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 unusually
large net charge or dipole moment, and how this might relate to specific
structural features of the protein, and thereby its function.
The results are displayed with jmol pictures, with the dipole and mass
moment vectors as red and grey-green lines, respectively.
Warning: the quadrapole moment and mass moment vector (RG) are being removed
from this server because their calculation is inaccurate or problematic.
This server is described in Clifford E. Felder, Jaime Prilusky, Israel Silman,
and Joel L. Sussman 2007, " A server and database for dipole moments of proteins",
Nucleic Acids Research, 35, special Web Servers Issue.
to get full descriptions of the table captions and the
the list of the average values and std. deviations
derived from the PISCES 90% homology set of 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:
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 ellipsoidal 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
databases containing this information calculated for a set of over 10000
representative, non-homologous biological unit proteins and their constituent,
unique (non-redundant) peptide chains, all with at least 50 residues,
according to the PISCES list of nonhomologous proteins to the 90%
homology level (See
http://dunbrack.fccc.edu/PISCES.php), as obtained 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
By definition the dipole vector points from the direction of net negative
charge to the direction of net positive charge. In other words, you would put
a (-) at the origin of the vector and a (+) at its end.
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.
In the pictures, the dipole vector is represented by a red line, and the
truncated mass moment vector is a short line, half red and half black. Both
vectors begin at the center-of-mass origin of the protein or chain. The origin
of the red dipole line corresponds with the net negative charge, and the far
end with the net positive charge of the dipole moment.
Note that the non-peptidyl portions of the structure have been removed, and a
new fictitious ligand representing the dipole and mass vectors has been added.
In order for the jmol pictures to
java plugin installed in your web browser. For more information about jmol, see
Ordinary jmol pictures including the non-peptide moieties can be obtained
from the RCSB PDB,
The drawn dipole vectors are scaled for large proteins. For short peptides,
select the ligand and ask for smaller atom balls and thinner bonds.
If you want to process a number of PDB entries using a script, or to link
this server from another server and automatically have it come up with the results
for a particular PDB entry, say entry 1abc, you can use URL
http://bip.weizmann.ac.il/dipol-bin/dipol2j.cgi?pdb_id=1abc If you want to display by chains and calculate the angles for residues 10 and 20, use
If the PDB-ID code specified is not in the PDB because it is obsolete, the
entry that replaces it will be used instead, automatically.