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Biology LibreTexts

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