JaMBW Chapter 3.1.6

Isoelectric Plot


Given a sequence of aminoacids, this program computes and plots the average net charge of the entire peptide, as function of the pH.

Mode of operation

The program uses 3 windows: the top one should be filled from the user, with the sequence of interest, the small window beneath is used by the program to return messages to the user, while the bottom one visualizes the results of the analysis. The following steps must be performed to use this program:
  1. Sequence input
  2. Compute
    Once the sequence is placed in the top window, by pressing the "COMPUTE" button the Net Charge of the entire protein is computed as function of the pH, at 0.5 unit interval and then visualized. The Isoelectric point is searched by computing the Net Charge at very fine grade. Its value, that is the pH at which the Net Charge of the entire polypeptide is zero, is displayed with red cross-bars and numerically is returned in the text window above the chart.

A Java-enabled browser would have in this place a window similar to this picture:

How to understand its output


  1. IUPAC-IUB Joint Commission on Biochemical Nomenclature (1984)Nomenclature and symbolism for Amino Acids and Peptides, Eur.J.Biochem., 138, 9-37
  2. Lehninger A., (1972) Biochimie Ed: Flammarion
  3. http://www-biol.univ-mrs.fr/d_abim/d_docs/doc-tab-pk.htmlTables of pK values.

Author:Luca I.G. TOLDO, Edition date: 28 February 1997