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rCSU
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New version of rCSU server is being prepared. To use the old version, go here.
This server generates contact maps of proteins by means of the
CSU-related algorithms as described in the paper:
"Determination of contact maps in proteins:
a combination of structural and chemical approaches" by
K. Wolek, A. Gomez-Sicila, and M. Cieplak, published in J. Chem. Phys. The default
parameters used are
as described in this paper.
The standard CSU algorithm is described in
V. Sobolev, R. C. Wade, G. Vriend, and M. Edelman, Proteins:
Struct. Funct. Bioinf. 25: 120 (1996). The resulting contact map
is denoted as oCSU ("o" stands for the original). The improved
contact map is denoted by rCSU ("r" stands for repulsive). The rCSU
map distinguishes between the proper and destabilizing (or
repulsive) atomic contacts:
two amino acids are declared to be in contact if the number of the
proper atomic contacts is bigger than the number of the
destabilizing ones. The server also identifies the chemical nature
of the resulting residue-residue contacts. Unlike the oCSU
approach, it identifies the ionic bridges.
The input to the calculations is the PDB structure file that
can be either downloaded or pasted in. If the file
contains more that one model, you will be asked to choose which
one you intend to use. Structural water, the presence of
ligands or of nucleic acids are not taken into account.
If the file contains more than one chain then you need to specify
which chain to consider. For the interchain contacts use
the "all chains" option.
Calculations should take a few seconds depending on parameters and
structure size. If they take longer or you get empty output file, please
contact us at kwolek@ifpan.edu.pl or mc@ifpan.edu.pl.
There are several contact maps in the output file:
1) rCSU contacts together with their chemical identification,
2) oCSU contacts,
3) OV contacts.
OV is the contact map obtained through the atomic overlaps as
described in M. Cieplak and T. X. Hoang, Biophys. J. 84:475 (2003).
In the OV procedure the atoms are represented by enlarged van der Waals
spheres. The van der Waals radii used in rCSU and OV
depend on the atom's location in
the side chain as derived by J. Tsai, R. Taylor, C. Chothia, and
M. Gerstein, J. Mol. Biol 290:290 (1999). The radii used in oCSU
are simplified to a smaller set of values as used in the
paper by Sobolev et al. The enlargement factor is 1.24.
Definition of contacts used in rCSU algorithm:
| Class | I | II | III | IV | V | VI | VII | VIII | IX | X |
| I | Hb | Hb | Hb | Dc | Dc | -- | -- | -- | Hb | Hb |
| II | Hb | Dc | Hb | Dc | Dc | -- | -- | -- | Hb | Dc |
| III | Hb | Hb | Dc | Dc | Dc | -- | -- | -- | Dc | Hb |
| IV | Dc | Dc | Dc | Ph | Ph | -- | -- | -- | Dc | Dc |
| V | Dc | Dc | Dc | Ph | Ar | -- | -- | -- | Dc | Dc |
| VI | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| VII | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| VIII | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| IX | Hb | Hb | Dc | Dc | Dc | -- | -- | -- | Dc | Ib |
| X | Hb | Dc | Hb | Dc | Dc | -- | -- | -- | Ib | Dc |
Atom classes:
I -- hydrophilic - N and O atoms which can be both donor and acceptor of hydrogen bond
II -- hydrogen bond acceptor
III -- hydrogen bond donor,
IV -- hydrophobic - all C atoms not connected to N or O and not in aromatic ring
V -- aromatic - all C atoms in aromatic rings
VI -- neutral - S atoms and C atoms which
VII -- neutral-donor - C atoms
VIII -- neutral-acceptor - C atoms
IX -- positively charged - atoms with positive charge
X -- negatively charged - atoms with negative charge
Types of contacts:
Hb -- hydrogen-bond,
Ph -- hydrophobic,
Ar -- aromatic - contacts between aromatic rings
Ib -- ionic bridge - contacts created by two atoms with different charges
Dc -- destabilizing contact - contacts which are in general repulsive,
``--'' denotes negligible other contacts.