Hi Thanks for your good help and I am wondering is there clear way to show these forces like H-bond. I tried KING and can see the VDW radii but not the visual representation. Does coot has any option for this. best Jiri
On Fri, Dec 8, 2017 at 8:57 AM, HERMAN VAN TILBEURGH < herman.van-tilbeu...@u-psud.fr> wrote: > 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 > herman.van-tilbeu...@u-psud.fr > > > > > > > Le 8 déc. 2017 à 08:52, KLAHOLZ bruno <klah...@igbmc.fr> 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 ). > 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 > > > > > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK > <CCP4BB@JISCMAIL.AC.UK>] *On Behalf Of *chemocev marker > *Sent:* 08 December 2017 07:55 > *To:* CCP4BB@JISCMAIL.AC.UK > *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 > > >
