In protein folding, a native contact is a contact between the side chains of two amino acids that are not neighboring in the amino acid sequence (i.e., they are more than four residues apart in the primary sequence in order to remove trivial i to i+4 contacts along alpha helices) but are spatially close in the protein's native state tertiary structure.
In protein folding, a native contact is a bond between two amino acids that aren't next to each other in the protein's linear sequence, but are close together when the protein folds into its final shape.