jiri, VDW forces are always acting and between any pair of atoms the optimal distance (most favourable interaction energy) depends on the pair of atoms involved in the interaction, but is a big bitter than the sum of atomic radii all the best herman Herman van Tilbeurgh Professor structural biology Directeur Adjoint Ecole Doctorale Innovation Thérapeutique: du fondamental à l'appliqué
Institut de Biologie Intégrative de la Cellule - I2BC UMR 9198 CNRS- Université Paris Sud Team: Fonction et Architecture des Assemblages MacroMoléculaires http://www.i2bc.paris-saclay.fr/spip.php?article256 Batiment 430 91405 Orsay France Tel: 33 1 69 15 31 55 fax: 33 1 69 85 37 15 [email protected] > Le 8 déc. 2017 à 08:52, KLAHOLZ bruno <[email protected]> a écrit : > > > Hello, > > van der Waals interactions are very weak, this is why we usually speak about > van der Waals contacts rather than interactions. > These are usually in the range of 3.5-3.8/4 Å (smaller than that may indicate > a close contact or steric clash of an atomic model under refinement), > corresponding to the packing of the van der Waals spheres of the individual > atoms. > In hydrogen bond interactions, the term “interaction” normally implies > sharing a hydrogen atom between two polar residues, for example between the > hydroxyl group of a threonine side chain with a carbonyl group of the main > chain peptide backbone; in there one should take into account the geometry as > well (e.g. ~120°-180° is favorable, 90° is not). Note that some positions > such as Calpha-H can be slightly polarized (these contribute to bifurcated > H-bonds in beta sheets for example, see e.g. > https://www.ncbi.nlm.nih.gov/pubmed/12220491 > <https://www.ncbi.nlm.nih.gov/pubmed/12220491> ). > In the context of series of van der Waals contacts between hydrophobic > residues there can be additive effects of the weak interactions with then sum > up, but in this context one should also consider entropic effects such as > de-solvatation which becomes favorable energetically. > > Hope this helps. > > Best regards, > > Bruno > > > ########################################################################### > Bruno P. Klaholz > Centre for Integrative Biology > Institute of Genetics and of Molecular and Cellular Biology > 67404 ILLKIRCH > FRANCE > http://igbmc.fr/Klaholz <http://igbmc.fr/Klaholz> > > > > > From: CCP4 bulletin board [mailto:[email protected] > <mailto:[email protected]>] On Behalf Of chemocev marker > Sent: 08 December 2017 07:55 > To: [email protected] <mailto:[email protected]> > Subject: [ccp4bb] Van der waals force > > Hi > I just have a basic question if the Van der waals interaction will exist > between the hydrophobic residues or it can also be contributed by the polar > residues as well. What distance is required for the Van der waals > interaction. > > best > > Jiri
