Hydrophilicity plot

A hydrophilicity plot is a quantitative analysis of the degree of hydrophobicity or hydrophilicity of amino acids of a protein. It is used to characterize or identify possible structure or domains of a protein.

The plot has amino acid sequence of a protein on its x-axis, and degree of hydrophobicity and hydrophilicity on its y-axis. There are a number of methods to measure the degree of interaction of polar solvents such as water with specific amino acids. For instance, the Kyte-Doolittle scale indicates hydrophobic amino acids, whereas the Hopp-Woods scale measures hydrophilic residues.

Analyzing the shape of the plot gives information about partial structure of the protein. For instance, if a stretch of about 20 amino acids shows positive for hydrophobicity, these amino acids may be part of alpha-helix spanning across a lipid bilayer, which is composed of hydrophobic fatty acids. On the converse, amino acids with high hydrophilicity indicate that these residues are in contact with solvent, or water, and that they are therefore likely to reside on the outer surface of the protein.

Kyte-Doolittle-Hydropathy Plot for Human RET proto-oncogene. Plot was created using the ExPASy Protscale tool (http://web.expasy.org/protscale/).
Hopp-Woods-Hydropathy Plot for Human RET proto-oncogene. Plot was created using the ExPASy Protscale tool (http://web.expasy.org/protscale/).
Amino Acid Hydropathy Scores [1]
Amino Acid One Letter Code Hydropathy Score
Isoleucine I 4.5
Valine V 4.2
Leucine L 3.8
Phenylalanine F 2.8
Cysteine C 2.5
Methionine M 1.9
Alanine A 1.8
Glycine G -0.4
Threonine T -0.7
Serine S -0.8
Tryptophan W -0.9
Tyrosine Y -1.3
Proline P -1.6
Histidine H -3.2
Glutamic acid E -3.5
Glutamine Q -3.5
Aspartic acid D -3.5
Asparagine N -3.5
Lysine K -3.9
Arginine R -4.5

The data in the above table was generated using a computer program that evaluates the average hydrophobicity of segments within a protein and uses data collected from literature.

References

  1. ^ Kyte, J; Doolittle, R. F. (1982). "A simple method for displaying the hydropathic character of a protein". Journal of Molecular Biology. 157 (1): 105–32. CiteSeerX 10.1.1.458.454. doi:10.1016/0022-2836(82)90515-0. PMID 7108955. {{cite journal}}: Cite uses deprecated parameter |citeseerx= (help)

Content Disclaimer

Informasi ini disarikan dari Wikipedia dan disajikan kembali untuk tujuan edukasi. Konten tersedia di bawah lisensi CC BY-SA 3.0. Kami tidak bertanggung jawab atas ketidakakuratan data yang bersumber dari kontribusi publik tersebut.

  1. The information displayed on this website is sourced in part or in whole from Wikipedia and has been adapted for the purpose of restating it. We strive to provide accurate and relevant information, however:
  2. There is no guarantee of absolute accuracy. Wikipedia is an open, collaborative project that can be edited by anyone, so information is subject to change.
  3. It is not intended to constitute professional advice. The content displayed is for informational and educational purposes only. For important decisions (e.g., medical, legal, or financial), please consult a professional.
  4. Content copyright. Wikipedia is licensed under the Creative Commons Attribution-ShareAlike License (CC BY-SA). This means that content may be reused with appropriate attribution and shared under a similar license.
  5. Responsible use. Any risk arising from the use of information from this website is entirely the responsibility of the user.