Figure 2. A three-dimensional representation of the complex 1E6J with the color-coding of the PRODIGY script (.pml).

This script can be downloaded from the PRODIGY output page. Interactor 1 is shown in light pink (chains L and H in this example) and Interactor 2 in light blue (chain P), respectively. The interacting residues are represented in sticks in blue and dark pink for Interactor 1 and Interactor 2, respectively.