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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 [log in to unmask] > Le 8 déc. 2017 à 08:52, KLAHOLZ bruno <[log in to unmask]> 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:[log in to unmask] <mailto:[log in to unmask]>] On Behalf Of chemocev marker > Sent: 08 December 2017 07:55 > To: [log in to unmask] <mailto:[log in to unmask]> > 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