Are binding residues conserved?

We present our attempt to quantify the evolutionary dynamics of functional residues in a representative set of protein structures and their homologous sequences. Using the log-odds formalism, the preference for all twenty amino acids to be conserved or participate in binding (or active) sites is examined. It appears that while there is a tendency for functional residues to be conserved, the two preference scales do not coincide. Remarkable differences between amino acid types emerge from this comparative study. The current approach is expected to lead towards a better understanding of functional site architecture in proteins.