Native contact explained

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.^{[1] [2]} The fraction of native contacts reproduced in a particular structure is often used as a reaction coordinate for measuring the deviation from the native state of structures produced during molecular dynamics simulations ^[3] or in benchmarks of protein structure prediction methods.^[4]

The contact 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 for downhill folding.

Notes and References

1. Taketomi . H. . Ueda . Y. . Gō . N. . 1975 . Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions . International Journal of Peptide and Protein Research . 7 . 6 . 445–459 . 0367-8377 . 1201909.
2. Web site: Demharter . Samuel . 2014-03-27 . native contacts Oxford Protein Informatics Group . 2024-01-22 . en-US.
3. Best . Robert B. . Hummer . Gerhard . Eaton . William A. . 2013-10-29 . Native contacts determine protein folding mechanisms in atomistic simulations . Proceedings of the National Academy of Sciences . en . 110 . 44 . 17874–17879 . 10.1073/pnas.1311599110 . 0027-8424 . 816414 . 24128758.
4. Onuchic . José Nelson . Socci . Nicholas D. . Luthey-Schulten . Zaida . Wolynes . Peter G. . 1996-12-01 . Protein folding funnels: the nature of the transition state ensemble . Folding and Design . 1 . 6 . 441–450 . 10.1016/S1359-0278(96)00060-0 . 1359-0278.
5. Plaxco . Kevin W . Simons . Kim T . Baker . David . 1998-04-10 . Contact order, transition state placement and the refolding rates of single domain proteins11Edited by P. E. Wright . Journal of Molecular Biology . 277 . 4 . 985–994 . 10.1006/jmbi.1998.1645 . 0022-2836.
6. Bonneau . Richard . Ruczinski . Ingo . Tsai . Jerry . Baker . David . August 2002 . Contact order and ab initio protein structure prediction . Protein Science . en . 11 . 8 . 1937–1944 . 10.1110/ps.3790102 . 0961-8368 . 2373674 . 12142448.