Name definition of HB1 and HB2

Alexandre Bonvin abonvin at LAPLACE.CSB.YALE.EDU
Mon Mar 4 09:51:40 EST 1996


>Dear x-plorers,
>
>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

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| Alexandre Bonvin PhD           | Phone: (203) 432-5066                 |
| Mol. Biophys. & Biochemistry   | Fax:   (203) 432-3923                 |
| Yale University                | Email: abonvin at laplace.csb.yale.edu   |
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