Skip to main content
Biology LibreTexts

G3. Prediction of Hydrophobicity

In a completely analogous fashion, a hydrophobic propensity or hydopathy can be calculated. In this system, empirical measures of the hydrophobic nature of the side chains are used to assign a number to a given amino acid. Many hydropathy scales are used. Several are based on the Dmo transfer of the side chains from water to a nonpolar solvent. Two commonly used scales are the Kyte-Doolittle Hydropathy and Hopp-Woods scales (used more like a hydrophilicity index to predict surface or water accessible structures that might be recognized by the immune system)

  Hydrophobicity Indices for Amino Acids

Amino Acid

 Kyte-Doolittle

 Hopp-Woods

Alanine

 1.8

 -0.5

Arginine

 -4.5

 3.0

Asparagine

 -3.5

 0.2

Aspartic acid

 -3.5

 3.0

Cysteine

 2.5

 -1.0

Glutamine

 -3.5

 0.2

Glutamic acid

 -3.5

 3.0

Glycine

 -0.4

 0.0

Histidine

 -3.2

 -0.5

Isoleucine

 4.5

 -1.8

Leucine

 3.8

 -1.8

Lysine

 -3.9

 3.0

Methionine

 1.9

 -1.3

Phenylalanine

 2.8

 -2.5

Proline

 -1.6

 0.0

Serine

 -0.8

 0.3

Threonine

 -0.7

 -0.4

Tryptophan

 -0.9

 -3.4

Tyrosine

 -1.3

 -2.3

Valine

 4.2

 -1.5

For a water-soluble protein, a  continuous stretch of amino acids found to have a high average hydropathy is probably buried in the interior of the protein.  Consider the example of bovine a-chymotrypsinogen, a 245 amino acid protein, whose sequence is shown below in single letter code.

1 CGVPAIQPVLSGLSRIVNGEEAVPGSWPWQVSLQDKTGFHFCGGSLINENWVVTAAHCGV
61 TTSDVVVAGEFDQGSSSEKIQKLKIAKVFKNSKYNSLTINNDITLLKLSTAASFSQTVSA
121 VCLPSASDDFAAGTTCVTTGWGLTRYTNANTPDRLQQASLPLLSNTNCKKYWGTKIKDAM
181 ICAGASGVSSCMGDSGGPLVCKKNGAWTLVGIVSWGSSTCSTSTPGVYARVTALVNWVQQ
241 TLAAN

A hydrophathy plot for chymotrypsinogen (sum of hydropathies of seven consecutive residues) shows many stretches that are presumably buried in the interior of the protein.

Figure:  hydrophathy plot for chymotrypsinogen