FIG. 3.

The location of important amino acids sites mapped onto the three-dimensional E protein structure of Japanese encephalitis virus (JEV) (PBD ID: 3P54, MMDB ID: 87213): (A) Node-defining amino acid substitutions specific to the Indonesian viruses sequenced in this study. (B) Sites identified by the directional evolution in protein sequences (DEP)S analysis to exhibit evidence of directional evolution. (C) Sites detected by the Spidermonkey algorithm to display evidence of co-evolution. Domain I is indicated in red, domain II in yellow, and domain III in blue. The image was created using MacPyMOL version 1.3. (Color image available online at www.liebertpub.com/vbz).