[ccp4bb] Buried Surface Area - summary

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

Previous message:
Subject: Electron Microscopist Position
From: Tuli Mukhopadhyay sumukhop {- at -} INDIANA {- dot -} EDU
Date: 2007-04-30

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Subject: Re: extra high B factor
From: Jiamu Du jiamudu {- at -} GMAIL {- dot -} COM
Date: 2007-05-01

Subject: Buried Surface Area - summary
From: Gloria Borgstahl gborgstahl {- at -} UNMC {- dot -} EDU
Date: 2007-04-30

Here was the query.
What is the easiest way, these days, to calculate the buried surface area
between two subunits of a protein?

Here are the software and links received (thank you all):

1. 4+ votes for PISA - This following website is great and does a very nice job
of analyzing protein interfaces (including, but not
limited to, buried surface area calculations):
http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html
FYI. the next website can also yield useful info
to figure out if an interface is physiologically
relevant or not (less detailed output though):
http://www.ebi.ac.uk/thornton-srv/databases/pita/

2. surface ( http://www.ccp4.ac.uk/dist/html/surface.html ).

3. Two or three votes for areaimol in CCP4 works well - but beware that for cases we have worked on the default value for point density needs to be increased to get accurate values.

With the subunits A and B and their surfaces surf(A) and surf(B) the equation should hold:

surf(A) + surf(B) = surf(A+B) +2x

where x is the surface between them. So if you calculate the surfaces of each subunit separately and of the complex that yields x.

4. NACCESS http://wolf.bms.umist.ac.uk/naccess/

5. CCP4mg will do this - and show you graphically..
http://www.ysbl.york.ac.uk/~ccp4mg/ccp4mg_help/analysis.html#sas

6. see the discussion and references in:
http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=84

7. Chimera.
http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-December/001131.html

Thanks again.

******************************************************************************
Gloria Borgstahl
Eppley Institute for Cancer Research and Allied Diseases
987696 Nebraska Medical Center
10732A Lied Transplant Center
Omaha, NE 68198-7696

http://sbl.unmc.edu
Office (402) 559-8578
FAX (402) 559-3739

Associate Professor
Interests:  Cancer, Biochemistry, DNA Metabolism,  Protein Crystallography,
Modulated Crystals,  Crystal Perfection, X-ray Topography,
Varley, Rowling, Avatar, BRAN, RAGBRAI, swimming & soccer
******************************************************************************

CCP4bb navigation

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

Previous message:
Subject: Electron Microscopist Position
From: Tuli Mukhopadhyay sumukhop {- at -} INDIANA {- dot -} EDU
Date: 2007-04-30

Next message:
Subject: Re: extra high B factor
From: Jiamu Du jiamudu {- at -} GMAIL {- dot -} COM
Date: 2007-05-01