CARP - CArbohydrate Ramachandran Plot - Help page
CARP is dedicated to evaluate linkage torsion agles between carbohydrate residues - comparable to the Ramachandran Plot used for protein backbone torsion angles.
InputInput is either a PDB id (e.g. 1AGM, 1CKL, ...) or a file in PDB format uploaded from a local PC. Using pdb2linucs, the given file is searched for carbohydrates and linkage torsions are analysed.
Background data sourceSince carbohydrate linkage torsions depend on the monosaccharides involved and on the kind of linkage, CARP generates a separate plot for each linkage type. To be able to evaluate the determined torsion angles, one needs data, to which they are compared. Here, the user can choose between to data sources:
Protein Data Bank.
This option uses scattered plots generated by GlyTorsion as plot backgrounds. Like in GlyTorsion, two different kinds of angel definitions can be chosen: NMR-like or crystallographic. (more info).
The amount of data available for the scattered plots depends on the occurrence of the specific linkage type in PDB entries. The more frequent a linkage is, the more data is available, of course.
Alternatively, plot backgrounds can be obtained from the GlycoMapsDB, a database of conformational maps generated from MD-simulation data.
GlycoMaps are only available for NMR-like definition of torsion angles.
For each map, a direct link to the respective GlycoMapsDB entry is established to get details on the used map. If more than one map is found in the database for the actual linkage, a link to a list of all available maps to choose from is offered.
Background source PDB Background source GlycoMapsDB
- Protein Data Bank.
Graphics TypePlots are generated by CARP either in SVG or in GIF file format. SVG graphics are scalable without quality loss (more info). In this graphics format, the user can click on a cross representing a linkage to view the corresponding structure using the Java applet Jmol or the Chime plugin.
To date, however, SVG files are not displayed by the browsers themselves, so that a plugin is needed. Therefore, if you do not have that plugin installed, the GIF format is recommended.
Further outputBelow each plot further information about each included linkage is displayed:
- The IUPAC-representation of the carbohydrate chain the linkage belongs to.
- The path from the reducing end to the respective linkage (to be able to distinguish linkages of the same type within one chain).
- The PDB residue names of the monosaccharides involved in the linkage. Clicking on these names yields the same structure view as clicking on a linkage within an SVG graphic (see above: ⇒ Graphics Type).
- The numerical values of the phi and psi angle for this linkage.
CARP input form