ProtScale

ProtScale [Reference / Documentation] allows you to compute and represent the profile produced by any amino acid scale on a selected protein.

An amino acid scale is defined by a numerical value assigned to each type of amino acid. The most frequently used scales are the hydrophobicity or hydrophilicity scales and the secondary structure conformational parameters scales, but many other scales exist which are based on different chemical and physical properties of the amino acids. This program provides 57 predefined scales entered from the literature.

Enter a UniProtKB/Swiss-Prot or UniProtKB/TrEMBL accession number (AC) (e.g. P05130) or a sequence identifier (ID) (e.g. KPC1_DROME):

Or you can paste your own sequence in the box below:

Please choose an amino acid scale from the following list. To display information about a scale (author, reference, amino acid scale values) you can click on its name.

 Molecular weight                         Number of codon(s)
 Bulkiness                                Polarity / Zimmerman
 Polarity / Grantham                      Refractivity
 Recognition factors                      Hphob. / Eisenberg et al.
 Hphob. OMH / Sweet et al.                Hphob. / Hopp & Woods
 Hphob. / Kyte & Doolittle                Hphob. / Manavalan et al.
 Hphob. / Abraham & Leo                   Hphob. / Black
 Hphob. / Bull & Breese                   Hphob. / Fauchere et al.
 Hphob. / Guy                             Hphob. / Janin
 Hphob. / Miyazawa et al.                 Hphob. / Rao & Argos
 Hphob. / Roseman                         Hphob. / Tanford
 Hphob. / Wolfenden et al.                Hphob. / Welling & al
 Hphob. HPLC / Wilson & al                Hphob. HPLC / Parker & al
 Hphob. HPLC pH3.4 / Cowan                Hphob. HPLC pH7.5 / Cowan
 Hphob. / Rf mobility                     HPLC / HFBA retention
 HPLC / TFA retention                     Transmembrane tendency
 HPLC / retention pH 2.1                  HPLC / retention pH 7.4
 % buried residues                        % accessible residues
 Hphob. / Chothia                         Hphob. / Rose & al
 Ratio hetero end/side                    Average area buried
 Average flexibility                      alpha-helix / Chou & Fasman
 beta-sheet / Chou & Fasman               beta-turn / Chou & Fasman
 alpha-helix / Deleage & Roux             beta-sheet / Deleage & Roux
 beta-turn / Deleage & Roux               Coil / Deleage & Roux
 alpha-helix / Levitt                     beta-sheet / Levitt
 beta-turn / Levitt                       Total beta-strand
 Antiparallel beta-strand                 Parallel beta-strand
 A.A. composition                         A.A. comp. in Swiss-Prot
 Relative mutability                     
Window size:
Relative weight of the window edges compared to the window center (in %):
Weight variation model (if the relative weight at the edges is < 100%): linear exponential
Do you want to normalize the scale from 0 to 1? yes no

If you need more information about how to set these parameters, please click here.