How can I calculate hydrogen bonds in a specific direction w.r.t. a C-alpha atom in a protein?

Question

[user366312]

I need to calculate H-bonds in a specific direction of a C-alpha atom of a protein. And, I need to calculate that from a PDB file.

Can anyone give me an idea regarding how to do that?

N.B. I need to write a python program.

Answer 1

[Mensur Dlakic]

If I understand correctly what you need - and it wouldn't hurt if you elaborated a bit - this is somewhat similar to half-sphere exposure (HSE), which calculates protein residue's solvent accessibility on the opposite sides of a C-alpha atom. There is a paper about it:

https://pubmed.ncbi.nlm.nih.gov/15688434/

And there is a BioPython code to calculate it:

https://biopython.org/docs/dev/api/Bio.PDB.HSExposure.html

This may give you some idea how to approach the problem, but it requires a thorough understanding of protein structure

[user366312]

the keyword in my question was "hydrogen bond". your supplied links do not say anything about hydrogen bonds.

[Mensur Dlakic]

I can read you keywords. I can also read this part:

Can anyone give me a general direction/idea regarding how to do that?

I said clearly that the links are about solvent accessibility, which is to say that I tried to give you a general idea. You can try that, or stock up with popcorn and soda and wait for someone to give you a complete solution.

[user366312]

I am sorry but your answer is not helpful. You are trying to explain a cat using a dog.