How do the three Wimley-White hydropathy scales differ from one another?
The hydropathy scales are based on experimentally determined whole-residue transfer free energies for each amino acid. The experiments involve partitioning to the POPC bilayer interface and into bulk-phase solvent (octanol, which imitates the hydrophobic core of a bilayer). The interface scale measures the free energy of transfer from water to the bilayer interface. The octanol scale measures the free energy of transfer from water to octanol. Therefore, if one were to subtract the octanol scale from the interface scale, one could see whether those segments that can partition on the interface would have favorable energy to become transmembrane helices. For additional information, see the Wimley-White Hydrophobicity Scale page.
