**************************************************************************** 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=6kda.pdb -o=6kda.out File name: 6kda.pdb no. of DNA/RNA chains: 2 [E=25,F=25] no. of nucleotides: 52 no. of atoms: 9004 no. of waters: 305 no. of metals: 0 **************************************************************************** List of 1 type of 2 modified nucleotides nt count list 1 SAH-a 2 A.SAH901,D.SAH901 **************************************************************************** List of 25 base pairs nt1 nt2 bp name Saenger LW DSSR 1 E.DA423 F.DT446 A-T WC 20-XX cWW cW-W 2 E.DA424 F.DT445 A-T WC 20-XX cWW cW-W 3 E.DT425 F.DA444 T-A WC 20-XX cWW cW-W 4 E.DT426 F.DA443 T-A WC 20-XX cWW cW-W 5 E.DG428 F.DC441 G-C WC 19-XIX cWW cW-W 6 E.DG429 F.DC440 G-C WC 19-XIX cWW cW-W 7 E.DA430 F.DT439 A-T WC 20-XX cWW cW-W 8 E.DA431 F.DT437 A-T -- -- cWW cW-W 9 E.DA431 F.DT438 A-T WC 20-XX cWW cW-W 10 E.DA432 F.DT436 A-T -- -- cWW cW-W 11 E.DA432 F.DT437 A-T WC 20-XX cWW cW-W 12 E.DA433 F.DT436 A-T WC 20-XX cWW cW-W 13 E.DA434 F.DT435 A-T WC 20-XX cWW cW-W 14 E.DT435 F.DA434 T-A WC 20-XX cWW cW-W 15 E.DT436 F.DA432 T-A -- -- cWW cW-W 16 E.DT436 F.DA433 T-A WC 20-XX cWW cW-W 17 E.DT437 F.DA432 T-A WC 20-XX cWW cW-W 18 E.DT438 F.DA431 T-A WC 20-XX cWW cW-W 19 E.DT439 F.DA430 T-A WC 20-XX cWW cW-W 20 E.DC440 F.DG429 C-G WC 19-XIX cWW cW-W 21 E.DC441 F.DG428 C-G WC 19-XIX cWW cW-W 22 E.DA443 F.DT426 A-T WC 20-XX cWW cW-W 23 E.DA444 F.DT425 A-T WC 20-XX cWW cW-W 24 E.DT445 F.DA424 T-A WC 20-XX cWW cW-W 25 E.DT446 F.DA423 T-A WC 20-XX cWW cW-W **************************************************************************** List of 1 helix 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[3] bps=22 strand-1 5'-AATTGGAAAAATTTTTCCAATT-3' bp-type |||||||||||||||||||||| strand-2 3'-TTAACCTTTTTAAAAAGGTTAA-5' helix-form BB.x......BB.....x.BB 1 E.DA423 F.DT446 A-T WC 20-XX cWW cW-W 2 E.DA424 F.DT445 A-T WC 20-XX cWW cW-W 3 E.DT425 F.DA444 T-A WC 20-XX cWW cW-W 4 E.DT426 F.DA443 T-A WC 20-XX cWW cW-W 5 E.DG428 F.DC441 G-C WC 19-XIX cWW cW-W 6 E.DG429 F.DC440 G-C WC 19-XIX cWW cW-W 7 E.DA430 F.DT439 A-T WC 20-XX cWW cW-W 8 E.DA431 F.DT438 A-T WC 20-XX cWW cW-W 9 E.DA432 F.DT437 A-T WC 20-XX cWW cW-W 10 E.DA433 F.DT436 A-T WC 20-XX cWW cW-W 11 E.DA434 F.DT435 A-T WC 20-XX cWW cW-W 12 E.DT435 F.DA434 T-A WC 20-XX cWW cW-W 13 E.DT436 F.DA433 T-A WC 20-XX cWW cW-W 14 E.DT437 F.DA432 T-A WC 20-XX cWW cW-W 15 E.DT438 F.DA431 T-A WC 20-XX cWW cW-W 16 E.DT439 F.DA430 T-A WC 20-XX cWW cW-W 17 E.DC440 F.DG429 C-G WC 19-XIX cWW cW-W 18 E.DC441 F.DG428 C-G WC 19-XIX cWW cW-W 19 E.DA443 F.DT426 A-T WC 20-XX cWW cW-W 20 E.DA444 F.DT425 A-T WC 20-XX cWW cW-W 21 E.DT445 F.DA424 T-A WC 20-XX cWW cW-W 22 E.DT446 F.DA423 T-A WC 20-XX cWW cW-W **************************************************************************** List of 3 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=4 strand-1 5'-AATT-3' bp-type |||| strand-2 3'-TTAA-5' helix-form BB. 1 E.DA423 F.DT446 A-T WC 20-XX cWW cW-W 2 E.DA424 F.DT445 A-T WC 20-XX cWW cW-W 3 E.DT425 F.DA444 T-A WC 20-XX cWW cW-W 4 E.DT426 F.DA443 T-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=14 strand-1 5'-GGAAAAATTTTTCC-3' bp-type |||||||||||||| strand-2 3'-CCTTTTTAAAAAGG-5' helix-form ......BB..... 1 E.DG428 F.DC441 G-C WC 19-XIX cWW cW-W 2 E.DG429 F.DC440 G-C WC 19-XIX cWW cW-W 3 E.DA430 F.DT439 A-T WC 20-XX cWW cW-W 4 E.DA431 F.DT438 A-T WC 20-XX cWW cW-W 5 E.DA432 F.DT437 A-T WC 20-XX cWW cW-W 6 E.DA433 F.DT436 A-T WC 20-XX cWW cW-W 7 E.DA434 F.DT435 A-T WC 20-XX cWW cW-W 8 E.DT435 F.DA434 T-A WC 20-XX cWW cW-W 9 E.DT436 F.DA433 T-A WC 20-XX cWW cW-W 10 E.DT437 F.DA432 T-A WC 20-XX cWW cW-W 11 E.DT438 F.DA431 T-A WC 20-XX cWW cW-W 12 E.DT439 F.DA430 T-A WC 20-XX cWW cW-W 13 E.DC440 F.DG429 C-G WC 19-XIX cWW cW-W 14 E.DC441 F.DG428 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#3[#1] bps=4 strand-1 5'-AATT-3' bp-type |||| strand-2 3'-TTAA-5' helix-form .BB 1 E.DA443 F.DT426 A-T WC 20-XX cWW cW-W 2 E.DA444 F.DT425 A-T WC 20-XX cWW cW-W 3 E.DT445 F.DA424 T-A WC 20-XX cWW cW-W 4 E.DT446 F.DA423 T-A WC 20-XX 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=2 GA E.DG422,E.DA423 2 nts=2 GA F.DG422,F.DA423 3 nts=3 CGA E.DC441,E.DG442,E.DA443 4 nts=3 CGA F.DC441,F.DG442,F.DA443 **************************************************************************** Nucleotides not involved in stacking interactions nts=1 C F.DC427 **************************************************************************** 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 2 internal loops 1 symmetric internal loop: nts=6; [1,1]; linked by [#1,#2] summary: [2] 1 1 [E.426 F.443 E.428 F.441] 4 14 nts=6 TCGCGA E.DT426,E.DC427,E.DG428,F.DC441,F.DG442,F.DA443 nts=1 C E.DC427 nts=1 G F.DG442 2 symmetric internal loop: nts=6; [1,1]; linked by [#2,#3] summary: [2] 1 1 [E.441 F.428 E.443 F.426] 14 4 nts=6 CGATCG E.DC441,E.DG442,E.DA443,F.DT426,F.DC427,F.DG428 nts=1 G E.DG442 nts=1 C F.DC427 **************************************************************************** List of 4 non-loop single-stranded segments 1 nts=1 G E.DG422 2 nts=1 G F.DG422 3 nts=1 a A.SAH901 4 nts=1 a D.SAH901 **************************************************************************** List of 4 splayed-apart dinucleotides 1 E.DT426 E.DC427 angle=167 distance=18.7 ratio=0.99 2 E.DC427 E.DG428 angle=143 distance=18.9 ratio=0.95 3 F.DT426 F.DC427 angle=164 distance=18.6 ratio=0.99 4 F.DC427 F.DG428 angle=144 distance=18.6 ratio=0.95 ---------------------------------------------------------------- Summary of 2 splayed-apart units 1 nts=3 TCG E.DT426,E.DC427,E.DG428 2 nts=3 TCG F.DT426,F.DC427,F.DG428 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >6kda nts=52 [whole] GAATTCGGAAAAATTTTTCCGAATT&GAATTCGGAAAAATTTTTCCGAATT&a&a .((((.((((((((((((((.((((&.)))).)))))))))))))).))))&.&. >6kda-E #1 nts=25 3.09(1.05) [chain] DNA GAATTCGGAAAAATTTTTCCGAATT .((((.((((((((((((((.(((( >6kda-F #2 nts=25 3.10(1.11) [chain] DNA GAATTCGGAAAAATTTTTCCGAATT .)))).)))))))))))))).)))) **************************************************************************** Summary of structural features of 52 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 . E.DG422 0.009 anti,~C2'-endo,BII,non-pair-contact,ss-non-loop 2 A ( E.DA423 0.012 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 3 A ( E.DA424 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 4 T ( E.DT425 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 5 T ( E.DT426 0.011 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate,splayed-apart 6 C . E.DC427 0.019 turn,anti,~C3'-endo,internal-loop,phosphate,splayed-apart 7 G ( E.DG428 0.004 anti,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate,splayed-apart 8 G ( E.DG429 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 9 A ( E.DA430 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 10 A ( E.DA431 0.006 anti,~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 11 A ( E.DA432 0.004 anti,~C2'-endo,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 12 A ( E.DA433 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 13 A ( E.DA434 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 14 T ( E.DT435 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 15 T ( E.DT436 0.007 anti,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 16 T ( E.DT437 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 17 T ( E.DT438 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 18 T ( E.DT439 0.006 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 19 C ( E.DC440 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 20 C ( E.DC441 0.003 anti,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 21 G . E.DG442 0.004 anti,BI,non-pair-contact,internal-loop 22 A ( E.DA443 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 23 A ( E.DA444 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 24 T ( E.DT445 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 25 T ( E.DT446 0.012 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,phosphate 26 G . F.DG422 0.012 anti,non-pair-contact,ss-non-loop 27 A ) F.DA423 0.018 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 28 A ) F.DA424 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 29 T ) F.DT425 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 30 T ) F.DT426 0.011 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate,splayed-apart 31 C . F.DC427 0.007 turn,anti,~C3'-endo,non-stack,internal-loop,phosphate,splayed-apart 32 G ) F.DG428 0.006 anti,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate,splayed-apart 33 G ) F.DG429 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 34 A ) F.DA430 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 35 A ) F.DA431 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 36 A ) F.DA432 0.004 anti,~C2'-endo,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 37 A ) F.DA433 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 38 A ) F.DA434 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 39 T ) F.DT435 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 40 T ) F.DT436 0.007 anti,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 41 T ) F.DT437 0.006 anti,~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 42 T ) F.DT438 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 43 T ) F.DT439 0.007 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 44 C ) F.DC440 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 45 C ) F.DC441 0.003 anti,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 46 G . F.DG442 0.007 anti,BI,non-pair-contact,internal-loop 47 A ) F.DA443 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 48 A ) F.DA444 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 49 T ) F.DT445 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 50 T ) F.DT446 0.010 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,phosphate 51 a . A.SAH901 0.065 modified,anti,~C2'-endo,ss-non-loop 52 a . D.SAH901 0.058 modified,anti,~C2'-endo,ss-non-loop **************************************************************************** List of 10 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