Two representations of the proteins analyzed by DOT.
Plastocyanin (the stationary molecule) is on the left, cytochrome c on the
right. The lower portion of the image shows the alpha carbon backbone of each
protein and gives a good feel for the proteins' general shapes. The top part
of the image shows a potential isosurface for each protein, displaying charge
characteristics, with red negative and blue positive. Plastocyanin
has a large negative lobe centered about tyrosine 83 (the pale red ring) and cytochrome c has a large positive lobe.