G3. Prediction of Hydrophobicity
- Page ID
- 4787
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 |
- Kyte-Doolittle Online Hydropathy Plot
- KD Hydropathy Plot
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