# Native contact

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{{Short description|Aspect of protein folding}}
{{More citations needed|date=January 2024}}

In [protein folding](/source/protein_folding), a '''native contact''' is a contact between the [side chain](/source/side_chain)s of two [amino acid](/source/amino_acid)s that are not neighboring in the [amino acid sequence](/source/primary_structure) (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](/source/native_state) [tertiary structure](/source/tertiary_structure).<ref>{{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 |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}}</ref><ref>{{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}}</ref> The fraction of native contacts reproduced in a particular structure is often used as a [reaction coordinate](/source/reaction_coordinate) for measuring the deviation from the native state of structures produced during [molecular dynamics](/source/molecular_dynamics) simulations <ref>{{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 }}</ref> or in benchmarks of [protein structure prediction](/source/protein_structure_prediction) methods.<ref>{{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|url-access=subscription }}</ref>

The [contact order](/source/contact_order) is a measure of the locality of a protein's native contacts;<ref name=kwp>{{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|url-access=subscription }}</ref> that is, the sequence distance between amino acids that form contacts. Proteins with low contact order are thought to fold faster<ref name=kwp/><ref>{{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}}</ref> and some may be candidates for [downhill folding](/source/downhill_folding).

== References ==
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{{DEFAULTSORT:Native Contact}}
Category:Protein structure

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Adapted from the Wikipedia article [Native contact](https://en.wikipedia.org/wiki/Native_contact) by Wikipedia contributors ([contributor history](https://en.wikipedia.org/wiki/Native_contact?action=history)). Available under [Creative Commons Attribution-ShareAlike 4.0 International](https://creativecommons.org/licenses/by-sa/4.0/). Changes may have been made.