Figure 1: Disarranged amino acid matches illustrated utilizing the homologous loops of two protein chains (Green and Blue) with dots representing the alpha carbons of noteworthy amino acids. The Blue Amino Acid and the Green Amino Acid 1 are truly homologous and calculated to be a structural match. However, the Blue Amino Acid also structurally matches to Green Amino Acid 2 due to their close proximity. If the remaining amino acids in the loop are matched correctly, the Green Amino Acid 2 will be disarranged in the amino acid sequence.