Characteristics of protein residue-residue contacts and their application in contact prediction
Contact sites between amino acids characterize important structural features of a protein. We investigated characteristics of contact sites in a representative set of proteins and their relations between protein class or topology. For this purpose, we used a non-redundant set of 5872 protein domains...
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| Format: | Online |
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Springer Berlin Heidelberg
2014
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4221654/ |
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pubmed-42216542014-11-11 Characteristics of protein residue-residue contacts and their application in contact prediction Wozniak, Pawel P. Kotulska, Malgorzata Original Paper Contact sites between amino acids characterize important structural features of a protein. We investigated characteristics of contact sites in a representative set of proteins and their relations between protein class or topology. For this purpose, we used a non-redundant set of 5872 protein domains, identically categorized by CATH and SCOP databases. The proteins represented alpha, beta, and alpha+beta classes. Contact maps of protein structures were obtained for a selected set of physical distances in the main backbone and separations in protein sequences. For each set a dependency between contact degree and distance parameters was quantified. We indicated residues forming contact sites most frequently and unique amino acid pairs which created contact sites most often within each structural class. Contact characteristics of specific topologies were compared to the characteristics of their protein classes showing protein groups with a distinguished contact characteristic. We showed that our results could be used to improve the performance of recent top contact predictor — direct coupling analysis. Our work provides values of contact site propensities that can be involved in bioinformatic databases. Springer Berlin Heidelberg 2014-11-06 2014 /pmc/articles/PMC4221654/ /pubmed/25374390 http://dx.doi.org/10.1007/s00894-014-2497-9 Text en © The Author(s) 2014 Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Wozniak, Pawel P. Kotulska, Malgorzata |
| spellingShingle |
Wozniak, Pawel P. Kotulska, Malgorzata Characteristics of protein residue-residue contacts and their application in contact prediction |
| author_facet |
Wozniak, Pawel P. Kotulska, Malgorzata |
| author_sort |
Wozniak, Pawel P. |
| title |
Characteristics of protein residue-residue contacts and their application in contact prediction |
| title_short |
Characteristics of protein residue-residue contacts and their application in contact prediction |
| title_full |
Characteristics of protein residue-residue contacts and their application in contact prediction |
| title_fullStr |
Characteristics of protein residue-residue contacts and their application in contact prediction |
| title_full_unstemmed |
Characteristics of protein residue-residue contacts and their application in contact prediction |
| title_sort |
characteristics of protein residue-residue contacts and their application in contact prediction |
| description |
Contact sites between amino acids characterize important structural features of a protein. We investigated characteristics of contact sites in a representative set of proteins and their relations between protein class or topology. For this purpose, we used a non-redundant set of 5872 protein domains, identically categorized by CATH and SCOP databases. The proteins represented alpha, beta, and alpha+beta classes. Contact maps of protein structures were obtained for a selected set of physical distances in the main backbone and separations in protein sequences. For each set a dependency between contact degree and distance parameters was quantified. We indicated residues forming contact sites most frequently and unique amino acid pairs which created contact sites most often within each structural class. Contact characteristics of specific topologies were compared to the characteristics of their protein classes showing protein groups with a distinguished contact characteristic. We showed that our results could be used to improve the performance of recent top contact predictor — direct coupling analysis. Our work provides values of contact site propensities that can be involved in bioinformatic databases. |
| publisher |
Springer Berlin Heidelberg |
| publishDate |
2014 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4221654/ |
| _version_ |
1613152748389269504 |