Arpeggio calculates interactions between atoms of molecules of interest, in macromolecular structures from the Protein Data Bank (PDB). These molecules include proteins, nucleic acids, carbohydrates as well as small molecules.
Interactions between atoms are stored as Structural Interaction Fingerprints (SIFts) that were described first by Deng et al.. Arpeggio implements 13 different interaction types such as hydrogen bonds, halogen bonds, carbonyl interactions and others. Arpeggio can also determine and visualise amide and aromatic ring interactions. Example interaction types calculable by Arpeggio are visualised below.
Interactions between the aromatic rings of PDB residues are recorded separately and classified into nine different interaction geometries.
Interactions between single atoms and aromatic rings can be energetically favourable and are frequently found in protein structures and their complexes. All occurrences of atoms within a certain distance of an aromatic ring's centroid are recorded including their interaction geometry and classified if possible. Examples for known atom-aromatic ring interactions are visualised below.