Comments (4)
cbaakman
commented on August 14, 2024
Non-conventional amino acids should work in DSSP as long as the four backbone atoms are present: N, CA, C, O. Your amino acid seems to have those, but the chain ids appear to be missing in your pdb format. Is this really the format you're using? Otherwise, could you send me the entire pdb file?
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luirink
commented on August 14, 2024
I thought so indeed, but I do have the N, CA, C, and O atoms in the non-natural amino acids.
I have attached an example pub file. It is a peptide of 24 residues, of which 2 non-natural. The output is for 22 residues and 3 chains, whereas the pdb file with the WT peptide gives the output for 24 residues and 1 chain. Thanks for helping!
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cbaakman
commented on August 14, 2024
My version of mkdssp makes the following file from your attached file:
==== Secondary Structure Definition by the program DSSP, CMBI version 3.0.6 ==== DATE=2019-04-25 .
REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 .
.
COMPND .
SOURCE .
AUTHOR .
23 1 0 0 0 TOTAL NUMBER OF RESIDUES, NUMBER OF CHAINS, NUMBER OF SS-BRIDGES(TOTAL,INTRACHAIN,INTERCHAIN) .
2729.3 ACCESSIBLE SURFACE OF PROTEIN (ANGSTROM**2) .
6 26.1 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(J) , SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS IN PARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS IN ANTIPARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-5), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-4), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-3), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-2), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-1), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+0), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+1), SAME NUMBER PER 100 RESIDUES .
1 4.3 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+2), SAME NUMBER PER 100 RESIDUES .
3 13.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+3), SAME NUMBER PER 100 RESIDUES .
2 8.7 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+4), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+5), SAME NUMBER PER 100 RESIDUES .
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 *** HISTOGRAMS OF *** .
0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 RESIDUES PER ALPHA HELIX .
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 PARALLEL BRIDGES PER LADDER .
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ANTIPARALLEL BRIDGES PER LADDER .
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 LADDERS PER SHEET .
# RESIDUE AA STRUCTURE BP1 BP2 ACC N-H-->O O-->H-N N-H-->O O-->H-N TCO KAPPA ALPHA PHI PSI X-CA Y-CA Z-CA CHAIN AUTHCHAIN
1 64 Q 0 0 186 0, 0.0 2,-0.3 0, 0.0 21,-0.1 0.000 360.0 360.0 360.0 115.7 39.0 28.9 20.1···························
2 65 E - 0 0 125 19,-0.1 2,-0.2 21,-0.0 21,-0.1 -0.915 360.0-120.0-161.8 163.0 38.9 32.7 20.5···························
3 66 A - 0 0 16 -2,-0.3 2,-0.3 19,-0.1 18,-0.1 -0.654 25.7-152.0 -97.4 165.3 39.1 35.9 18.3···························
4 67 L - 0 0 129 -2,-0.2 2,-0.2 2,-0.0 -2,-0.0 -0.967 10.7-122.9-142.7 153.8 41.6 38.7 18.5···························
5 68 E - 0 0 92 -2,-0.3 2,-0.3 4,-0.0 3,-0.0 -0.576 23.1-171.8 -89.1 159.2 42.0 42.5 17.7···························
6 69 E >> - 0 0 96 -2,-0.2 4,-2.3 1,-0.0 3,-1.7 -0.934 43.8 -92.4-146.3 167.6 44.7 44.1 15.4···························
7 70 R H 3> S+ 0 0 216 -2,-0.3 4,-2.6 1,-0.3 5,-0.2 0.794 121.6 59.9 -62.0 -38.8 45.6 47.7 14.8···························
8 71 A H 34 S+ 0 0 74 1,-0.2 -1,-0.3 2,-0.2 -3,-0.0 0.666 116.6 35.0 -63.9 -24.1 43.1 48.1 11.7···························
9 72 X H X4 S+ 0 0 37 -3,-1.7 3,-1.2 2,-0.1 -1,-0.2 0.809 114.7 57.2 -85.4 -36.4 40.2 47.2 14.1···························
10 73 N H 3< S+ 0 0 84 -4,-2.3 -2,-0.2 1,-0.3 -3,-0.2 0.800 104.8 51.1 -72.7 -26.4 41.8 49.0 17.1···························
11 74 E T 3< S+ 0 0 113 -4,-2.6 -1,-0.3 -5,-0.2 2,-0.2 0.344 87.1 105.9 -92.6 2.0 42.0 52.5 15.3···························
12 75 L S < S- 0 0 83 -3,-1.2 -3,-0.0 -5,-0.2 -4,-0.0 -0.610 71.3-133.8 -83.4 147.5 38.3 52.6 14.1···························
13 76 S S S+ 0 0 138 -2,-0.2 2,-0.3 2,-0.1 -1,-0.1 0.261 85.5 56.9 -76.8 2.9 35.7 54.9 15.8···························
14 77 M S S- 0 0 141 -5,-0.2 -2,-0.1 0, 0.0 2,-0.1 -0.984 79.7-119.6-139.9 144.4 33.0 52.1 16.1···························
15 78 T - 0 0 162 -2,-0.3 -2,-0.1 1,-0.1 -5,-0.0 -0.420 40.4 -91.0 -73.3 162.0 32.9 48.6 17.6···························
16 79 R > - 0 0 79 -2,-0.1 3,-0.6 1,-0.0 2,-0.3 -0.562 32.9-138.6 -69.3 125.9 32.2 45.4 15.7···························
17 80 P T 3 S+ 0 0 145 0, 0.0 -1,-0.0 0, 0.0 0, 0.0 -0.747 85.7 8.7 -84.1 135.1 28.6 44.2 15.4···························
18 81 G T 3 S- 0 0 88 -2,-0.3 2,-0.7 1,-0.2 -2,-0.0 0.747 80.5-178.9 66.3 37.0 28.1 40.3 15.9···························
19 82 X < + 0 0 86 -3,-0.6 -1,-0.2 2,-0.1 2,-0.1 -0.447 8.4 179.2 -65.5 105.9 31.7 39.6 17.0···························
20 83 T - 0 0 107 -2,-0.7 -17,-0.1 2,-0.3 -1,-0.0 -0.304 43.2 -98.4 -98.9-176.4 32.0 35.9 17.6···························
21 84 F S S+ 0 0 175 -19,-0.1 2,-0.3 -2,-0.1 -19,-0.1 0.372 94.9 85.1 -77.1 -4.6 34.8 33.4 18.7···························
22 85 Y 0 0 192 -21,-0.1 -2,-0.3 -19,-0.0 -19,-0.1 -0.896 360.0 360.0-101.3 150.5 35.6 32.3 15.0···························
23 86 R 0 0 164 -2,-0.3 -21,-0.0 -21,-0.1 -2,-0.0 -0.988 360.0 360.0-146.9 360.0 37.9 34.0 12.4···························
Notice that residues 72 and 82 are present. Residue 87 is missing, because it has no 'O' atom.
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luirink
commented on August 14, 2024
I see that using xssp directly gives me the same result. I previously used it through Gromacs do_dssp.
Not sure why there is a difference.. Will have a look.
I need percentages of amount of structure in longer trajectories, an output given by the gromacs program.
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