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
For backward compatability, the old server is located at
For the new version of this server with jmol molecular pictures and dipole
If you don't know the id-code for your protein,
use the PDB Browser
to find it.
Please note the following:
- 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
- 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
- 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.
- 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.
- 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
- 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.
- 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.
- This server is limited to proteins up to 200,000 heavy protein atoms and
10000 residues; larger proteins will produce unpreditable results.
- An option is provided to analize the protein by individual peptide strands,
instead of one overall calculation encompassing the entire complex of unique
- 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.
- 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.
- 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