Magnetic skyrmions are prime candidates for future spintronic devices. However, incorporating them as information carriers hinges on their interaction with defects ubiquitous in any device. Here we map from first-principles, the energy profile of single skyrmions interacting with single-atom impurities, establishing a generic shape as function of the defect's electron filling. Depending on their chemical nature, foreign 3d and 4d transition metal adatoms or surface implanted defects can either repel or pin skyrmions in PdFe/Ir(111) thin films, which we relate to the degree of filling of bonding and anti-bonding electronic states inherent to the proximity of the non-collinear magnetic structure. Similarities with key concepts of bond theories in catalysis and surface sciences imbue the universality of the shape of the interaction profile and the potential of predicting its interaction. The resulting fundamental understanding may give guidance for the design of devices with surface implanted defects to generate and control skyrmions.