Overview¶

GlyContact is an open-source Python package designed specifically for glycan structure analysis that can be entirely operated with glycan sequences (in any chosen nomenclature). It enables retrieving and processing three-dimensional glycan structures, performing sophisticated conformational analyses, and investigation of structure-function relationships.

Many functionalities within GlyContact allow users to produce and retrieve heatmap plots or overlays of glycan sequences. Below are some code examples and their associated outputs.

Glycan Contact Maps¶

Contact maps reveal the spatial relationships between monosaccharides in a glycan structure. These maps help identify which parts of the glycan are in close proximity, providing insights into potential functional regions.

from glycontact.process import get_contact_tables
# Get monosaccharide contact tables
glycan = "Gal(b1-4)GlcNAc(b1-2)Man(a1-3)[Gal(b1-4)GlcNAc(b1-2)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)[Fuc(a1-6)]GlcNAc"
contact_tables = get_contact_tables(glycan, level="monosaccharide")

from glycontact.visualize import draw_contact_map
# Visualize the first contact map
draw_contact_map(contact_tables[0], size=1.0)

png

Surface Accessibility and Flexibility¶

The solvent-accessible surface area (SASA) and flexibility of monosaccharides are crucial determinants of glycan-protein interactions. GlyContact calculates these properties and allows visualization of their distribution across the glycan structure.

from glycontact.visualize import plot_glycan_score
plot_glycan_score(glycan, attribute="SASA")

png

Glycosidic Torsion Angles¶

Glycosidic torsion angles (phi/psi) determine the overall shape of glycans. GlyContact can analyze these angles across multiple structures to identify preferred conformations, similar to protein Ramachandran plots.

from glycontact.visualize import ramachandran_plot
ramachandran_plot("GlcNAc(b1-4)GlcNAc")

png