Figure 2: The omega loop problem illustrated utilizing two homologous protein chains with dots representing the alpha carbons of noteworthy amino acids. Amino Acids 1, 2, 4, and 5 for both proteins will be structurally matched. However, to which amino acid composing the omega loop (3A, 3B, 3C, 3D, or 3E) will Amino Acid 3 match? Assuming three of the four amino acids composing the omega loop were evolutionarily inserted (as opposed to the loop being deleted in the opposing protein), the original homologous amino acid can be any one of the loop amino acids. Conversely, utilizing only structural coordinates, the amino acid opposing the omega loop can be homologous to any of the amino acids composing the loop.