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

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.

protein-prediction homology-modeling pdb
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updated by Ram Ram • written by Mahmoud Ahmed • Mahmoud Ahmed

2 answers

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,

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written by Ibrahim Tanyalcin Ibrahim Tanyalcin

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

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written by DG DG

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