Re: [ccp4bb] questions about hydrophobic core

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

Previous message:
Subject: questions about hydrophobic core
From: Sebastiano Pasqualato sebastiano {- dot -} pasqualato {- at -} IFOM-IEO-CAMPUS {- dot -} IT
Date: 2007-06-19

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

Subject: Re: questions about hydrophobic core
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-06-19

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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CCP4bb navigation

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

Previous message:
Subject: questions about hydrophobic core
From: Sebastiano Pasqualato sebastiano {- dot -} pasqualato {- at -} IFOM-IEO-CAMPUS {- dot -} IT
Date: 2007-06-19

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