If you look in the monomer library $CLIBD/monomers/ener_lib.cif
There is a first approximation to expected VDW radi for all the atom types.
This gives a rough guide to expected VDW contact distances - which of
course needs to be modified by local chemistry etc..
Eleanor
Jiamu Du wrote:
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]
<mailto:[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)
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