I am looking at residue-residue contacts in proteins and need to set up
criteria for when two side chains from different secondary structure
potentially can be in direct contact.
I want to base the criteria on two things:
* Cbeta-Cbeta distance between the two residues.
* Angle between Calpha-Cbeta bond vectors for the two residues.
Given a Cbeta-Cbeta distance between to residues and the angle
between Calpha-Cbeta bond vectors for the two residues I want to be able
to say if the two amino acid side chains are likely to be in direct
contact of not.
Being a quite basic thing I am sure that some studies have been done on
this previously. However, I have not been able to find anything in the
literature.
If anybody is aware of any such criteria being set up or examined before,
I would be very grateful if you could point me in the right direction.
With thanks.
Per
______________________________________________________________________
Per Kallblad, Drug Design Group Email: pk215 at cam.ac.uk
Department of Pharmacology Phone: +44 1223 331982
University of Cambridge Fax +44 1223 331740
Tennis Court Road CAMBRIDGE CB2 1QJ UK
______________________________________________________________________
