CCP4 has a program called "contact" where you can specify the chains, distances and atoms you want to explore for contacts and it will give a list of all contacts that fit that criteria, along with the distance. It works best if you already have an idea for which chain interfaces you want to explore. A much slower way is to use coot to bring up the model and look at the residue environments. Again, much better if you already know which residues to use.
A better predictor for unknown interfaces would be PISA, accessible either directly through EMBL-EBI or indirectly through ExPASy.
Regina
--- On Mon, 8/17/09, protein.chemist protein.chemist <[log in to unmask]> wrote:
> From: protein.chemist protein.chemist <[log in to unmask]>
> Subject: [ccp4bb] Protein Protein interactions
> To: [log in to unmask]
> Date: Monday, August 17, 2009, 1:13 PM
> Hello All,
>
> Can anyone tell me what are the programs used to find out
> the different interactions in a protein.
> I am talking about both intra and intermolecular
> interactions.
>
> Thanks in advance.
>
> Mariah
>
>
>
>
> --
> Mariah Jones
> Department of Biochemistry
> University of Florida
>
>
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