Is there any standard value like two non-bonded residues or atoms are considered to form a contact if their distance is less than ?
I usually use like 1.4 nm for short range non-bonded LJ cut-off and short-range electrostatic cutoff in gromacs for MD simulation, but since water molecules/lipids can come in between atom pairs, is there any definitive non-bonded distance for forming a contact?
Interpret the structures energetically: calculate residue-residue non-bonded interaction energies.
Setting a contact/no-contact threshold distance is arbitrary enough and subject to multiple conditions (e.g., are residues of interest charged) even for a direct contact. Then, if one wants to account for water-mediated contacts it gets just intractable. The easiest would be to consider as a "true contact" only those contacts with a significant LJ force involved, that is, about 0.4 nm.
A rationalized criteria for interactions can be derived using the Non-Covalent Interactions index (NCI), freely available here: http://www.lct.jussieu.fr/pagesperso/contrera/nciplot.html
It has a promolecular library, and therefore can work only with simple pdb geometries. For more information, refer to the work of C. Gatti et al.
It may take a little time, specially if you are not into quantum chemistry, but I'd say it is a much more sound criteria that arbitrary distances...
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