glycosciences.de - GlyVicinity - Statistical Analysis of Amino Acids in the Vicinity of Carbohydrate Residues

GlyVicinity: Analysis of Amino Acids in the Vicinity of Carbohydrate Residues contained in the Protein Data Bank (PDB)

Introduction
Besides the amino acids in sequential neighbourhood of glycosylation sites (analysed by GlySeq), those in the spatial vicinity of carbohydrate residues determine the characteristics of glycoproteins. The latter ones are of special interest for the examination of carbohydrate-binding proteins. Since carbohydrate moieties are not covalently bound in these cases, sequence analysis comparable to that for glycosylation sites is not possible there.
GlyVicinity performes statistical analyses on the types of amino acids around carbohydrate chains and on the atoms forming the closest contacts between protein and carbohydrate residues. Results are based on weekly updated datasets derived from the Protein Data Bank (PDB).

Contact: Thomas Lütteke

References

General Settings

Graphics Size:	x pixel	In this section you can set some general parameters influencing output in subsequent steps. You can adjust the size of graphics (gif or svg diagrams) and of 3D structure display to the resolution of your monitor. Structure viewer selects your preferred program to view 3D structures within the browser window.
Structure Viewer:	Jmol Chime
Viewer Size:	x pixel

Analysis Parameters

Resolution (Å)		Only data received from pdb-files with an resolution better or equal to the selected value is analysed. To switch off resolution check, put in "0.0"
Radius (Å)	-	Radius around the carbohydrate residues in which amino acids are analysed. Values may be between 0.0 and 4.0.
Chain length		Defines the minimal number of monosaccharides of which the chain a residue belongs to consists. Type in "0" to switch off chain length check.
Depth	-	Depth marks the distance of a residue from the reducing end of a carbohydrate chain. The monosaccharide located at the reducing end has detph 1, those attached to this residue have depth 2, and so on. "0" switches off depth check.

Residue

Enter directly:

or choose from list:

Chain

Type:

LINUCS:

Output:
	Text only
	Text + GIF graphic
	Text + SVG graphic ?
	Print information about avarage residue distances
	Order amino acids:

Select PDB entries:

Retrieve a list of all PDB entries matching the specifications given above. Further analysis will be done for the selected entries only.
This option enables comparison of different kind of proteins or proteins from different species.

When citing glyvicinity, 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.