Re: [ccp4bb] domain contact surface

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

Previous message:
Subject: Re: domain contact surface
From: Jane Bailey jbailey {- dot -} xtal {- at -} GOOGLEMAIL {- dot -} COM
Date: 2010-02-19

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From: Gerard Bricogne gb10 {- at -} GLOBALPHASING {- dot -} COM
Date: 2010-02-19

Subject: Re: domain contact surface
From: Pierre Rizkallah rizkallahp {- at -} CARDIFF {- dot -} AC {- dot -} UK
Date: 2010-02-19

Hello Again,

The buried surface area is twice the interface area, because the interface is
counted twice when working out the solvent accessible area which disappeared
upon interfacing, once on molecule 1 and once on molecule 2. This is a matter
of definition. While I prefer to quote the interface area, quite a number of
people prefer the buried surface area. Either one should be alright, as long as
you say clearly which one you are reporting.

Pierre

********************************************************
Dr. Pierre Rizkallah, Senior Lecturer in Structural Biology,
WHRI, School of Medicine, Cardiff University, Heath Park, CF14 4XN
email: rizkallahp@cf.ac.uk phone + 44 29 2074 2248
>>> Jane Bailey 19/02/10 4:57 PM >>>
Ed Pozharski wrote:
> http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html
>
> Try PISA server - it will identify contacts and report total buried
> surface area per contact.
>
> On Fri, 2010-02-19 at 16:42 +0100, Jane Bailey wrote:
>
>> Dear all,
>>
>> I am trying to calculate the domain-domain contact surface from one
>> chain. I see AREAIMOL to only tell you the accessible surface
>> area/residue. Could any other software/webserve could specify residues
>> in the contact surface and calculate the total contact area?
>>
>> Thanks
>>
>> J.
>>
>
>
>
Dear all,

Thanks very much for the answers. I managed to get the interface from
PISA by assign two chain IDs onto two domains, as suggested by Pierre
and Amy. It gave the interface Solvent-accessible area of each domain:
274.2, 312.2, but not the BSA. However I saw it gave the BSA of
individual residue from the interface. Do people get the total interface
BSA by adding them up?

best
Jane

CCP4bb navigation

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

Previous message:
Subject: Re: domain contact surface
From: Jane Bailey jbailey {- dot -} xtal {- at -} GOOGLEMAIL {- dot -} COM
Date: 2010-02-19

Next message:
Subject: Re: anomalous difference fourier maps
From: Gerard Bricogne gb10 {- at -} GLOBALPHASING {- dot -} COM
Date: 2010-02-19