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.

Revised Version: Corrected Quadrapole Moment, User can enter his own data.

For an overview of this server's purpose, please click here. For backward compatability, the old server is located at http://bioportal.weizmann.ac.il/dipol/dipol.html

For the new version of this server with jmol molecular pictures and dipole vectors, click here.

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

Alternatively, if the above box is blank, you can enter your own data in PDB format, at least the HEADER and ATOM records, and ending in TER and END RECORDS here:

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 PISCES 90% homology set of 9249 proteins from the OCA browser:

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 the protein, 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.

  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 a set of 9249 representative proteins according to the PISCES list of nonhomologous proteins to the 90% homology level (See . http://dunbrack.fccc.edu/PISCES.php), as obtained on 2 May 2005 from the OCA browser at http://bioportal.weizmann.ac.il/oca/

  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, metals, hetero-atoms and groups and solvent are all ignored in this calculation.

  5. All of the peptide chains present explicitly in the specified PDB entry's ATOM records are used in the calculation. Symmetry-related chains or coordinates that comprise the complete X-ray crystallographic or biological structure are not included.

  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 200,000 heavy protein atoms and 10000 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. The quadrapole moments are now calculated according to the formula, for each atom i, Qx(i) = 0.5q(i)*( 3x(i)**2 - r(i)**2 ), and similar for Qy and Qz, where q(i) is the atom's partial charge, x(i) is its X-coordinate and r(i) is its distance from the center-of-mass origin.

  12. Note: the database averages have not been updated since 2 May 2005, 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