Figure 2. Unique amino acid replacements in Cytochrome C oxidase subunit 1 form tight spatial clusters.

The twenty-three unique amino acid replacements in the cytochrome C oxidase subunit 1 (COI) protein of snakes form seven pairs and one triplet of spatially clustered amino acid replacements, concentrated at the core functional region of the COI protein. The seven spatially adjacent pairs of amino acid residues, strongly suggestive of coevolutionary adaptive change, are shown in blue/red paired spacefill combinations, and one triplet cluster is shown in a blue/purple/red combination. Unique sites that did not form clusters are shown in gray spacefill representations. The two heme groups are shown in gold spacefill shapes, the COI backbone in white, and the magnesium and copper atoms are shown as magenta and green balls, respectively. Two different perspectives are depicted, one in A and B, and a second in C and D; Figure sets A/B and C/D are the same views with B and D showing the ribbon structure of the COI backbone in transparent grey.