native contact

{{Short description|Aspect of protein folding}}

{{More citations needed|date=January 2024}}

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.{{Cite journal |last1=Taketomi |first1=H. |last2=Ueda |first2=Y. |last3=Gō |first3=N. |date=1975 |title=Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions |url=https://pubmed.ncbi.nlm.nih.gov/1201909/ |journal=International Journal of Peptide and Protein Research |volume=7 |issue=6 |pages=445–459 |doi=10.1111/j.1399-3011.1975.tb02465.x |issn=0367-8377 |pmid=1201909}}{{Cite web |last=Demharter |first=Samuel |date=2014-03-27 |title=native contacts {{!}} Oxford Protein Informatics Group |url=https://www.blopig.com/blog/tag/native-contacts/ |access-date=2024-01-22 |language=en-US}} 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 {{Cite journal |last1=Best |first1=Robert B. |last2=Hummer |first2=Gerhard |last3=Eaton |first3=William A. |date=2013-10-29 |title=Native contacts determine protein folding mechanisms in atomistic simulations |journal=Proceedings of the National Academy of Sciences |language=en |volume=110 |issue=44 |pages=17874–17879 |doi=10.1073/pnas.1311599110 |doi-access=free |issn=0027-8424 |pmc=816414 |pmid=24128758|bibcode=2013PNAS..11017874B }} or in benchmarks of protein structure prediction methods.{{Cite journal |last1=Onuchic |first1=José Nelson |last2=Socci |first2=Nicholas D. |last3=Luthey-Schulten |first3=Zaida |last4=Wolynes |first4=Peter G. |date=1996-12-01 |title=Protein folding funnels: the nature of the transition state ensemble |url=https://www.sciencedirect.com/science/article/pii/S1359027896000600 |journal=Folding and Design |volume=1 |issue=6 |pages=441–450 |doi=10.1016/S1359-0278(96)00060-0 |pmid=9080190 |issn=1359-0278}}

The contact order is a measure of the locality of a protein's native contacts;{{Cite journal |last1=Plaxco |first1=Kevin W |last2=Simons |first2=Kim T |last3=Baker |first3=David |date=1998-04-10 |title=Contact order, transition state placement and the refolding rates of single domain proteins11Edited by P. E. Wright |url=https://www.sciencedirect.com/science/article/pii/S002228369891645X |journal=Journal of Molecular Biology |volume=277 |issue=4 |pages=985–994 |doi=10.1006/jmbi.1998.1645 |pmid=9545386 |issn=0022-2836}} that is, the sequence distance between amino acids that form contacts. Proteins with low contact order are thought to fold faster{{Cite journal |last1=Bonneau |first1=Richard |last2=Ruczinski |first2=Ingo |last3=Tsai |first3=Jerry |last4=Baker |first4=David |date=August 2002 |title=Contact order and ab initio protein structure prediction |journal=Protein Science |language=en |volume=11 |issue=8 |pages=1937–1944 |doi=10.1110/ps.3790102 |issn=0961-8368 |pmc=2373674 |pmid=12142448}} and some may be candidates for downhill folding.