[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[ccp4bb]: Tables of amino acid volumes

***  For details on how to be removed from this list visit the  ***
***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***

Many thanks to all those who helped me with finding tables of amino 
acid volumes. The following information was very helpful and since a 
few people asked "me too" here is what I found with attribution

Structure 1994 Jul 15;2(7):641-9 Volume changes on protein folding. 
Harpaz Y, Gerstein M, Chothia C
	Gabby Rudenko

Andersson & Hovm÷ller (1998). The average atomic volume and density 
of proteins. Z. Kristallogr. 213, 369-273. Also the latest Acta Cryst 
	Salam Al-Karadaghi

A very rough but not too bad approximation is to say that the average 
volume of any atom including H is 10A**3, and get it from there.
	Eleanor J. Dodson

Proteins: Structure and molecular properties by Thomas E. Creighton. Second Ed
	Darren D'Arcy, Ilana M. Nodelman, Daniel Picot, David J. Schuller

The values in Creighton are derived from Chothia, C. (1975) 
Structural invariants in protein folding. Nature 254 304--308 which 
is an interesting paper in its own right.

David Schuller also sent me some fortran code for calculating side 
chain volumes which proved very useful.

Craig Marshall          mailto:craig.marshall@otago.ac.nz
Biochemistry Department http://biochem.otago.ac.nz/staff/marshall/cmarshall.htm
University of Otago     Phone +64 3 479 7570 Fax +64 3 479 7866