carp: CArbohydrate Ramachandran Plot
Introduction
The "Ramachandran Plot", where backbone torsion angles are plotted against each other, is a frequently used tool to evaluate the quality of a protein 3D structure. For carbohydrate structures, linkage torsions can be evaluated in a similar way. Preferred Phi/Psi values of the torsion angles of glycosidic bonds depend strongly on the types of monosaccharides involved in the linkage, the kind of linkage (1-3, 1-4, etc) as well as the degree of branching of the structure.
CARP analyses carbohydrate data given in PDB files using the pdb2linucs algorithm. For each different linkage type a separate plot is generated. The user can choose between two sources for plot background information for comparison: data obtained from PDB (Fig.1) or GlycoMapsDB (Fig.2). GlycoMapsDB provides calculated conformational maps, which show energetically preferred regions for a specific linkage, while PDB data is based on experimentally solved structures. For seldom occuring linkages, however, PDB data is often rare, so maybe not sufficient background information for comparison will be available from this source.

Enter PDB ID:
or select file to upload:

Fig.1: Background data source PDB
Select data source for plot background:
PDB (NMR-like definition)?
PDB (crystallographic definition)
GlycoMapsDB

Select graphics type:
GIF
SVG ?

Find carbohydrates in
Assign connections by atom distances


Select structure viewer / size:
Jmol
Chime
 /  x pixel


Fig.2: Background data source GlycoMapsDB




When citing carp, please refer to:

 Lütteke T , Frank M , von der Lieth CW:
Carbohydrate Structure Suite (CSS): analysis of carbohydrate 3D structures derived from the PDB
Nucleic Acids Res 2005, 33: D242-6.

back to top

© 1997-2009 German Cancer Research Center Heidelberg, Central Spectroscopic Division, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
© 2010-2014 Justus-Liebig University Giessen, Institute of Veterinary Physiology and Biochemistry, Frankfurter Str. 100, 35392 Giessen, Germany
All rights reserved.