How to determine if an amino acid is part of a-helix or B-sheet in pdb file

Question

[Mahmoud Ahmed]

Now I worked on "protein structure prediction" project and need to extract data from .pdb file , in this step I have to extract amino acid residue and determine if it was alpha-helix or beta-sheet ?

I had copy all content of the secondary structure section in pdb file but cant recognize my specified amino acid in it.

Answer 1

[Ibrahim Tanyalcin]

Dear Mahmoud,

You can download Swiss-Pdb Viewer (DeepView) at http://spdbv.vital-it.ch/ . You can open your pdb using it, and then go to Window(top right) and then select control panel. There on the leftmost side you will see S or H denoting strand or helix. You can also open the alignment window and see the same information in rectangular layout. I am pretty sure, you can do this by other commercially available pdb viewer packages as well.

Good luck,

Answer 2

[DG]

Typically the PDB file lists the first and last residues of a particular secondary structure element. So you would extract those from the various secondary structure lines and determine which, if any, your residue lies in based on those ranges. However, a given particular residue may lie in a loop region, and thus not be in any of the helix or sheet secondary structure designations.

PDB file format descriptions