Equivalent amino acids for similarity searches

[Simon Brocklehurst Bioc]

Notwithstanding all that has preceeded this thread, it is probably worth
pointing out that the physico-chemical properties of amino-acids ARE
of course reflected in the pattern amino acid substitutions that are
observed in divergently evolved families of proteins.  When this doesn't
happen, it's often because a particular position a fold doesn't have 
ANY real preference for a type of residue e.g a lot of surface positions
fall into this catagory.

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Simon M. Brocklehurst
Cambridge Centre for Molecular Recognition
Department of Biochemistry
University of Cambridge
Cambridge
UK

E-mail: s.m.brocklehurst at bioc.cam.ac.uk