How can I get B factor value of a specific amino acid of a protein sequence, from DSSP?

Question

[Qingyang Xiao]

How can I get B factor value of a specific amino acid of a protein sequence, from DSSP?

https://swift.cmbi.umcn.nl/gv/dssp/

It seems no functions/buttons that could generate the B-factor value from the website.

If it doesn't work, are there some other tools for collecting B factor values given a protein sequence?

Thanks!

Answer 1

[Mensur Dlakic]

You need a PDB structure file to extract B factors, as protein sequences do not contain that information.

Individual amino-acids don't have B factors, but you can calculate them as an average of B factors of all atoms that belong to that residue. B factors are stored in columns 61-66 of PDB files. If you don't want to count, that would be the last numerical column in the printout below (values 15.74, 15.48, etc). Averaging their sum would give you a B factor for this MET residue.

ATOM      1  N   MET A   1      21.182  23.095  19.731  1.00 15.74           N
ATOM      2  CA  MET A   1      21.175  22.975  18.256  1.00 15.48           C
ATOM      3  C   MET A   1      22.352  22.067  17.886  1.00 14.01           C
ATOM      4  O   MET A   1      23.494  22.373  18.208  1.00 15.09           O
ATOM      5  CB  MET A   1      21.350  24.356  17.631  1.00 17.44           C
ATOM      6  CG  MET A   1      20.916  24.451  16.185  1.00 22.09           C
ATOM      7  SD  MET A   1      21.223  26.088  15.485  1.00 26.05           S
ATOM      8  CE  MET A   1      19.716  26.929  15.949  1.00 27.39           C

[Qingyang Xiao]

This is what I want! Thanks!

Answer 2

[GenoMax]

Did you see this: https://swift.cmbi.umcn.nl/servers/html/listavb.html