<html> <head> <title> SCA, SCALE </title> </head> <h1 align=center> SCA, SCALE </h1> <hr size="3"> <font color=#880000> <b> NAME <br> </b> </font> SCA, SCALE - select hydrophobicity scale. <br><br> <font color=#880000> <b> SYNOPSIS <br> </b> </font> SCA keyword <br> SCALE keyword <br><br> <font color=#880000> <b> DESCRIPTION <br> </b> </font> 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 <a href="http://blanco.biomol.uci.edu"> Stephen White laboratory </a> . 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. <br><br> Hard-coded program default is Eisenberg scale. <br><br> <font color=#880000> <b> KEYWORDS <br> </b> </font> <table border=2 cellspacing=2 cellpading=0> <td align="left"> KEYWORD <br> (SHORT) </td> <td align="left"> KEYWORD <br> (LONG) </td> <td align="left"> DESCRIPTION </td> <tr> <td align="left"> EIS </td> <td align="left"> EISENBERG </td> <td align="left"> Default: Eisenberg normalized consensus hydrophobicity <br> scale (reference 1, see the bottom of this page!). </td> <tr> <td align="left"> KD </td> <td align="left"> KD </td> <td align="left"> Kyte-Doolittle hydropathy scale (reference 2). </td> <tr> <td align="left"> INT </td> <td align="left"> INTERFACE </td> <td align="left"> Interface scale from the Stephen White laboratory (ref. 3). </td> <tr> <td align="left"> OCT </td> <td align="left"> OCT </td> <td align="left"> Octanol scale from the Stephen White laboratory (ref. 4). <br> The keyword OCT was introduced in version 1.4 of garlic, <br> to replace the keyword WHI (WHITE). </td> <tr> <td align="left"> IN2 </td> <td align="left"> IN2 </td> <td align="left"> Modified interface scale: HIS, ASP and GLU neutral. </td> <tr> <td align="left"> DIF </td> <td align="left"> DIFFERENTIAL </td> <td align="left"> Differential scale: octanol minus interface. </td> </table> <br> <font color=#880000> <b> HYDROPHOBICITY SCALES <br> </b> </font> 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: <br> <a href="http://blanco.biomol.uci.edu/hydrophobicity_scales.html"> http://blanco.biomol.uci.edu/hydrophobicity_scales.html </a> <br> <table border=2 cellspacing=2 cellpading=0> <td align="center"> NAME </td> <td align="right"> EIS </td> <td align="right"> KD </td> <td align="right"> INT </td> <td align="right"> OCT </td> </td> <td align="right"> IN2 </td> <td align="right"> DIF </td> <tr> <td align="center"> ALA </td> <td align="right"> 0.62 </td> <td align="right"> 1.80 </td> <td align="right"> -0.17 </td> <td align="right"> -0.50 </td> <td align="right"> -0.17 </td> <td align="right"> -0.33 </td> <tr> <td align="center"> ARG </td> <td align="right"> -2.53 </td> <td align="right"> -4.50 </td> <td align="right"> -0.81 </td> <td align="right"> -1.81 </td> <td align="right"> -0.81 </td> <td align="right"> -1.00 </td> <tr> <td align="center"> ASN </td> <td align="right"> -0.78 </td> <td align="right"> -3.50 </td> <td align="right"> -0.42 </td> <td align="right"> -0.85 </td> <td align="right"> -0.42 </td> <td align="right"> -0.43 </td> <tr> <td align="center"> ASP </td> <td align="right"> -0.90 </td> <td align="right"> -3.50 </td> <td align="right"> -1.23 </td> <td align="right"> -3.64 </td> <td align="right"> 0.07 </td> <td align="right"> -2.41 </td> <tr> <td align="center"> CYS </td> <td align="right"> 0.29 </td> <td align="right"> 2.50 </td> <td align="right"> 0.24 </td> <td align="right"> 0.02 </td> <td align="right"> 0.24 </td> <td align="right"> -0.22 </td> <tr> <td align="center"> GLN </td> <td align="right"> -0.85 </td> <td align="right"> -3.50 </td> <td align="right"> -0.58 </td> <td align="right"> -0.77 </td> <td align="right"> -0.58 </td> <td align="right"> -0.19 </td> <tr> <td align="center"> GLU </td> <td align="right"> -0.74 </td> <td align="right"> -3.50 </td> <td align="right"> -2.02 </td> <td align="right"> -3.63 </td> <td align="right"> 0.01 </td> <td align="right"> -1.61 </td> <tr> <td align="center"> GLY </td> <td align="right"> 0.48 </td> <td align="right"> -0.40 </td> <td align="right"> -0.01 </td> <td align="right"> -1.15 </td> <td align="right"> -0.01 </td> <td align="right"> -1.14 </td> <tr> <td align="center"> HIS </td> <td align="right"> -0.40 </td> <td align="right"> -3.20 </td> <td align="right"> -0.96 </td> <td align="right"> -2.33 </td> <td align="right"> -0.17 </td> <td align="right"> -1.37 </td> <tr> <td align="center"> ILE </td> <td align="right"> 1.38 </td> <td align="right"> 4.50 </td> <td align="right"> 0.31 </td> <td align="right"> 1.12 </td> <td align="right"> 0.31 </td> <td align="right"> 0.81 </td> <tr> <td align="center"> LEU </td> <td align="right"> 1.06 </td> <td align="right"> 3.80 </td> <td align="right"> 0.56 </td> <td align="right"> 1.25 </td> <td align="right"> 0.56 </td> <td align="right"> 0.69 </td> <tr> <td align="center"> LYS </td> <td align="right"> -1.50 </td> <td align="right"> -3.90 </td> <td align="right"> -0.99 </td> <td align="right"> -2.80 </TD > <td align="right"> -0.99 </td> <td align="right"> -1.81 </td> <tr> <td align="center"> MET </td> <td align="right"> 0.64 </td> <td align="right"> 1.90 </td> <td align="right"> 0.23 </td> <td align="right"> 0.67 </td> <td align="right"> 0.23 </td> <td align="right"> 0.44 </td> <tr> <td align="center"> PHE </td> <td align="right"> 1.19 </td> <td align="right"> 2.80 </td> <td align="right"> 1.13 </td> <td align="right"> 1.71 </td> <td align="right"> 1.13 </td> <td align="right"> 0.58 </td> <tr> <td align="center"> PRO </td> <td align="right"> 0.12 </td> <td align="right"> -1.60 </td> <td align="right"> -0.45 </td> <td align="right"> -0.14 </td> <td align="right"> -0.45 </td> <td align="right"> 0.31 </td> <tr> <td align="center"> SER </td> <td align="right"> -0.18 </td> <td align="right"> -0.80 </td> <td align="right"> -0.13 </td> <td align="right"> -0.46 </td> <td align="right"> -0.13 </td> <td align="right"> -0.33 </td> <tr> <td align="center"> THR </td> <td align="right"> -0.05 </td> <td align="right"> -0.70 </td> <td align="right"> -0.14 </td> <td align="right"> -0.25 </td> <td align="right"> -0.14 </td> <td align="right"> -0.11 </td> <tr> <td align="center"> TRP </td> <td align="right"> 0.81 </td> <td align="right"> -0.90 </td> <td align="right"> 1.85 </td> <td align="right"> 2.09 </td> <td align="right"> 1.85 </td> <td align="right"> 0.24 </td> <tr> <td align="center"> TYR </td> <td align="right"> 0.26 </td> <td align="right"> -1.30 </td> <td align="right"> 0.94 </td> <td align="right"> 0.71 </td> <td align="right"> 0.94 </td> <td align="right"> -0.23 </td> <tr> <td align="center"> VAL </td> <td align="right"> 1.08 </td> <td align="right"> 4.20 </td> <td align="right"> -0.07 </td> <td align="right"> 0.46 </td> <td align="right"> -0.07 </td> <td align="right"> 0.53 </td> <tr> <td align="center"> ASX </td> <td align="right"> -0.84 </td> <td align="right"> -3.50 </td> <td align="right"> -0.83 </td> <td align="right"> -2.25 </td> <td align="right"> -0.18 </td> <td align="right"> -1.38 </td> <tr> <td align="center"> GLX </td> <td align="right"> -0.80 </td> <td align="right"> -3.50 </td> <td align="right"> -1.30 </td> <td align="right"> -2.20 </td> <td align="right"> -0.29 </td> <td align="right"> -0.90 </td> <tr> <td align="center"> UNK </td> <td align="right"> 0.00 </td> <td align="right"> -0.49 </td> <td align="right"> -0.14 </td> <td align="right"> -0.52 </td> <td align="right"> -0.38 </td> <td align="right"> -0.29 </td> </table> <br> <font color=#880000> <b> EXAMPLES <br> </b> </font> <table border=2 cellspacing=2 cellpading=0> <td align="left"> COMMAND </td> <td align="left"> DESCRIPTION </td> <tr> <td align="left"> sca eis <br> </td> <td align="left"> Use the scale prepared by David Eisenberg. </td> <tr> <td align="left"> sca int </td> <td align="left"> Use the experimental interface scale from <br> the Stephen White laboratory. </td> </table> <br> <font color=#880000> <b> NOTES <br> </b> </font> (1) Many hydrophobicity scales may be found in literature. However, most of these scales are mutually highly correlated. <br><br> (2) The keyword WHI (WHITE) was replaced by the keyword OCT (OCTANOL) in version 1.4 of garlic! <br><br> <font color=#880000> <b> RELATED COMMANDS <br> </b> </font> PLOT is used to draw averaged hydrophobicity and other hydrophobicity functions. color HYPHOB is used to color the structure according to hydrophobicity of residues. <br><br> <font color=#880000> <b> REFERENCES <br> </b> </font> (1) Eisenberg, D., Schwarz, E., Komaromy, M. and Wall, R. (1984). J. Mol. Biol. 179, p. 125. <br> (2) Kyte, J. and Doolittle, R. F. (1982). J. Mol. Biol. 157, p. 105. <br> (3) Wimley, W. C. and White, S. H. (1996). Nature Struct. Biol. 3, p. 842. <br> (4) Wimley, W. C., Creamer, T. P. and White, S. H. (1996). Biochemistry 35, p. 5109. <br> (5) White, S. H. and Wimley, W. C. (1998). Biochim. Biophys. Acta 1376, p 339. <br> (6) White, S. H. and Wimley, W. C. (1999). Annu. Rev. Biophys. Biomol. Struc. 28, p. 319. <br><br> <hr size="3"> </html>
