Web Server to Calculate Dipole Moments of Proteins

Clifford Felder and Joel Sussman, Dept. of Structural Biology
Weizmann Institute, 761000 Rehovot, Israel

With this server you can discover if your protein might have an unusally large net charge or dipole moment, and how this might relate to specific structural features of the protein, and thereby its function.

For an overview of this server's purpose, please click here.

This is an OLD version of the server. For a newer version, click http://bioportal.weizmann.ac.il/dipol/dipole.html.

Please enter PDB-ID Code of the protein you want to analize:

Click here to calulate the dipole for each peptide strand.

Optionally enter a string of up to 20 residues, separated by commas, for which you want the dipole angles calculated:

Click here to run calculation:

Click here to get the list of the average values and std. deviations derived from the PDB_select set of over 1000 proteins:

If you don't know the id-code for your protein, use the PDB Browser to find it.

Please note the following:

  1. The following information are returned: number of heavy atoms used, number of residues, mean radius of gyration, overall shape (spherical, spherical, prolate or oblate ellpsoidal or other), numbers of positively and negatively charges residues, net molecular charge, molecular dipole moment in Debyes, quadrapole moment, and the ratios of charge and of dipole moment over number of atoms. Also returned is the overall protein shape, spherical, prolate or oblate ellipsoidal, or other elongated.

  2. Besides providing this information for the particular protein requested, the server compares them against the corresponding average values from a database containing this information calculated for over 1000 proteins, according to the PDB-select list by Hobyuhm and Sander of EMBL-Heidelberg up to 45%? sequence identity.

  3. What this server returns is the number of standard deviation units the given value for your protein is above (+) or below (-) the average value. While values close to 0. indicate an average behavior, those close to +/- 1. deviate significantly from the average. Values of +/- 2. or more deviate very significantly, and if it is the charge, dipole or quadrapole moment, indicates an unusual property that may have a special function.

  4. Only the non-hydrogen atoms of the standard amino acids of the protein itself are included in the dipole calculation. DNA, RNA, hetero-atoms and groups and solvent are all ignored in this calculation.

  5. Only that portion of the structure comprising the unique set of polypeptide strands is included in the calculation. Duplicate strands are ignored. This is to avoid the problem of some PDB entries including full biological units while others have just partial units.

  6. The Parse set of partial atomic charges is used. To compensate the absence of backbone amino hydrogens HN in alpha helices, the charges of main chain atoms C and O are doubled.

  7. All GLU, ASP, LYS, ARG and C- and N-termini residues are 100% ionized, and all other residues are completely non-ionized. Note that N-terminus GLU and ASP and C-terminus LYS and ARG residues are considered uncharged, though they are Zwitterionic. N-terminus LYS and ARG and C-terminus GLU and ASP are counted like two residues.

  8. This server is limited to proteins up to 20,000 heavy protein atoms and 5000 residues; larger proteins will produce unpreditable results.
  9. An option is provided to analize the protein by individual peptide strands, instead of one overall calculation encompassing the entire complex of unique peptide strands.

  10. You can also obtain the angle between the dipole moment vector and the Beta carbon of one or more residues that you can specify. This can let you know how the dipole moment lines up against key structural or binding regions of the protein, and might offer a clue to an electrostatic role assisting in the binding of certain substrates or inhibitors.

  11. Note: the database averages have not been updated since 9 March 2000, and there is no plan to update them in the forseable future.

If you have any questions, please feel free to email me at Clifford.Felder@weizmann.ac.il