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Hi According to the documentation, the solvent accessible surface of a protein is defined (Lee and Richards (1971)) as the locus of the centre of a probe sphere (representing a solvent molecule) as it rolls over the Van der Waals surface of the protein, whereas as you say, the contact area is defined as the area on the Van der Waals surface of an atom that can be contacted by a sphere of the given probe radius. So the contact surface coincides with the VDW surface, except where the latter is re-entrant (i.e. can't be contacted by the probe sphere), whereas the accessible surface lies 1.4 Ang (or whatever the probe radius is set to) above the contact surface. Also according to the documentation, it will attempt to identify isolated areas of surface (which could be cavities either within the molecule, or formed as a result of intermolecular contacts): i.e. areas which cannot be accessed by water from outside the crystal (assuming of course that the structure is completely rigid and can't move aside to let the water in!). So in all there are 4 different areas to consider! -- Ian > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On > Behalf Of [EMAIL PROTECTED] > Sent: 28 September 2005 10:38 > To: [email protected] > Subject: [ccp4bb]: AREAIMOL: "accessible area" vs. "contact area"? > > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > > Hello, > > I recently started using 'areaimol' in the CCP4 program suite, > > CCP4 5.0 > AREAIMOL 5.0 > 30/01/04 > > I am using default settings to look at 'simple area calculation' of a > protein. The results file has two major sections, > > 1) ACCESSIBLE AREAS (for the residue/chain/oligomer) > 2) CONTACT AREAS (for the residue/chain/oligomer) > > What is the difference between these two measures? (Are they > even related > measures, or do they measure different physical properties of the > molecule?) > > From the manual I read... > > "The contact area is defined as the area on the Van der Waals > surface of > an atom that can be contacted by a sphere of the given probe radius." > > but that sounds just like the ASA? > > I am a beginner with these concepts, so I don't see how (if > at all) the > two measures are related, or why two measures are needed. > > Thanks for any help, > > Dan. > > > > > > ********************************************************************** CONFIDENTIALITY NOTICE This email contains confidential information and may be otherwise protected by law. Its content should not be disclosed and it should not be given or copied to anyone other than the person(s) named or referenced above. If you have received this email in error, please contact [EMAIL PROTECTED] **********************************************************************
