 41 G ) B.DG28 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 42 G ) B.DG29 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 43 C ) B.DC30 0.003 anti,canonical,non-pair-contact,helix,stem 44 A ) B.DA31 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 45 A ) B.DA32 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 46 T ) B.DT33 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 47 T ) B.DT34 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 48 T ) B.DT35 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 49 G ) B.DG36 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 50 T ) B.DT37 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 51 C ) B.DC38 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 52 A ) B.DA39 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 53 C ) B.DC40 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 54 A ) B.DA41 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 55 g ) B.GS42 0.070 modified,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 56 g ) B.GS43 0.070 modified,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 57 t ) B.PST44 0.046 modified,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 58 T ) B.DT45 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 59 A ) B.DA46 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 60 T ) B.DT47 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 61 C ) B.DC48 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 62 C . B.DC49 0.002 anti,~C2'-endo,non-pair-contact,ss-non-loop **************************************************************************** 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-2ndstrs.bpseq -- secondary structure in bpseq format 5 dssr-2ndstrs.ct -- secondary structure in connectivity table format 6 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 7 dssr-torsions.txt -- backbone torsion angles and suite names 8 dssr-stacks.pdb -- an ensemble of base stacks 9 dssr-rotmat.txt -- position vector and rotation matrix 10 dssr-viewV.pdb -- vertical view of the principal moment of inertia 11 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 12 dssr-viewT.pdb -- top view of the principal moment of inertia