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G3. Prediction of Hydrophobicity

  • Page ID
    4787
  • [ "article:topic", "authorname:jjakubowskih" ]

    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