About Arpeggio
Interatomic Interaction Types
Summary
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.
Structural Interaction Fingerprints (SIFts)
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.
Hydrogen bonds
Water-mediated hydrogens bonds are supported in CREDO as well.
Weak hydrogen bonds
Halogen bonds
Ionic interactions
Metal complexes
Hydrophobic interactions
Carbonyl interactions
Interactions between aromatic rings
Interactions between the aromatic rings of PDB residues are recorded separately and classified into nine different interaction geometries.
Atom-aromatic ring interactions
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.
Carbon-pi
Here, the atom acts as a weak hydrogen bond donor and the pi electrons from the aromatic ring as acceptor.
Cation-pi
Here, the atom is positively ionisable and forms an electrostratic interaction with the negatively charged pi-electron cloud.
Donor-pi
Here, the atom is a hydrogen bond donor that can form a hydrogen bond with the pi-electrons that act as acceptor.