Name definition of HB1 and HB2
abonvin at LAPLACE.CSB.YALE.EDU
Mon Mar 4 09:51:40 EST 1996
>I have two questions about NMR structure calculations in XPLOR:
>1. In stereospecific assignments, how does the atom name definition of HB1 and HB2
> in XPLOR match IUPAC-IUB definition of H beta 2 and H beta 3? As the definition
> of atom names HB1 and HB2 is essential to the correct setup of NOE restraints.
The current convention in X-PLOR is based on the IUPAC like rules, i.e. looking
from the backbone down the side chain, the first proton encountered in a clockwise
rotation being HB1 and the second one HB2 (according to IUPAC these should
be in fact HB2 and HB3). This notation is always consistent.
The current X-PLOR notation follows the old IUPAC rules that
are the one apparently recommended in the IUPAC-IUBMB-IUPAB task group on the
standardisation of data bases on protein structures determined by NMR in solution
(draft from Wuthrich et al to be published in various journals).
>2. If the disulfide bonds of a protein have been determined, must the PSF file contain
> the disulfide linkage? Could one exclude the disulfide linkage in the PSF file
> and use patch DISU topology statements to add S-S bonds instead when necessary for
> structure calculations? As from my own experience, I found the latter has an
> advantage over the former.
If you check the standard X-PLOR scripts for NMR structure calculations that's
what is happening. In particular for DG calculation S-S bonds should be deleted
from the topology and replaced by distance restraints.
| Alexandre Bonvin PhD | Phone: (203) 432-5066 |
| Mol. Biophys. & Biochemistry | Fax: (203) 432-3923 |
| Yale University | Email: abonvin at laplace.csb.yale.edu |
| New Haven CT 06520-8114, USA | |
| http://xplor.csb.yale.edu/group/people/alex_bonvin/alex_bonvin.html |
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