Re: [ccp4bb] questions about hydrophobic core

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

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

Hi,

There exists a formal analytical way in doing this using the "survol"
command in BRUGEL package.
In short, this command define the accessible surface (external and
cavities) to the probe you choose and creates
separate masks (ensembles) of all atoms/residues that define these surfaces.
The way to go, then, would be to create a collection mask of all
accessible atoms/residues and subtract this
from your protein mask to be left with the mask that contains the core
residues.
You could also use a cutoff of 5-10% ASA max (there are different ways
of calculating these !).
On the other hand, taking away even residues that display very little
ASA (< 5%) would certainly leave you with
genuine core residues.
Hope this helps.

Greetings,

Pr. Nadir T. Mrabet
Cellular & Molecular Biochemistry
INSERM U-724
UHP - Nancy 1, School of Medicine
Avenue de la Foret de Haye, BP 184
54505 Vandoeuvre-les-Nancy Cedex
France
Phone: +33 (0)3.83.68.32.73
Fax: +33 (0)3.83.68.32.79
E-mail: Nadir.Mrabet@medecine.uhp-nancy.fr
Cell.: +33 (0)6.11.35.69.09

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

Next message:
Subject: Survey on computer usage in crystallography
From: P Hubbard dienoylcoa {- at -} HOTMAIL {- dot -} COM
Date: 2007-06-19