Model viewing programs were used to compare characteristics of the cAR2 model to the Brd template. The size of the amino acid is important to consider because bumping between amino acids could occur. The bulky amino acids in the template structure were observed and the model was checked for similar placements. Another protein viewing program, Rasmol was used to show differences by coloring chosen groups, components that make of the structure, and charge. Also, the Brd structure was colored to show the differences in charge.
High values are blue and low values are red.
Most of the protein is colored in red, which indicates a trend in uncharged amino acids. IF was colored to highlight the different components of the structures. The helices are magenta, loops are purple, and all others are white. The same cAR2 model was colored to show the differences in charge. Most of the protein is colored in green and yellow, which indicates slightly more charged amino acids than the Brd.