dssp with non-natural amino acid
luirink opened this issue · 4 comments
Hi, I would like to calculate secondary structure with xssp for a peptide with a non-natural amino acid incorporated.
The non-natural amino acid is as written below (pdb). My attempt showed that it skipped the particular non-natural amino acids and divides the peptide in separate chains , which results in results that are not usable.
Is there a way to work around this issue, and consider the non-natural amino acid as well?
ATOM 128 N LAL 72 41.040 39.610 18.280 1.00 0.00
ATOM 129 H LAL 72 41.390 40.530 18.450 1.00 0.00
ATOM 130 CA LAL 72 39.600 39.500 17.930 1.00 0.00
ATOM 131 HA LAL 72 39.050 39.210 18.830 1.00 0.00
ATOM 132 CB LAL 72 39.110 40.880 17.500 1.00 0.00
ATOM 133 HB1 LAL 72 39.700 41.230 16.640 1.00 0.00
ATOM 134 HB2 LAL 72 39.180 41.560 18.340 1.00 0.00
ATOM 135 CG LAL 72 37.650 40.860 17.210 1.00 0.00
ATOM 136 HG1 LAL 72 37.070 40.340 17.980 1.00 0.00
ATOM 137 HG2 LAL 72 37.440 40.520 16.190 1.00 0.00
ATOM 138 CD LAL 72 37.090 42.270 17.460 1.00 0.00
ATOM 139 HD1 LAL 72 37.040 42.490 18.520 1.00 0.00
ATOM 140 HD2 LAL 72 36.020 42.220 17.230 1.00 0.00
ATOM 141 CE LAL 72 37.710 43.370 16.570 1.00 0.00
ATOM 142 HE LAL 72 38.780 43.500 16.510 1.00 0.00
ATOM 143 CZ LAL 72 36.850 44.210 15.880 1.00 0.00
ATOM 144 HZ LAL 72 35.780 44.120 15.870 1.00 0.00
ATOM 145 CN LAL 72 37.480 45.340 15.060 1.00 0.00
ATOM 146 HN1 LAL 72 38.140 44.870 14.310 1.00 0.00
ATOM 147 HN2 LAL 72 38.200 45.820 15.720 1.00 0.00
ATOM 148 C LAL 72 39.220 38.440 16.870 1.00 0.00
ATOM 149 O LAL 72 38.160 37.920 17.030 1.00 0.00
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?
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!
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.
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.