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 <[email protected]> wrote: > From: protein.chemist protein.chemist <[email protected]> > Subject: [ccp4bb] Protein Protein interactions > To: [email protected] > 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 > >
