DSSP: P secondary structure

Question

[Nelson]

Some of the DSSP prediction files that can be downloaded from their website contain a "P" code in the secondary structure column. What does it mean? "P" is not one of the secondary structure codes included in the website or in the article.

[Mensur Dlakic]

You are right, acceptable codes are H,G,E,B,I,T,S,C. Sometimes there is a ! which means chain break.

Can you give an example of such a DSSP file? Looking at it and its PDB structure may provide a clue.

[Nelson]

This is one of the files, 1maa.dssp:

==== Secondary Structure Definition by the program DSSP, NKI version 3.0                           ==== DATE=2021-09-20        .
REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637                                                              .
HEADER    HYDROLASE                               04-NOV-98   1MAA                                                             .
COMPND    MOL_ID: 1; MOLECULE: ACETYLCHOLINESTERASE; CHAIN: A, B, C, D; FRAGMENT: CATALYTIC DOMAIN; SYNONYM: MACHE; EC: 3.1... .
SOURCE    MOL_ID: 1; ORGANISM_COMMON: HOUSE MOUSE; GENE: MOUSE ACHE; STRAIN: BLACK6CBA CROSS F1; ORGANISM_SCIENTIFIC: MUS M... .
AUTHOR    Y.Bourne; P.Taylor; P.E.Bougis; P.Marchot                                                                            .
 2157  6 12 10  2 TOTAL NUMBER OF RESIDUES, NUMBER OF CHAINS, NUMBER OF SS-BRIDGES(TOTAL,INTRACHAIN,INTERCHAIN)                .
 73078.7   ACCESSIBLE SURFACE OF PROTEIN (ANGSTROM**2)                                                                         .
 1427 66.2   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(J)  , SAME NUMBER PER 100 RESIDUES                              .
  188  8.7   TOTAL NUMBER OF HYDROGEN BONDS IN     PARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES                              .
  129  6.0   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                              .
   12  0.6   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-3), SAME NUMBER PER 100 RESIDUES                              .
    7  0.3   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                              .
  146  6.8   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+2), SAME NUMBER PER 100 RESIDUES                              .
  275 12.7   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+3), SAME NUMBER PER 100 RESIDUES                              .
  571 26.5   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+4), SAME NUMBER PER 100 RESIDUES                              .
   38  1.8   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 13 12  3  8  3  1  4  9  4  5  4  0  2  2  0  2  2  0  0  0  0  0  0  0  0  0  0    RESIDUES PER ALPHA HELIX         .
 10  4  8  8  6  0  6  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      .
  6  5  5  8  4  0  2  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  .
  4  4  2  0  0  0  0  0  0  2  0  2  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
    1    4 A E              0   0  204      0, 0.0     3,-0.0     0, 0.0     5,-0.0   0.000 360.0 360.0 360.0 -70.6   93.4  147.7   47.2

Then in position 50:

   49   52 A P  E>    -N   35   0D  87      0, 0.0   -14,-0.3     0, 0.0   -15,-0.1  -0.304  48.6-103.5 -59.1 129.2   68.1  135.5   52.1
   50   53 A K  PP    -     0   0   67    -16,-1.4     3,-0.1     1,-0.1   -14,-0.0  -0.254  39.5-116.5 -50.9 134.4   71.1  136.9   53.9
   51   54 A R  PP    -     0   0  162      1,-0.1    -1,-0.1    -3,-0.1   -40,-0.1  -0.553  39.5 -90.7 -76.0 148.5   70.4  140.5   54.9
   52   55 A P  P<    -     0   0  103      0, 0.0     2,-0.3     0, 0.0   -40,-0.2  -0.227  45.4-140.9 -58.9 143.9   72.6  143.2   53.3
   53   56 A W        -     0   0   44    -42,-1.7   -40,-0.3     2,-0.1     2,-0.3  -0.802   4.1-125.1-114.6 154.9   75.8  144.2   55.1

and position 588:

  585   46 B R  T <  S+     0   0   12     -3,-1.2    -4,-0.1     1,-0.2   111,-0.1  -0.399  81.6   4.0 -66.6 134.1   42.8   46.6   29.5
  586   47 B F  T 3  S+     0   0    2    109,-0.6   122,-0.5     1,-0.3    -1,-0.2   0.201 108.7 117.6  77.5 -16.5   44.3   49.0   31.9
  587   48 B M  S><  S-     0   0   31     -3,-1.0    -1,-0.3     1,-0.1   118,-0.1  -0.404  75.4 -92.6 -79.1 157.5   45.3   46.1   34.1
  588   49 B P  PP    -     0   0   43      0, 0.0     2,-0.2     0, 0.0    -1,-0.1  -0.173  52.0 -90.4 -66.6 160.9   48.9   45.1   34.9
  589   50 B P  P<    -     0   0   22      0, 0.0     3,-0.0     0, 0.0   -12,-0.0  -0.550  33.1-152.7 -77.4 136.6   50.6   42.5   32.7
  590   51 B E        -     0   0   71    -12,-0.5   -12,-2.7    -2,-0.2     3,-0.1  -0.907  37.0 -91.8-105.2 137.2   50.3   38.9   33.5
  591   52 B P  B>    -H  577   0J  85      0, 0.0   -14,-0.3     0, 0.0     2,-0.3  -0.060  46.8 -90.6 -48.8 146.7   53.2   36.7   32.3
  592   53 B K  PP    -     0   0   66    -16,-1.1     3,-0.1   -15,-0.1   -14,-0.0  -0.467  43.6-126.0 -64.3 120.6   53.1   35.0   28.9
  593   54 B R  PP    -     0   0  150     -2,-0.3    -1,-0.1    -3,-0.1   -40,-0.1  -0.505  36.8 -92.4 -68.6 137.6   51.6   31.5   29.4
  594   55 B P  P<    -     0   0  100      0, 0.0     2,-0.3     0, 0.0   -40,-0.2  -0.060  43.0-155.4 -52.8 147.9   53.8   28.7   28.0
  595   56 B W        -     0   0   45    -42,-2.4     2,-0.3     2,-0.1   -40,-0.2  -0.857   7.9-128.7-124.4 162.3   53.3   27.6   24.4
  596   57 B S        +     0   0  117     -2,-0.3     2,-0.1   -42,-0.1   -42,-0.0  -0.740  68.5  21.6-108.8 157.4   54.0   24.4   22.6

Several other positions also are assigned the code P, you can check the complete file here. Thanks!

Answer 1

[Mensur Dlakic]

This is what I get around position 50 after running a local copy of dssp on 1maa:

   47   50 A P        -     0   0   18      0, 0.0   -12,-0.0     0, 0.0   122,-0.0  -0.224  32.9-141.5 -69.2 156.9   66.5  129.3   54.6
   48   51 A E  E     -N   36   0D  92    -12,-0.6   -12,-2.6    -3,-0.1     3,-0.1  -0.951  28.8 -94.2-118.8 145.3   66.1  133.1   54.4
   49   52 A P  E     -N   35   0D  87      0, 0.0   -14,-0.3     0, 0.0   -15,-0.1  -0.304  48.6-103.5 -59.1 129.2   68.1  135.5   52.1
   50   53 A K        -     0   0   67    -16,-1.4     3,-0.1     1,-0.1   -14,-0.0  -0.254  39.5-116.5 -50.9 134.4   71.1  136.9   53.9
   51   54 A R        -     0   0  162      1,-0.1    -1,-0.1    -3,-0.1   -40,-0.1  -0.553  39.5 -90.7 -76.0 148.5   70.4  140.5   54.9
   52   55 A P        -     0   0  103      0, 0.0     2,-0.3     0, 0.0   -40,-0.2  -0.227  45.4-140.9 -58.9 143.9   72.6  143.2   53.3
   53   56 A W        -     0   0   44    -42,-1.7   -40,-0.3     2,-0.1     2,-0.3  -0.802   4.1-125.1-114.6 154.9   75.8  144.2   55.1
   54   57 A S  S    S+     0   0  118     -2,-0.3   -42,-0.0   -42,-0.1   -43,-0.0  -0.627  72.1   0.6 -89.9 148.7   77.7  147.4   55.8
   55   58 A G  S    S-     0   0   53     -2,-0.3   -42,-0.9     1,-0.1     2,-0.8  -0.171 108.9 -32.9  72.9-165.4   81.4  147.8   54.9
   56   59 A V  E     -b   13   0A  56    -44,-0.1     2,-0.4   -48,-0.0   -42,-0.2  -0.834  57.2-145.1 -99.3 108.3   83.7  145.2   53.2

In places where you have a P there are spaces in my .dssp file, which is equivalent to C or a coil. The same is true for all other positions where you have a P, so from this limited example it would appear that P and C are equivalent.

It is a separate issue why there is a different program version that outputs that P to begin with, since it isn't part of the DSSP code.

[Nelson]

Thanks Mensur. You are right, the outputs we're taking about come from different versions of the program, the newest version now predicts poly-proline helices, and they are encoded as 'P'. This is explained in the Github version of the manual.

Answer 2

[Robbie]

Nelson is completely right. Please note that the legacy DSSP format will be phased out because it doesn't scale to the large structure models that are now available. Consider using the mmCIF output instead as this is more future-proof.