Amino acids in protein active sites

It is difficult to generalise which amino acids are likely to be in a protein active/functional site as this greatly depends on the type of function. With that in mind, below are preferences for the 20 amino acids to lie within functional regions on proteins (after Holm & Sander, Intelligent Systems for Molecular Biology, 5, 140-146, 1997). These were worked out by considering how often particular amino acids were in contact with bound non-protein atoms in protein three-dimensional structures. Postive values mean that the amino acid makes more contacts than one would expect by chance; negative values mean that it makes fewer. The below does not include protein-protein, or protein-peptide interactions, where many of the amino acids with negative values (e.g. tryptophan or proline) can play critical roles.

His 0.360
Cys 0.210
Ser 0.130
Lys 0.100
Thr 0.100
Asn 0.080
Arg 0.055
Gln 0.050
Glu 0.050
Asp 0.045
Ala 0.025
Met 0.025
Ile -0.005
Tyr -0.040
Val -0.060
Gly -0.070
Phe -0.120
Trp -0.140
Leu -0.180
Pro -0.200

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Please cite: M.J. Betts, R.B. Russell. Amino acid properties and consequences of subsitutions.
In Bioinformatics for Geneticists, M.R. Barnes, I.C. Gray eds, Wiley, 2003.