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Inprotein folding, anative contact is a contact between theside chains of twoamino acids that are not neighboring in theamino 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'snative statetertiary structure.[1][2] The fraction of native contacts reproduced in a particular structure is often used as areaction coordinate for measuring the deviation from the native state of structures produced duringmolecular dynamics simulations[3] or in benchmarks ofprotein structure prediction methods.[4]
Thecontact order is a measure of the locality of a protein's native contacts;[5] that is, the sequence distance between amino acids that form contacts. Proteins with low contact order are thought to fold faster[5][6] and some may be candidates fordownhill folding.
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