while evaluating it, you might want to check the importance of buried residues by looking at how conserved they are in homologs. tommi
Quoting Eleanor Dodson <[EMAIL PROTECTED]>: > I dont know the answer but have you looked at the PISA site at the eBI - > > there is extensive documentation addressing these sorts of questions. > http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html > Eleanor > Sebastiano Pasqualato wrote: > > > > Hi all, > > a few days ago I sent a post in which I was asking if anybody knew a > > program to automatically define the hydrophobic core of a protein, > > given the pdb. > > Unfortunately I got no answers, and indeed a more thorough googling > > around revealed that such a program might not exist. > > So it seems I have to define my hydrophobic core residues by hand... > > So now my question would be: how to define the hydrophobic core > residues? > > I would tend to say that those that bury more than ## % (say 70%, 80% > > ??) of their otherwise solvent accessible surface area could be > > defined as such, but how can I get such a /per residue/ percentage? > > (NB: this is not the asa buried upon interaction, so I don't know how > > to get the asa of the "free" amino acid) > > Alternatively, are there other simple and defined rules to state which > > > are the hydrophobic core residues? > > Any help appreciated, > > thanks in advance, > > ciao > > s > > > > > > > > -- > > Sebastiano Pasqualato, PhD > > IFOM-IEO Campus > > Dipartimento di Oncologia Sperimentale > > Istituto Europeo di Oncologia > > via Adamello, 16 > > 20139 Milano > > Italy > > > > tel +39 02 9437 5094 > > fax +39 02 574 303 310 > > > > > ------------------------------------------------------------------------ > > > > > > > > No virus found in this outgoing message. > > Checked by AVG Free Edition. > > Version: 7.5.472 / Virus Database: 269.9.0/853 - Release Date: > 6/18/2007 3:02 PM > > > -- Tommi Kajander, Ph.D. Macromolecular X-ray Crystallography Research Program in Structural Biology and Biophysics Institute of Biotechnology PO box 65 (Street address: Viikinkaari 1, 4th floor) University of Helsinki FIN-00014 Helsinki, Finland Tel. +358-9-191 58903 Fax +358-9-191 59940
