# SCA, SCALE

NAME
SCA, SCALE - select hydrophobicity scale.
SYNOPSIS
SCA keyword
SCALE keyword
DESCRIPTION
The command SCALE selects the specified hydrophobicity scale. Since version 1.4, six scales are available: Eisenberg normalized consensus scale, Kyte-Doolittle hydropathy scale and four experimentally determined scales from the Stephen White laboratory . The scale is assigned to the structure which is currently being handled (the structure which was caught using the command CATCH). It is also used as default hydrophobicity scale for the sequence in the main sequence buffer. The hydrophobicity scale is used to calculate the averaged hydrophobicity and hydrophobic moment. It may be also used to color the protein structure according to hydrophobicity.
Hard-coded program default is Eisenberg scale.
KEYWORDS

KEYWORD (SHORT) | KEYWORD (LONG) | DESCRIPTION
EIS | EISENBERG | Default: Eisenberg normalized consensus hydrophobicity scale (reference 1, see the bottom of this page!).
KD | KD | Kyte-Doolittle hydropathy scale (reference 2).
INT | INTERFACE | Interface scale from the Stephen White laboratory (ref. 3).
OCT | OCT | Octanol scale from the Stephen White laboratory (ref. 4). The keyword OCT was introduced in version 1.4 of garlic, to replace the keyword WHI (WHITE).
IN2 | IN2 | Modified interface scale: HIS, ASP and GLU neutral.
DIF | DIFFERENTIAL | Differential scale: octanol minus interface.

HYDROPHOBICITY SCALES
The table below contains numeric data for four hydrophobicity scales which are used in garlic. The original scales from the Stephen White laboratory contain the free energy changes for a transfer of whole residues from water to bilayer interface or octanol. In garlic, these free energy changes are multiplied by minus one and used as hydrophobicity values. The experimental values and nice theoretical explanations may be found at:
http://blanco.biomol.uci.edu/hydrophobicity_scales.html

NAME | EIS | KD | INT | OCT | IN2 | DIF
ALA | 0.62 | 1.80 | -0.17 | -0.50 | -0.17 | -0.33
ARG | -2.53 | -4.50 | -0.81 | -1.81 | -0.81 | -1.00
ASN | -0.78 | -3.50 | -0.42 | -0.85 | -0.42 | -0.43
ASP | -0.90 | -3.50 | -1.23 | -3.64 | 0.07 | -2.41
CYS | 0.29 | 2.50 | 0.24 | 0.02 | 0.24 | -0.22
GLN | -0.85 | -3.50 | -0.58 | -0.77 | -0.58 | -0.19
GLU | -0.74 | -3.50 | -2.02 | -3.63 | 0.01 | -1.61
GLY | 0.48 | -0.40 | -0.01 | -1.15 | -0.01 | -1.14
HIS | -0.40 | -3.20 | -0.96 | -2.33 | -0.17 | -1.37
ILE | 1.38 | 4.50 | 0.31 | 1.12 | 0.31 | 0.81
LEU | 1.06 | 3.80 | 0.56 | 1.25 | 0.56 | 0.69
LYS | -1.50 | -3.90 | -0.99 | -2.80 | -0.99 | -1.81
MET | 0.64 | 1.90 | 0.23 | 0.67 | 0.23 | 0.44
PHE | 1.19 | 2.80 | 1.13 | 1.71 | 1.13 | 0.58
PRO | 0.12 | -1.60 | -0.45 | -0.14 | -0.45 | 0.31
SER | -0.18 | -0.80 | -0.13 | -0.46 | -0.13 | -0.33
THR | -0.05 | -0.70 | -0.14 | -0.25 | -0.14 | -0.11
TRP | 0.81 | -0.90 | 1.85 | 2.09 | 1.85 | 0.24
TYR | 0.26 | -1.30 | 0.94 | 0.71 | 0.94 | -0.23
VAL | 1.08 | 4.20 | -0.07 | 0.46 | -0.07 | 0.53
ASX | -0.84 | -3.50 | -0.83 | -2.25 | -0.18 | -1.38
GLX | -0.80 | -3.50 | -1.30 | -2.20 | -0.29 | -0.90
UNK | 0.00 | -0.49 | -0.14 | -0.52 | -0.38 | -0.29

EXAMPLES

COMMAND | DESCRIPTION
sca eis | Use the scale prepared by David Eisenberg.
sca int | Use the experimental interface scale from the Stephen White laboratory.

NOTES
(1) Many hydrophobicity scales may be found in literature. However, most of these scales are mutually highly correlated.
(2) The keyword WHI (WHITE) was replaced by the keyword OCT (OCTANOL) in version 1.4 of garlic!
RELATED COMMANDS
PLOT is used to draw averaged hydrophobicity and other hydrophobicity functions. color HYPHOB is used to color the structure according to hydrophobicity of residues.
REFERENCES
(1) Eisenberg, D., Schwarz, E., Komaromy, M. and Wall, R. (1984). J. Mol. Biol. 179, p. 125.
(2) Kyte, J. and Doolittle, R. F. (1982). J. Mol. Biol. 157, p. 105.
(3) Wimley, W. C. and White, S. H. (1996). Nature Struct. Biol. 3, p. 842.
(4) Wimley, W. C., Creamer, T. P. and White, S. H. (1996). Biochemistry 35, p. 5109.
(5) White, S. H. and Wimley, W. C. (1998). Biochim. Biophys. Acta 1376, p 339.
(6) White, S. H. and Wimley, W. C. (1999). Annu. Rev. Biophys. Biomol. Struc. 28, p. 319.