Figure 2.
The relationship between the effective number of amino acids Ω and the relative solvent accessibility (RSA) of sites depends on whether amino-acid distributions are pooled across similar sites. (a) Without pooling, an Ω value is calculated at each site, and then Ω is averaged over all sites within the same RSA percentile. This procedure yields relatively low Ω values, between 2 and 10, and a nearly linear increase of Ω with increasing RSA. (b) Alternatively, amino-acid distributions are pooled among all sites within the same RSA percentile, and then a single Ω value is calculated for each pooled distribution. This procedure yields much higher Ω values (> 10), and it shows a maximum at intermediate RSA values. Protein sequences and structural data for this analysis were taken from (34). We selected 266 distinct enzymes for which each available alignment consisted of at least 400 sequences.