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COCOMAPS (bioCOmplexes COntact MAPS) is a web application to easily and effectively analyse and visualize the interface in biological complexes (such as protein-protein, protein-DNA and protein-RNA complexes), by making use of intermolecular contact maps.
A user-friendly interface allows the user to download input files directly from the wwPDB or upload her/his own PDB formatted files. The user is also requested to specify the chain identifiers for the molecules involved in the interaction to be analyzed. More chains can be selected for each interacting partner.
COCOMAPS output includes three different contact maps: a "classical map", a "distance range map" and a "property map" (see below). Contact maps represent a sort of fingerprint of the complex reporting crucial information in a ready-to-read form. They allow to identify uniquely and intuitively the surface of interaction, allowing to immediately discriminate between similar and different binding solutions. This is of immediate applicability in the analysis and comparison both of experimental structures of complexes sharing at least one molecular partner, and of the best scored solutions of a docking simulation.
Detailed information, organized in tables, is also provided about the interacting residues, defined on the basis of a cut-off distance that can be customized by the user, the residues at the interface, defined on the basis of the buried surface upon complex formation, and the inter-molecular H-bonds, with specification of the acceptor and donor atom. Accessible areas and H-bonds are calculated by NACCESS (Hubbard and Thornton, 1993) and HBPLUS (McDonald and Thornton, 1993), respectively.
A 3D visualization of the complex in JMol (http://www.jmol.org/) is also provided online and a ready-to-run Pymol (Delano Scientific, 2002) script, which generates a visualization of the interface, is downloadable.
COCOMAPS outputs are displayed on the results HTML page for one month and archived in a downloadable ZIP file. A link to the online resource is also emailed to the user, if requested (see Advanced Options).
COCOMAPS is freely available to the scientific community as a complementary tool in the analysis of the surface of interaction in biological complexes.
Input page:
OPTION 1: Choose this option if you want to use a biological complex present in the wwPDB.PDB code: Enter a single pdb code of the biological complex. (e.g. 2za4 )
Chain/s Molecule1: Type a white-space separated single letter/s to identify the chain/s belonging to the first interacting partner (molecule1). (e.g A or A B)
Chain Molecule2: Type a white-space separated single letter/s to identify the chain/s belonging to the second interacting partner (molecule2). (e.g C or C D)
The order of Molecule1 and Molecule2 is not influent.
OPTION 2: Choose this option if you want to upload and analyse your own PDB file/s.
1 file: Click on this option if you have only one file with the coordinates of both interacting molecules to upload.
PDB File: Click on this button to upload the PDB file from your pc.
Chain Molecule1: Type white-space separated single letter/s to identify the chain/s belonging to the first interacting partner (molecule1). (e.g A or A B)
Chain Molecule2: Type a white-space separated single letter/s to identify the chain/s belonging to the second interacting partner (molecule2). (e.g C or C D)
The order of Molecule1 and Molecule2 is not influent.
2 files: Click on this option if you have two separate PDB files for the two interacting molecules to upload.
PDB File 1: Click on this button to upload the PDB file of the first interacting molecule.
PDB File 2: Click on this button to upload the PDB file of the second interacting molecule.
Chain Molecule1: Write a white-space separated single letters to identify the chain/s belonging to the first interacting partner (PDB file1). (e.g A or A B)
Chain Molecule2: Write a white-space separated single letters to identify the chain/s belonging to the second interacting partner (PDB file2). (e.g C or C D)
The order of PDB file1 and PDB file2 is not influent. Please note that Chain Molecule1 is referred to the PDB file1, while Chain Molecule2 is referred to the PDB file 2.
Cut-off (A): This is the maximum distance value to report an atom-atom interaction. The default value is 8 Å .
Submit: Click on this button to submit the analysis
Advanced option (Optional fields)
Project Name: Optional. Any string can indentify your result. If you leave it blank, a default name will be used. Don't use white-space separated words.E-mail: Optional. If a valid e-mail address is provided, a link to a page on the server is e-mailed to the user, where she/he can access to her/his results (which are also displayed online) for one month.
Name Molecule 1: Optional. Insert the name of the first interacting molecule of the complex (e.g. barnase). Otherwise, the generic name "Molecule 1" will be used.
Name Molecule 2: Optional. Insert the name of the second interacting molecule of the complex (e.g. barstar). Otherwise, the generic name "Molecule 2" will be used.
Output page:
Download section: Clicking on it, you can download maps and table as a zipped file.Chart: Chart section includes three contact maps as .png files.
The first “classical black and white map” presents a black dot at the crossover of two residues i and j, belonging to Molecule1 and Molecule2, respectively, if any atom of the two residues are closer than the cut-off distance chosen by the user (default value being 8 Å).
2) The "distance Range map" reports inter-molecular contacts at increasing distances, as coloured dots in a white background. Red, yellow, green, and blue indicate contacts within 7 Å, 10 Å, 13 Å and 16 Å, respectively.
3) The "property map" is similar to the first one, but with each contact colored according to the physico-chemical nature of the two interacting residues, violet = hydropohilic-hydrophilic,green = hydrophobic-hydrophobic, yellow = hydrophilic-hydropholic.
The user can download the three maps, or each maps separately, clicking on the download links.
H-Bonds Table: includes a list of the intermolecular hydrogen bonds, calculated by HBPLUS (McDonald and Thornton, 1994), where the acceptor and donor atoms are specified, together with the H-X and the CA-CA distances in Å and the atom category (S = side-chain atom, M = main-chain atom). Above each column, there are possible filters to apply and arrows to order it alphabetically or numerically.
Distance Table: reports a list of all the atom pairs “in contact” (i.e. within the distance cutoff) with relative distances in Å. The hydprophobic/hydrophilic character of the corresponding residues is also specified.
Table of minimum distance: this is a short table reporting, for each pair of interacting residues, the atom pair at minimum distance. Above each column, there are possible filters to apply and arrows to order it alphabetically or numerically.
ASA Table for Molecule 1: this section includes a list of molecule1 residues at the interface, defined as those having an ASA (Accessible Surface Area) decreased by > 1.0 Å upon the complex formation. ASA values in the complex and in the isolated molecule (“free”), and the difference between them are reported for each residue. The percentage of buried surface upon complex formation is also reported.
ASA Table for Molecule 2: this section includes a list of molecule2 residues at the interface, defined as those having an ASA (Accessible Surface Area) decreased by > 1.0 Å upon the complex formation. ASA values in the complex and in the isolated molecule (“free”), and the difference between them are reported for each residue. The percentage of buried surface upon complex formation is also reported.
