*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk ***
VdW interactions are based on weak London Dispersion forces (i.e., electronic dipole polarization exchange) and follow the typical LJ potential curve. In short, they have a distinct maximum at the sum of the VdW radii and rapidly decay at larger distances (and cause strong repulsion at distances any closer than the sum of VdW radii). However, even at the maximum interaction, a single VdW interaction does not contribute much to the binding energy, about -0.5 to -0.7 kcal/mol, which is about RT (0.62) at physiological temperature. It is the *sum of many of those* that can make a significant contribution to binding/interaction energies. Thus, a definition of one general 'cutoff' for VdW interactions is not really meaningful on an energetic scale. > I found some important contact in my strcuture, but the > distance is about 3.5-4 angstrom. Depends on what specific A-B contact and how far off the ideal VdW distance. See kcal warning above as far as 'important' goes. br ________________________________ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jiamu Du Sent: Monday, January 15, 2007 8:44 PM To: Anastassis Perrakis Cc: [email protected] Subject: Re: [ccp4bb]: what distance is the van der Waals contact limited? Dear Perrakis: What I want to know is that in common protein strucuture articles, what is the van der Waals contact limit distance. I found some important contact in my strcuture, but the distance is about 3.5-4 angstrom. I am not so sure that if this is still within the distance limit of van der Waals contact. I have found some article mentioned van der Waals contact in their structure, but with none mention the distance limit they used. So I need a accurite number to define van der Waals contact. Thank you very much. On 1/16/07, Anastassis Perrakis <[EMAIL PROTECTED]> wrote: http://en.wikipedia.org/wiki/Van_der_Waals_force <http://en.wikipedia.org/wiki/Van_der_Waals_force> ... or any basic protein structure Book ! (they can be still useful!) A. On Jan 15, 2007, at 16:21, Jiamu Du wrote: > Dear All: > Another question is that after I find the contact information, how > to define a dsitance limit commonly? > Which limit can be accepted? > Thanks. > > Jiamu Du > Key Laboratory of Proteomics > Institute of Biochemistry and Cell Biology Shanghai Institutes for > Biological Sciences > Chinese Academy of Sciences (CAS) -- Jiamu Du Key Laboratory of Proteomics Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS)
