The hydrophobicity of an amino acid is a measure of the thermodynamic interaction between the side chain and water. In general, side chains have strong feelings about water, with hydrophilic side chains demonstrating an affinity for water and hydrophobic groups demonstrating an aversion to water. Hydrocarbon side chains such as those of leucine and phenylalanine interact unfavorably with water. Just as oil-water mixtures separate spontaneously into two phases, there is a tendency for hydrophobic side chains to gather together in the interior of a protein, away from contact with water. This hydrophobic effect provides an important component of the driving force for protein folding.

A hydrophobicity scale attempts to indicate how hydrophobic or hydrophilic the various side chains are, that is, which particular amino acids are buried in the interior in the interior of a protein or exposed to the solvent.

Free amino acids are zwitterions at pH 7 and are soluble in water. How, then, can you measure the hydrophobicities of the side chains? By using model compounds which mimic the structure of an amino acid residue in a polypeptide chain. For example, you could convert the free amino acid to the corresponding α-N-acetyl derivative, thereby removing the positive charge of the α amino group. You could also remove the negative charge on the carboxyl group by converting it to an amide, but then the solubilities in water would be too low to measure accurately. That leaves the α-N-acetyl amino acids as your model. The rankings in a hydrophobicity scale are based on the free energy changes for transfer of the α-N-acetyl amino acids from water to an organic solvent, such 1-octanol. By substracting the free energy change of transfer of N-acetylglycine derivative from the free energy change for the other α-N-acetyl amino acids, one can estimate the free energy change of transfer of the side chain for water to octanol. The implication in forming a scale based on ΔΔG values is that the interior of a protein resembles octanol in its interactions with hydrophobic side chains.

Different hydrophobicity scales have appeared over the past three decades, based on personal preferences for different models and solvents. They are similar to each other, although the details of the rankings differ. The amino acids whose side chains are alkanes, namely leucine, isoleucine, and valine, are the most hydrophobic amino acids. The amino acids with charged side chains at pH 7 (arginine, lysine, glutamate, and aspartate) are the most hydrophilic. Alanine, glycine, and proline reside in the middle. These rankings are in accord with the distribution of amino acids between the surface and the interior of proteins in crystallographic models.