C2H2-ZF domain divergence with respect to <i>D. melanogaster</i> reference.

<p>(A) Schematic of a C2H2-ZF protein—DNA interface under the 7-contact model [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005011#pgen.1005011.ref053" target="_blank">53</a>]. Amino acids within the depicted finger are numbered according to their relative position from the start of the alpha helix within the C2H2-ZF domain, with <i>a_-1</i> indicating the position before the start of the helix. Bases <i>b₁, b₂, b₃</i> and <i>b₄</i> are numbered sequentially from 5’ to 3’ of the primary DNA strand; the complementary bases are denoted by <i>b₁’, b₂’, b₃’</i> and <i>b₄’</i>. Contacts between amino acids and bases are shown in arrows, with four specificity-determining amino acids <i>a_-1, a₂, a₃</i> and <i>a₆</i> making these contacts. Solid arrows depict the four “canonical” contacts between ZF domains and DNA [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005011#pgen.1005011.ref052" target="_blank">52</a>], and dashed arrows depict three additional contacts that are used in our predictions of binding specificity [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005011#pgen.1005011.ref053" target="_blank">53</a>]. (B) Histogram showing the percent divergence per species by position within the C2H2-ZF domain’s alpha-helix (-1 to 6) for all canonically linked domains. The columns with blue labels in the <i>x</i>-axis correspond to positions that interact with DNA in the 7-contact model. (C) Percent of all (black), canonically linked (blue) and non-canonically linked (red) aligned domains in each non-reference fly species with a divergent residue (as compared to the <i>D. melanogaster</i> reference) in positions -1, 2, 3, and/or 6.