Hydropathy index or Hydrophobicity index are values which can be define as the relative hydrophobicity of amino acid residues. Two of the most commonly used hydropathy index are incorporated into the hydropathy analysis: (i) Kyte-Doolitle (ii) Hopp-Woods scale (See table below). More positive the value of hydrophobicity, the more hydrophobic are the amino acids located in that region of the protein (Kyte-Doolitle hydropathy index). These hydropathy index are usually helpful to predict the transmembrane alpha-helices of membrane proteins. When successively measuring amino acids of a protein, changes in hydropathic value indicate attraction of specific protein regions towards the hydrophobic region inside lipid bilayer. For more clear understanding look for hydropathy plot.
In case of globular proteins, amino acids with ionic (charged) or strongly polar neutral groups (e.g., Asp, Gln, and Lys in this protein) are located on the external surface, where they interact optimally with solvent water. Residues with nonpolar side chains (such as Ala and Ile) are situated in the interior, where they escape the polar environment. Threonine is of intermediate polarity and could be found either in the interior or on the exterior surface (see hydropathy scale).
Two of the most commonly used hydrophobicity index are incorporated into the hydropathy analysis: (i) Kyte-Doolitle (ii) Hopp-Woods scale