Figure 7

Site-specific amino acid frequencies sampled from the PDB, ${\pi }_{c_i/〈c〉}^{obs}$(a), versus the probabilities ${\pi }_{c_i/〈c〉}^{pred}$(a) predicted through the mean-field model with optimal mutation parameters. All amino acids and all sites are shown. Observed and predicted frequencies are divided by the frequencies expected under mutation alone w_AA(a). The four frames refer to (a) mutation model 2 ('constant'), (b) mutation model 3 ('#codons'), (c) mutation model 4 ('opt. freq.'), and (d) mutation model 5 ('CpG'), respectively.