[ccp4bb]: summary of interaction surface calculation

[jinghua@mailer.sb.fsu.edu (Jinghua Tang)]

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  To keep the spirit of the CCP4 BB, here is a summary
of my question on how to calculate the interaction surface
area and replies. Thank all the people who reply to me!

========================================================================
Dr. Norbert Straeter

Use CCP4 program areaimol to calculate the accessible surface area for
each of the individual proteins and than calculate the surface of the
complex. The buried surface area is S(1) + S(2) - S(1-2) and the
interaction surface area is half of this value. 

========================================================================
Dr. Andrea Schmidt

 create the surface for each monomer in GRASP (it gives you the area for
the monomer in the little textbox) and then create the surface over the 
dimer (which gives you the area for the dimer)

  The difference is the area (A) covered:  A(interact per molecule) = 
(A(monomer)+A(monomer)-A(dimer))/2 gives you the area of interaction per 
monomer (or molecule).

========================================================================
Dr. Marko Hyvonen 

The way you do your calculation is correct. You do not specify if you
calculated the accessible surface area or the molecular surface area,
which are two different things. Although the results for most cases are 
very similar. To divide by two or not, is your choice. Just  make clear
which way you do it. See Jones and Thornton (1996) PNAS 93:13--20, 
Lo Conte et al. (1999) J. Mol. Biol 285:2177--2198 and Stanfield and
Wilson (1995) Curr. Opinion Struct. Biol 5:103--113, for a few different
ways of analysing protein-protein interfaces. Jones and Thornton use the
half-values, Lo Conte et al. the total area and Stanfield and
Wilson calculate molecular surfaces instead of solvent accessible
surfaces. 

You can also calculate the interface area directly in GRASP by following
menus Calculate - Area of a Surface/Molecule - Molecule - Excluded area.
The program will then list the area of the subunits in complex and free
and the difference of the two. You can then use this information to
project the data to the surface of a molecule. See manual for more info. 
  

========================================================================
Drs. Mary Canady, Mike Sierk, David Buckler and Marko Hyvonen suggest the 
protein-protein interaction server at UCL:

  http://www.biochem.ucl.ac.uk/bsm/PP/server/

========================================================================
Dr. David Buckler

  You can use the CCP4 module AREAIMOL in DIFFMODE COMPARE.  Create
two individual XYZIN (pdb) files, one with all components and a second
with one or more of the components removed.  Output files will be
generated showing regions with altered surface accessibility for the
common coordinates.  An aside -- this program was useful to us because
it can also give quantitative information about crystal packing
interactions.  See the documentation for all details:
http://www.dl.ac.uk/CCP/CCP4/html/areaimol.html
http://www.dl.ac.uk/CCP/CCP4/newsletter38/03_surfarea.html