Fig. 1: GlyContact is a powerful platform to process and analyze glycan 3D structures across multiple conformers.

a Schematic overview of the main capabilities of GlyContact. Aided by functionality from glycowork¹⁵, GlyContact extracts glycan-relevant information from PDB files and then can be used to analyze coordinates within and across structures, as well as calculate biophysical parameters, from solvent-accessible surface area (SASA) to monosaccharide conformations, as well as glycan 3D alignments. b Monosaccharide contact map of example glycolipid. Across all beta conformers of the shown glycan, using the draw_contact_map and inter_structure_variability_table functions, we compared how stable the contacts between two monosaccharides were across conformers. c Calculating monosaccharide-level SASA values. Using the plot_glycan_score function, we calculated SASA values for all monosaccharides of the shown glycan (weighted and averaged across its beta conformers), mapped the values to the glycan graph, and visualized them via GlycoDraw¹⁷ as normalized SASA values (0-1) in the form of a color gradient. d Calculating monosaccharide-level flexibilities. Similar to (c), we used the plot_glycan_score function to visualize the distance-based flexibility, weighted across beta conformers, of each monosaccharide for an example structure. e Conformational and torsion angle analysis of example structure. For a single alpha-conformer of the disialyl-T antigen, we used the get_ring_conformations function to obtain ring puckering (Q), polar angle (θ), and ring conformations (Conf) for each monosaccharide and the get_glycosidic_torsions function to obtain the torsion angles (φ, ψ, ω) for all disaccharide connections. f Aligning glycan structures. Using the superimpose_glycans and plot_superimposed_glycans functions, we visualized the best alignment between all conformers of sialyl-Lewis A (blue) and sialyl-Lewis X (gray), including their root mean square distance (RMSD) in Å. All glycans in this work have been drawn with GlycoDraw¹⁷ in the Symbol Nomenclature For Glycans (SNFG).