Sorry, a bit late here (2:00 AM) after a long day. I meant (for CH2/CH2 contacts!): Dij < 1.8 + 1.8 + 2x1.4 = 6.4 Ang.
Best, Nadir Mrabet Pr. Nadir T. Mrabet Structural & Molecular Biochemistry N-gere - INSERM U-954 University of Lorraine, Nancy School of Sciences and Technologies & School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: Nadir.Mrabet <at> univ-lorraine.fr LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail, or any action taken (or not taken) in reliance on it, is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately. ----- Mail original ----- > Hi Kavya, > My guess is that you are referring to the van der Waals (vdw) > contribution of the hydrophobic effect (the other being of entropic > nature). > If this is the case, then the most reasonable consensus is that Dij < > Ri + Rj + 2 R(H2O), where Dij is the distance between atoms i and j, > Ri is the vdw radius of atom i, Rj, the vdw radius of atom j and > R(H2O) the vdw radius of the water molecule. > Doing so, you state that as far as two atoms are close enough to > avoid being solvated (either one!), then they are close enough to > engage in vdw interaction and if the atoms being considered are both > nonpolar, that would correspond to what you call hydrophobic > "interaction". > Therefore, the distances that you state are likely meaningless, > depending on the sizes of the atoms concerned. > I suppose you are using unified atoms; in which case, e.g., CH2 is > about 1.8 Ang. If you take R(H2O) = 1.4 Ang, then 1.8 + 1.8 + 2x1.4 > = 5.0 Ang. > 8 Ang is far too much for CH2/CH2! > HTH, > Nadir Mrabet > Pr. Nadir T. Mrabet > Structural & Molecular Biochemistry > N-gere - INSERM U-954 > University of Lorraine, Nancy > School of Sciences and Technologies > & School of Medicine > 9, Avenue de la Foret de Haye, BP 184 > 54505 Vandoeuvre-les-Nancy Cedex > France > Phone: +33 (0)3.83.68.32.73 > Fax: +33 (0)3.83.68.32.79 > E-mail: Nadir.Mrabet <at> univ-lorraine.fr > LEGAL NOTICE > Unless expressly stated otherwise, this message is confidential and > may be privileged. It is intended for the addressee(s) only. > Access to this E-mail by anyone else is unauthorized. > If you are not an addressee, any disclosure or copying of the > contents of this E-mail, or any action taken (or not taken) in > reliance on it, > is unauthorized and may be unlawful. > If you are not an addressee, please inform the sender immediately. > ----- Mail original ----- > > Dear users, > > > Sorry for an off-topic question. > > > What is the limits for hydrophobic > > > interactions in protein? > > > Some prefer 5Ang some prefer upto 8Ang. > > > Any reference or suggestions are welcome. > > > Thanking you > > > Regards > > > Kavya > > > -- > > > This message has been scanned for viruses and > > > dangerous content by MailScanner, and is > > > believed to be clean. >
