2.5.3: G3. Prediction of Hydrophobicity
- Page ID
- 64234
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)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
