From chemistry-request@ccl.net Sun Oct 27 20:01:30 1991 Date: Sun, 27 Oct 91 17:41:35 EST From: shenkin@avogadro.barnard.columbia.edu (Peter S. Shenkin) To: chemistry@ccl.net Subject: IUPAC definition of chi1 for VAL Status: R I am having a bit of trouble "grokking" the IUPAC definitions of the chi angles (side-chain dihedral angles) for amino acids. I _think_ I have it right, but I'd like someone who thinks he/she knows for sure to confirm my reading of the definitions. The only cases I'm uncertain about is where there are two "identical" (but non-symmetrical) 4th atoms in the torsion, as in chi1 of VAL or chi2 of LEU; in this case the IUPAC dictates which of the atoms is to be labeled the "main" branch. If this naming convention is followed, then, as I understand it, chi1 of VAL would be defined by N-CA-CB-CG1, and chi2 of LEU would be CA-CB-CG-CD1. In Brookhaven files, most VALs and LEUs have their terminal branches numbered consistently as shown below; however, there are a number of exceptions. Anyway, here is my understanding of how the angles and corresponding rotamers should be named for VAL, using Newman projections looking down the CB-CA bond, with CB closer to you. I also have the chirality of the alpha-carbon right, I believe/hope. O / / C This is the t (trans) conformation. | | Chi1, the dihedral angle specified CG1 | \ | by N-CA-CB-CG1, is ~180 deg. \ | \-----) It would seem to make sense that ( \ ) ( \ ) this rotamer is lowest in energy, ( * ) ( | ) since it has the fewest 1-4 heavy- ( | ) (--|--) atom interactions, and in fact, | \ | \ Ponder & Richards state that the | \ CG2 NH trans conformation is observed for VAL in proteins about 67% of the time. O / / C | | GG2 This is the - (gauche -) conf. | / | / Chi1 is ~ -60 deg. | / (-----/ ( / ) ( / ) ( * ) ( | ) ( | ) (--|--) | \ | \ | \ CG1 NH O / / C | CG2 | GG1 This is the + (gauche +) conf. \ | / \ | / Chi1 is ~ +60 deg. \ | / \-----/ ( \ / ) ( \ / ) ( * ) ( ) ( ) (-----) \ \ \ NH So, someone out there please tell me if I am right. Incidentally, in the molecular modeling package Insight, if I pick "Torsion" from the "Transform" menu, and, in two-atom mode, define a torsion about CA-CB, the program uses the atoms C-CA-CB-CG1, not what I believe is the IUPAC definition of chi1, as the dihedral angle. -P. ************************f*u*cn*rd*ths*u*cn*gt*a*gd*jb************************* Peter S. Shenkin, Department of Chemistry, Barnard College, New York, NY 10027 (212)854-1418 shenkin@avogadro.barnard.columbia.edu shenkin@cunixc.BITNET ********** "I've got algorithm -- who could ask for anything more?" **********