Essential Amino Acids Hydrophobicity Scales – see hyd.xls
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=1140
7414&dopt=Abstract –Oxford Journals
Several hydrophobicity scales have been published for various uses. Some of them
are presented in Table 1.
1. Kyte-Doolittle scale [Kyte and Doolittle, 1982]1:
a. used for detecting hydrophobic regions in proteins. Regions with a positive
value are hydrophobic.
b. can be used for identifying both surface-exposed regions as well as
transmembrane regions. Short window sizes of 5-7 generally works well for
predicting putative surface-exposed regions. Large window sizes of 19-21 is
well suited for finding transmembrane domains if the values calculated are
above 1.6.
2. Engelman scale [Engelman et al., 1986]2:
a. also known as the GES-scale
b. can be used for prediction of protein hydrophobicity
c. useful for prediction transmembrane regions in proteins.
3. Eisenberg scale [Eisenberg et al., 1984]3:
a. a normalized consensus hydrophobicity scale
4. Hopp-Woods scale [Hopp and Woods, 1983]4:
a. developed for identification of potential antigenic sites in proteins
b. is a hydrophilic index where apolar residues have been assigned negative
values. Antigenic sites are likely to be predicted when using a window size of
7
5. Cornette scale [Cornette et al., 1987]5:
a. an optimal hydrophobicity scale based on 28 published scales
b. suitable for prediction of alpha-helices in proteins.
6. Rose scale [Rose et al., 1985]6:
a. a scale correlated to the average area of buried amino acids in globular
proteins
b. is a scale which is showing the surface accessibility of a protein
7. Janin scale [Janin, 1979]7:
a. based on the accessible and buried amino acid residues of globular proteins.
8. Wimley-White scale [Wimley and White, 1996]8:
9. Hessa et al. scale [Hessa et al, 2005]9:
10.Bumble scale [Bumble, 1999]10:
11.Wolfenden et al [Wolfenden, 1981]11:
12.Sweet-Eisenberg [Sweet & Eisenberg., 1983]12:
13.Abraham-Leo13
14.Bull & Breese14
15.Guy15
16.Miyazawa et al.16
17.Roseman17
18.Welling & al18
19.Parker & al19: HPLC
20.Cowan20: HPLC pH = 7.5
21.Manavalan et al.21: Average surrounding hydrophobicity
22.Black22: Hydrophobicity of physiological L-alpha amino acids
23.Fauchere et al.23: Hydrophobicity scale (pi-r).
24.Rao & Argos24: Membrane buried helix parameter
25. Wilson et al25: Hydrophobic constants derived from HPLC peptide retention times
26.Cowan-Whittaker26: Hydrophobicity indices at ph 3.4 determined by HPLC
TABLE I Distribution Coefficients of the 19 Amino Acid Side Chains
Amino acid
ILE
LEU
PHE
VAL
CYS
MET
ALA
TRP
THR
TYR
GLY
SER
ASN
HIS
GLN
ARG
GLU
LYS
ASP
RH (side chain)
Least polar
n-butane
isobutane
toluene
propane
methanethiol
methylethylsulfide
methane
3-methylindole
ethanol
4-methylphenol
hydrogen
methanol
acetamide
4-methylimidazole
propionamide
N-propylguanidine
propionic acid
n-butylamine
acetic acid
Most polar
r2 versus VHh
r2 versus CHh
p versus VHi
v>wa
c>wb
VHc
CHd
GUe
WWf
WWthg
2.15
2.28
–0.76
1.99
–1.24
–1.48
1.94
–5.88
–4.88
–6.11
2.39
–5.06
–9.68
–10.27
–9.38
–19.92
–10.24
–9.52
–10.95
4.92
4.92
2.98
4.04
1.28
2.35
1.81
2.33
–2.57
–0.14
0.94
–3.40
–6.64
–4.66
–5.54
–14.92
–6.81
–5.55
–8.72
–0.60
–0.55
–0.32
–0.31
–0.13
–0.10
0.13
0.30
0.52
0.68
0.74
0.84
2.05
2.06
2.36
2.58
2.68
2.71
3.49
0.24
–0.02
0.00
0.09
0.00
–0.24
–0.29
–0.59
–0.71
–1.02
–0.34
–0.75
–1.18
–0.94
–1.53
–2.71
–0.90
–2.05
–1.02
2.04
1.76
2.09
1.18
ND
1.32
0.52
2.51
0.27
1.63
0.00
0.04
–0.01
0.95
–0.07
–1.32
–0.79
0.08
ND
2.16
2.29
2.68
1.61
1.23
1.71
0.87
2.96
0.95
1.67
1.01
0.85
0.30
0.92
0.30
2.99
–2.53
2.49
–2.46
–1.12
–1.25
–1.71
–0.46
–0.02
–0.67
0.50
–2.09
0.25
–0.71
1.15
0.46
0.85
2.33
0.77
1.81
3.63
2.80
3.64
0.73
0.82
0.000001
0.83
0.80
<0.0000001
(1.0)
0.66
0.66
(1.0)
0.59
0.48
0.00003
0.30
0.00
0.003
0.77
0.35
Distribution coefficients of the 19 amino acid side chains (RH) at pH 7, expressed in kcal/mol at
25°C, sorted according to their decreasing tendencies (VH) to be found in a transmembrane helix
(Hessa et al., 2005). Experimental scales are shown in bold, theoretical scale in normal type.
a
Side-chain Kd values for side-chain transfer from vapor to water (Wolfenden et al., 1981).
b
Side-chain Kd values for transfer from cyclohexane to water (Radzicka and Wolfenden, 1988).
c
Tendency of amino acid residue to be found in a transmembrane helix (Hessa et al., 2005).
d
Tendency of amino acid residue to be buried in the interior of a globular protein (Chothia, 1976).
e
Amino acid side-chain Kd values for transfer from wet octanol to water (Guy, 1985).
f
Pentapeptide Kd values for transfer from water to wet octanol (Wimley et al., 1996).
g
Theoretical pentapeptide Kd values for transfer from water to wet octanol, after adjustment for the
estimated effects of occlusion by neighboring residues (Wimley et al., 1996, Table II, column 3).
h
Value of the correlation coefficient (r) obtained by linear regression of distribution coefficients
against the VH or the CH scales.
i
Probability that this experimental scale is not related to the VH scale, i.e., that the null hypothesis
is true.
Kyte J, Doolittle RF. A Simple Method for Displaying the Hydropathic Character of a
Protein. J Mol Biol 1982;157:105-132.
2
Engelman DM, Steitz TA, Goldman A. Identifying nonpolar transbilayer helices in
amino acid sequences of membrane proteins. Annu Rev Biophys Biophys Chem
1986;15:321-353.
3
Eisenberg D, Schwarz E, Komaromy M, Wall R. Analysis of membrane and surface
protein sequences with the hydrophobic moment plot. J Mol Biol 1984;179:125-142.
4
Hoop TP, Woods KR. Prediction of protein antigenic determinants from amino acid
sequences. Proc Natl Acad Sci USA 1981;78:3824-3828.
1
Cornette JL, Cease KB, Margalit H, Spouge JL, Berzofsky JA, DeLisi C. Hydrophobicity
scales and computational techniques for detecting amphipathic structures in proteins.
J Mol Biol 1987;195:659-685.
6
Rose GD, Geselowitz AR, Lesser GJ, Lee RH, Zehfus MH. Hydrophobicity of amino
acid residues in globular proteins. Science 1985;229:834-838.
7
Janin J. Surface and inside volumes in globular proteins. Nature 1979;277:491-492.
8
Wimley WC, White SH, Experimentally determined hydrophobicity scale for proteins
at membrane interfaces. Nature Struct Biol 1996;3:842-848.
9
Hessa T, Kim H, Bihlmaier K, Lundin C, Boekel J, Andersson H, Nilsson I, White SH,
von Heijne G. Recognition of transmembrane helices by the endoplasmic reticulum
translocon. Nature 2005;433:377-381, supplementary data.
10
Bumble S. The Design of Life: Information Technology, “Knapsack” and “Synprops”
Used to Engineer the Sequence of Amino Acid Residues in Proteins [online] [cited June
1, 2007]. http://science-advisor.net/article/cond-mat/0305442
&&& Bumble S.
Computer Generated Physical Properties, CRC Press, LLC, Boca Raton, 1999
11
Wolfenden R, Andersson L, Cullis P, Southgate C. Affinities of Amino Acid Side
Chains for Solvent Water. Biochemistry 1981;20:849-855.
12
Sweet RM, Eisenberg D. Correlation of sequence hydrophobicities measures
similarity in three-dimensional protein structure. J Mol Biol 1983;171:479-488.
13
Abraham D.J., Leo A.J. Extension of the fragment method to calculate amino acid
zwitterions and side chain partition coefficients. Proteins 1987;2:130-152.
14
Bull HB, Breese K. Surface tension of amino acid solutions: A hydrophobicity scale
of the amino acid residues. Arch Biochem Biophys 1974;161:665-670.
15
Guy HR. Amino acid side-chain partition energies and distribution of residues in
soluble proteins. Biophys J 1985;47:61-70.
16
Miyazawa S, Jernigen RL. Estimation of Effective Interresidue Contact Energies from
Protein
Crystal
Structures:
Quasi-Chemical Approximation.
Macromolecules
1985;18:534-552.
17
Roseman MA. Hydrophilicity of polar amino acid side-chains is markedly reduced by
flanking peptide bonds. J Mol Biol 1988;200:513-522.
18
Welling GW, Weijer WJ, Van der Zee R, Welling-Wester S. Prediction of sequential
antigenic regions in proteins. FEBS Lett 1985;188:215-218.
19
Parker JMR, Guo D, Hodges RS. New Hydrophilicity Scale Derived from HighPerformance Liquid Chromatography Peptide Retention Data: Correlation of Predicted
Surface Residues with Antigenicity and X-ray-Derived Accessible Sites? Biochemistry
1986;25:5425-5431.
20
Cowan R., Whittaker R.G. Hydrophobicity indices for amino acid residues
asdetermined by HPLC. Peptide Research 1990;3:75-80.
21
Manavalan P, Ponnuswamy PK. Hydrophobic character of amino acid residues in
globular proteins. Nature 1978;275:673-674.
22
Black SD, Mould DR. Development of Hydrophobicity Parameters to Analyze
Proteins Which Bear Post- or Cotranslational Modifications. Anal Biochem
1991;193:72-82. Available online: URL:
http://psyche.uthct.edu/shaun/SBlack/aagrease.html
23
Fauchere J-L, Pliska VE. Hydrophobic parameters of amino-acid side-chains from
the partitioning of N-acetyl-amino-acid amide. Eur J Med Chem 1983;18:369-375.
24
Rao MJK, Argos P. A conformational preference parameter to predict helices in
integral membrane proteins. Biochim Biophys Acta 1986;869:197-214.
25
Wilson KJ, Honegger A, Stotzel RP, Hughes GJ. The behaviour of peptides on
reverse-phase supports during high-pressure liquid chromatography. Biochem J
1981;199:31-41.
26
Cowan R, Whittaker RG. Hydrophobicity indices for amino acid residues
asdetermined by HPLC. Peptide Research 1990;3:75-80.
5