Subject: re amino acid atom names

From: Kim Henrick <[email-masked]>
Date: Mon, 23 Jul 2001 12:18:33 +0100 (BST)

The amino acid atoms names are defined in the IUPAC-IUB
pages and please note for pro-chiral atoms there is
a difference between CD1 and CD2 as defined by the torsion
angles see http://www.chem.qmw.ac.uk/iupac/misc/ppep4.html
and pages ppep3.html /ppep1.html

software like procheck's clean will check torsion angles

prochirality rules also determine the names of some
of the hydrogens see for example
http://www.bmrb.wisc.edu/ref_info/aa_chem.html

see the paper 
J. L. Markley, Y. Arata, A. Bax, C. W. Hilbers, R. Kaptein, B. D.
       Sykes, P. E. Wright, and K. Wuethrich,"Recommendations for the
       Presentation of NMR Structures of Proteins and Nucleic Acids,"
       Pure & Appl. Chem. 70, 117-142 (1998). 

link to pdf file on http://www.bmrb.wisc.edu/

kim henrick

Kim HENRICK    [email-masked] ::telephone:  +44 (0) 1223 494629