Peptides (version 1.0.1)

hydrophobicity: Compute the hydrophobicity index

Description

This function calculates the GRAVY hydrophobicity index of an amino acids sequence using one of the 24 scales availables on ExPASy "protscale"

Usage

hydrophobicity(seq,scale)

Arguments

seq

amino acid sequence string in upper case

scale

a character string specifying the hydophobicity scale to be used; must be one of "KyteDoolittle", "AbrahamLeo", "BullBreese","Guy", "Miyazawa", "Roseman", "Wolfenden"

source

http://web.expasy.org/protscale/

References

Gasteiger, E., Hoogland, C., Gattiker, A., Wilkins, M. R., Appel, R. D., & Bairoch, A. (2005). Protein identification and analysis tools on the ExPASy server. In The proteomics protocols handbook (pp. 571-607). Humana Press.

Eisenberg D., Schwarz E., Komarony M., Wall R. Normalized consensus hydrophobicity scale. J. Mol. Biol. 179:125-142(1984).

Sweet R.M., Eisenberg D. Optimized matching hydrophobicity (OMH). J. Mol. Biol. 171:479-488(1983).

Hopp T.P., Woods K.R. Hydrophilicity. Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828(1981).

Kyte J., Doolittle R.F. Hydropathicity. J. Mol. Biol. 157:105-132(1982).

Manavalan P., Ponnuswamy Average surrounding hydrophobicity. P.K. Nature 275:673-674(1978).

Abraham D.J., Leo A.J. Hydrophobicity (delta G1/2 cal). Proteins: Structure, Function and Genetics 2:130-152(1987).

Black S.D., Mould D.R. Hydrophobicity of physiological L-alpha amino acids. Anal. Biochem. 193:72-82(1991).

Bull H.B., Breese K. Hydrophobicity (free energy of transfer to surface in kcal/mole). Arch. Biochem. Biophys. 161:665-670(1974).

Fauchere J.-L., Pliska V.E. Hydrophobicity scale (pi-r). Eur. J. Med. Chem. 18:369-375(1983).

Guy H.R. Hydrophobicity scale based on free energy of transfer (kcal/mole). Biophys J. 47:61-70(1985).

Janin J. Free energy of transfer from inside to outside of a globular protein. Nature 277:491-492(1979).

Miyazawa S., Jernigen R.L. Hydrophobicity scale (contact energy derived from 3D data). Macromolecules 18:534-552(1985).

Rao M.J.K., Argos P. Membrane buried helix parameter. Biochim. Biophys. Acta 869:197-214(1986).

Roseman M.A. Hydrophobicity scale (pi-r). J. Mol. Biol. 200:513-522(1988).

Tanford C. Hydrophobicity scale (Contribution of hydrophobic interactions to the stability of the globular conformation of proteins). J. Am. Chem. Soc. 84:4240-4274(1962).

Wolfenden R.V., Andersson L., Cullis P.M., Southgate C.C.F. Hydration potential (kcal/mole) at 25C. Biochemistry 20:849-855(1981).

Welling G.W., Weijer W.J., Van der Zee R., Welling-Wester S. Antigenicity value X 10. FEBS Lett. 188:215-218(1985).

Wilson K.J., Honegger A., Stotzel R.P., Hughes G.J. Hydrophobic constants derived from HPLC peptide retention times. Biochem. J. 199:31-41(1981).

Parker J.M.R., Guo D., Hodges R.S. Hydrophilicity scale derived from HPLC peptide retention times. Biochemistry 25:5425-5431(1986).

Cowan R., Whittaker R.G. Hydrophobicity indices at ph 3.4 determined by HPLC. Peptide Research 3:75-80(1990).

Cowan R., Whittaker R.G. Hydrophobicity indices at ph 7.5 determined by HPLC. Peptide Research 3:75-80(1990).

Rose G.D., Geselowitz A.R., Lesser G.J., Lee R.H., Zehfus M.H. Mean fractional area loss (f) [average area buried/standard state area]. Science 229:834-838(1985)

Examples

# COMPARED TO GRAVY Grand average of hydropathicity (GRAVY) ExPASy
# http://web.expasy.org/cgi-bin/protparam/protparam
# SEQUENCE: QWGRRCCGWGPGRRYCVRWC
# GRAVY: -0.950

hydrophobicity("QWGRRCCGWGPGRRYCVRWC","KyteDoolittle")
# [1] -0.95
hydrophobicity("QWGRRCCGWGPGRRYCVRWC","AbrahamLeo")
# [1] 0.09
hydrophobicity("QWGRRCCGWGPGRRYCVRWC","BullBreese")
# [1] 0.16
hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Guy")
# [1] 0.19
hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Miyazawa")
# [1] 5.74
hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Roseman")
# [1] -0.5
hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Wolfenden")
# [1] -6.31
hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Wilson")
# [1] 3.16
hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Cowan3.4")
# [1] 0.08
hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Aboderin")
# [1] 3.84
hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Sweet")
# [1] -0.11
hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Eisenberg")
# [1] -0.33
hydrophobicity("QWGRRCCGWGPGRRYCVRWC","HoppWoods")
# [1] -0.14
hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Manavalan")
# [1] 13.04
hydrophobicity("QWGRRCCGWGPGRRYCVRWC","BlackMould")
# [1] 0.5
hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Fauchere")
# [1] 0.53
hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Janin")
# [1] -0.1
hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Rao")
# [1] 0.81
hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Tanford")
# [1] -0.29
hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Cowan7.5")
# [1] 0.06
hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Chothia")
# [1] 0.26
hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Rose")
# [1] 0.76