Analyzing 3D protein structure. Finding out which amino acids are close to each other?

Question

[donkichote]

Hi,

I' working on the protein (cytochrome oxidase), that is a complex of 3 to 13 chains. There is a very good model 3D model. The first subunit is quite big and has few transmembrane domains. I would like to choose one amino acid and check which other amino acids are close to my chosen one (there is an interaction between them). Which software could show that?

Thanks,

Answer 1

[João Rodrigues]

Pymol can do it, as can Chimera or VMD or other visualization program. You can also script it if visualization is not necessary. In Pymol, you load your structure and use the "around" or "within" selectors.

For example, to select residues within 5Å of histidine 34 you would write the following:

select my_selection, byres( resi 34 around 5 )

[donkichote]

Hi,

Thanks for your help. It's all working.

[João Rodrigues]

If the answer was helpful, instead of replying to the question with another answer, mark the question as solved so that others can find it more easily.

Cheers