Hi Miguel!
if min. two consecutive residues are having the same kind of H-Bond "pitch" , the residues in between are assigned to belong to the helix.display them as helix, but color them in a different color?
What do we do about helixes with pitch 3 and pitch 5?
But, what are the critera for recognizing them?
e.g. 2hhb helix:http://srs.embl-heidelberg.de:8000/srs5bin/cgi-bin/wgetz?-e+[DSSP-ID:'2HHB'] )
35 35 A S H < S+ 0 0 17 -4,-2.5 -2,-0.2 1,-0.3 -3,-0.2 0.795 130.1 29.7 -86.5 -29.7 12.7 -7.9 -7.4
36 36 A F >< + 0 0 38 -4,-2.6 3,-2.4 -5,-0.3 4,-0.3 -0.675 67.5 178.5-130.8 76.8 9.2 -6.8 -8.4
37 37 A P G > S+ 0 0 45 0, 0.0 3,-1.8 0, 0.0 4,-0.3 0.708 72.3 74.4 -59.3 -21.4 8.4 -8.4 -11.7
38 38 A T G > S+ 0 0 38 1,-0.3 3,-1.6 2,-0.2 4,-0.1 0.801 84.7 67.8 -64.0 -23.8 4.9 -6.9 -11.9
39 39 A T G X S+ 0 0 3 -3,-2.4 3,-1.6 -7,-0.3 -1,-0.3 0.739 82.7 73.8 -67.9 -16.4 6.5 -3.6 -12.7
40 40 A K G X S+ 0 0 66 -3,-1.8 3,-1.5 -4,-0.3 -1,-0.3 0.673 75.5 80.4 -71.0 -15.8 7.6 -5.0 -16.1
41 41 A T G < S+ 0 0 10 -3,-1.6 -1,-0.3 -4,-0.3 -2,-0.2 0.672 89.5 54.3 -64.3 -16.7 3.9 -4.7 -17.2
42 42 A Y G < S+ 0 0 21 -3,-1.6 -1,-0.3 1,-0.2 -2,-0.2 0.587 108.7 48.9 -91.8 -8.3 4.5 -1.0 -17.9
43 43 A F X + 0 0 32 -3,-1.5 3,-1.7 -4,-0.2 -1,-0.2 -0.248 59.7 133.3-122.5 46.5 7.6 -1.7 -20.1
44 44 A P T 3 S+ 0 0 66 0, 0.0 -1,-0.1 0, 0.0 -3,-0.1 0.763 75.7 57.3 -69.6 -15.8 6.4 -4.4 -22.6
45 45 A H T 3 S+ 0 0 127 -3,-0.1 2,-0.3 2,-0.1 -2,-0.1 0.401 94.3 87.7 -94.2 4.1 7.9 -2.3 -25.4
46 46 A F S < S- 0 0 46 -3,-1.7 2,-1.0 8, 0.0 -3,-0.1 -0.787 79.5-123.9-104.1 147.8 11.4 -2.3 -23.9
47 47 A
residues 36 is Hbonded to 39 and 37 to 40, and so on. The starts of the H-Bonds are labeled with ">", ends with "<". If a residues is start and end of helix - hbond pattern it is labeled "X". The3- helix residues are labeled with "G"
Here DSSP assignes a 3-Helix from 37 - 42. Note that residue 43 is not part of the helix, although this residues is "start" of a 3-Helix hbond pattern ("3"). Since neither the residue before nor after are start of a 3-helix pattern, it is neglected. DSSP is "cutting off" the terminal residues of the helices. IMHO this can be criticised, after all there are two residues skipped, that are involved into the HBond pattern.... Not sure why this rule has been chosen.
If residues are assigned to several types of helices, alpha helix has priority over the other ones.
Cheers, Andreas
-- --------------------------------------------------
Andreas Prlic Wellcome Trust Sanger Institute
Hinxton, Cambridge CB10 1SA, UK
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