A description of the interaction types used in the CREDO database can be found in the table below. All images have been recreated using the PyMOL interface of the credoscript API. The visualisation of bonds, i.e. dash gap, dash color, etc. can be configured in the credo.ini configuration file. Besides the types listed below, interactions are also distinguished by distance only into covalent (inter-atomic distance is less than or equal to the sum of the covalent radii), van der Waals clashes (distance less than or equal to the sum of the van der Waals radii) and van der Waals (distance less than or equal to van der Waals radii + 0.5A). The maximum allowed distance is 5.0A for proximal contacts. Interactions are not mutually exclusive, i.e. more than one interaction can be set in the interaction vector at the same time (e.g. hydrogen bonds and ionic interactions).

Visualisation	Description
	Metal complexes: interacting atoms are considered to form a metal complex if one atom is a metal (usually the ligand) and the other a hydrogen bond acceptor and the inter-atomic distance equal to or less than 2.8A. From Marcou, G. & Rognan, D. Optimizing fragment and scaffold docking by use of molecular interaction fingerprints. Journal of Chemical Information and Modeling 47, 195-207 (2007)
	Cation-Pi interactions: These interaction occur where the distance between a positively ionisable atom and the centroid of an aromatic ring is equal to or less than 4.0A and the arcsin of the angle between the normal vector of the plane and the vector between the ionisable atom and the centroid is equal to or greater than 45 degrees.
	Aromatic interactions: Ring interactions are considered aromatic if the distance between their centroids is less than or equal to 4.5A and the ring system is aromatic. The interaction geometry is further classified into a combination of EDGE,FACE,OFFSET,TILTED according to Chakrabarti, P. & Bhattacharyya, R. Geometry of nonbonded interactions involving planar groups in proteins. Progress in Biophysics and Molecular Biology 95, 83-137 (2007).
	Donor-Pi interactions: These interactions are recorded if the distance between a hydrogen bond donor and the centroid of an aromatic ring is equal to or less than 4.0A and the arcsin of the angle between the normal vector of the plane and the vector between the donor atom and the centroid is equal to or greater than 45 degrees. From Desiraju, G. R. & Steiner, T. The Weak Hydrogen Bond In Structural Chemistry and Biology, vol. 9 (Oxford University Press, Oxford, 2001)
	Carbon-Pi interactions: These interaction occur where the distance between a weak hydrogen bond donor and the centroid of an aromatic ring is equal to or less than 4.0A and the arcsin of the angle between the normal vector of the plane and the vector between the weak donor atom and the centroid is equal to or greater than 60 degrees.
	Carbonyl interactions: Interactions are classified as carbonyl interactions if one of the atoms is a carbonyl carbon, the other a carbonyl oxygen and the inter-atomic distance equal to or less than 3.6A. Taken from Allen, F. H., Baalham, C. A., Lommerse, J. P. M. & Raithby, P. R. Carbonyl-carbonyl interactions can be competitive with hydrogen bonds. Acta Crystallographica Section B 54, 320-329 (1998)
	Hydrogen bonds: Interactions between atoms identified as hydrogen bonds acceptors and donors are classified as hydrogen bonds if the inter-atomic distance is less than or equal to 3.9A and the angle between the donor atom, the hydrogen and the acceptor is greater than or equal to 90 degrees. Hydrogen atoms are automatically added with the help of the OEChem toolkit in order to calculate these angles. (Based on HBPLUS)
	Weak hydrogen bonds (Ch...O): Interactions between atoms identified as hydrogen bonds acceptors and weak donors are classified as weak hydrogen bonds if the inter-atomic distance is less than or equal to 3.8A and the angle between the donor atom, the hydrogen and the acceptor is greater than or equal to 130 degrees. Hydrogens are automatically added with the help of the OEChem toolkit in order to calculate these angles. From Pierce, A. C., Sandretto, K. L. & Bemis, G. W. Kinase inhibitors and the case for ch..o hydrogen bonds in protein-ligand binding. Proteins: Structure, Function, and Genetics 49, 567-576 (2002)
	Hydrophobic interactions: Interactions between hydrophobic atoms are classified as hydrophobic contacts if the inter-atomic distance is less than or equal to 4.5A. From Marcou, G. & Rognan, D. Optimizing fragment and scaffold docking by use of molecular interaction fingerprints. Journal of Chemical Information and Modeling 47, 195-207 (2007)
	Water-mediated hydrogen bonds: These interactions are recorded if a water molecule (oxygen atom) with a B factor less than or equal to 30.0 is in hydrogen bond distance of both a ligand and a protein atom.
	Halogen bonds: Definition taken from Voth, A. R., Hays, F. A. & Ho, P. S. Directing macromolecular conformation through halogen bonds. Proceedings of the National Academy of Sciences of the United States of America 104, 6188-6193 (2007)
	Ionic interactions: Interactions are classified as ionic if the distance between a positively ionisable and a negative ionisable atom (based on SMARTS queries) is less than or equal to 4.0A thus not dependent on the protonation state.