rCSU
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, submitted to J. Chem. Phys. [link to the manuscript]. 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.

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Radii used by: Tsai et al Sobolev and Edelman
Fibonacci number (between 10 and 20):
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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.