Re: [ccp4bb] questions about hydrophobic core

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: questions about hydrophobic core
From: Liz Potterton lizp {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-06-19

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Subject: Re: questions about hydrophobic core
From: "Nadir T {- dot -} Mrabet" Nadir {- dot -} Mrabet {- at -} MEDECINE {- dot -} UHP-NANCY {- dot -} FR
Date: 2007-06-19

Subject: Re: questions about hydrophobic core
From: Tommi Kajander tommi {- dot -} kajander {- at -} HELSINKI {- dot -} FI
Date: 2007-06-19

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 :

> 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
> >
> >
> ------------------------------------------------------------------------
> >
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>

--
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

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: questions about hydrophobic core
From: Liz Potterton lizp {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-06-19

Next message:
Subject: Re: questions about hydrophobic core
From: "Nadir T {- dot -} Mrabet" Nadir {- dot -} Mrabet {- at -} MEDECINE {- dot -} UHP-NANCY {- dot -} FR
Date: 2007-06-19