High Quality Content by WIKIPEDIA articles! Hydrophobicity scales are ranking lists for the relative hydrophobicity of amino acid residues. In general, the more positive the value, the more hydrophobic are the amino acids located in that region of the protein (while the more negative the value, the more hydrophillic those amino acids). These scales are commonly used to predict the transmembrane alpha-helices of membrane protein -- because as you measure the amino acid values consecutively along the protein, each time the values change from positive to negative (or vice versa) it is an indication that the amino acids are either attracted to (positive) or repelled from (negative) the hydrophobic region located inside the phospholipid membrane.