conserved amino acid changes

Shaun D. Black SHAUN%JASON.DECNET at relay.the.net
Wed May 19 15:55:48 EST 1993


Dear ProteiNetters,
     Conservative replacements have been well defined by Margaret Dayhoff 
in her PAM matrices (see Atlas of Protein Sequences, front of any edition). 
It shows quantitatively how often each amino acid replaces another.  The 
mentioned conservative replacements (S<->T, D<->E, etc) pop out as high 
frequency results.
     It might also be of some interest to point you to our work on amino 
acid side chain hydrophobicity/hydrophilicity.  Essentially, most 
conservative substitutions are similar in polarity, probably because 
hydrophobicity is probably the principal driving 'force' in protein 
folding.  We've characterized the standard 20 amino acids and about twenty 
post- or co-translational modifications of these.  The reference is Black, 
S.D. and Mould, D.R. (1991) Anal. Biochem. 193, 72-82, "Development of 
Hydrophobicity Parameters to Analyze Proteins Which Bear Post- or Co-
translational Modifications".  Hope this helps.  Cheers.  -Shaun
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  = Shaun D. Black, PhD     | Internet:  shaun%jason.decnet at relay.the.net = 
  = Dept. of Biochemistry   | Bitnet:    shaun%jason.decnet at thenic.bitnet = 
  = UT Health Center, Tyler | Phone:    (903)877-2806  FAX: (903)877-7558 = 
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