You are right, NH1 and NH2 are distinct in a way that CD1 and CD2 in Phenylalanine are not, since the torsion angle that exchanges them is not freely rotatable (except perhaps in a highly acidic solution).
The practical difference is that the convention for defining labels in Phe and the others cuts the most populated region in half. Even for models that obey the convention you can have two extremely similar conformations that appear very different because the atom labels are swapped. This means that your comparison software has to have some way to sometimes match CD1 with CD1 in the other side chain and other times match CD1 with CD2. You pick the match that gives the lowest rms difference. This problem should never occur in Arginine because the definition of the labels cuts through an unpopulated region of the torsion angle distribution. NH1 should always be matched to NH1. However, I continually run into models where the labeling convention for NH1/NH2 is violated. You can either add an initial pass through the models fixing the labeling when comparing models, or use the code you all ready have to have for Phenylalanine and the like to decide the match using rms's. Dale Tronrud Charlie Bond wrote: > Hi Gerard, > > Interesting - isn't it the case that for Arg, the the NH1 and NH2 atoms > are chemically distinguishable and the convention is unambiguous (NH1 > cis to CD and NH2 trans, if I recall correctly). > > The truly symmetric sidechains of Asp, Glu, Tyr, Phe, and the > pseudosymmetric sidechains of Asn, Gln and His are more straightforward, > but for Arg I would have thought quite a strong case would have to be > made for ignoring the convention for RMSD purposes. Put differently, I > find it hard to envision a scenario where swapping the names of NH1 and > NH2 for the purposes of an RMSD would be useful. Would one also not have > to include NE in the redundancy? > > Cheers, > Charlie > > Gerard DVD Kleywegt wrote: >>> Is there any convention to define the order of the two terminal >>> nitrogens (NH1 and NH2) of the arginine side chain. For example, >>> should the name NH1 be assigned to the nitrogen that is in trans >>> position with respect to the CD carbon, and NH2 to the nitrogen in >>> cis (or viceversa)? >> >> Yes there is a convention. Programs such as LSQMAN >> (http://xray.bmc.uu.se/usf/lsqman_man.html#S32) and WhatCheck can >> detect/fix these for you. This is something you would normally do at >> the end of your refinement. When you compare two models using all >> atoms, it's not so important that you use the correct convention but >> rather the one that gives the smallest RMSD (as the atoms are >> chemically indistinguishable). See: >> http://xray.bmc.uu.se/usf/lsqman_man.html#S33 >> >> --dvd >> >> ****************************************************************** >> Gerard J. Kleywegt >> Dept. of Cell & Molecular Biology University of Uppsala >> Biomedical Centre Box 596 >> SE-751 24 Uppsala SWEDEN >> >> http://xray.bmc.uu.se/gerard/ mailto:ger...@xray.bmc.uu.se >> ****************************************************************** >> The opinions in this message are fictional. Any similarity >> to actual opinions, living or dead, is purely coincidental. >> ****************************************************************** >> >
