FIG 2.

Effects of all amino acid mutations at each site in the E protein as measured in the deep mutational scanning. (A) The preference of each site for each amino acid. The height of each letter is proportional to the enrichment of that amino acid after selection relative to its frequency before selection, so taller letters indicate more strongly preferred amino acids. The letters immediately above each logo stack indicate the wild-type amino acid in the parental MR766 E protein, the first color bar (DOM) indicates the domain of the E protein as defined in Dai et al. (27), and the second color bar (SS) indicates the secondary structure of that region as defined using DSSP (49) on PDB structure 5IRE (7). (B) An alternative representation of the same data shown in panel A. In this representation, the height of each letter represents the estimated effect of that mutation, where letters above the black line indicate favorable mutations (there are relatively few of these) and letters below the black line indicate unfavorable mutations. The effect of a mutant amino acid is equal to the logarithm of the ratio of its preference divided by the preference for the wild-type amino acid at that site.