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Characteristics of protein residue-residue contacts and their application in contact prediction.

Wozniak PP, Kotulska M - J Mol Model (2014)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biomedical Engineering and Instrumentation, Wroclaw University of Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wroclaw, Poland, pawel.p.wozniak@pwr.edu.pl.

ABSTRACT
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.

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Related in: MedlinePlus

Values of Wc for different amino acid types at cutoff 12 Å. Class alpha and separation 7 (dark blue), class alpha and separation 15 (bright blue), class beta and separation 7 (red), class beta and separation 15 (orange). Standard deviations for every Wc value were added to the figure
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Fig5: Values of Wc for different amino acid types at cutoff 12 Å. Class alpha and separation 7 (dark blue), class alpha and separation 15 (bright blue), class beta and separation 7 (red), class beta and separation 15 (orange). Standard deviations for every Wc value were added to the figure

Mentions: Figures 4 and 5 present bar plots of Wc values (see Amino acids frequency of forming contact sites, Eq. 1) for different amino acid types and contact sites parameters. Comparison between results for class alpha and results for class beta shows that their characteristics are similar. The only difference is a higher level reached by bars for class beta. It stems from the fact that the occurrence of contact sites in class beta is higher than in class alpha. Furthermore, the change of cutoff and separation parameters affects Wc values for all amino acids in the same way. With the increase of the cutoff values, the Wc values grow for all amino acids. The difference between bar heights for two adjoining amino acids on the x-axis remains the same. However, similarly to what was observed in the previous paragraph, the change of the separation has lower impact on contact sites occurrence than a change of the cutoff.Fig. 4


Characteristics of protein residue-residue contacts and their application in contact prediction.

Wozniak PP, Kotulska M - J Mol Model (2014)

Values of Wc for different amino acid types at cutoff 12 Å. Class alpha and separation 7 (dark blue), class alpha and separation 15 (bright blue), class beta and separation 7 (red), class beta and separation 15 (orange). Standard deviations for every Wc value were added to the figure
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4221654&req=5

Fig5: Values of Wc for different amino acid types at cutoff 12 Å. Class alpha and separation 7 (dark blue), class alpha and separation 15 (bright blue), class beta and separation 7 (red), class beta and separation 15 (orange). Standard deviations for every Wc value were added to the figure
Mentions: Figures 4 and 5 present bar plots of Wc values (see Amino acids frequency of forming contact sites, Eq. 1) for different amino acid types and contact sites parameters. Comparison between results for class alpha and results for class beta shows that their characteristics are similar. The only difference is a higher level reached by bars for class beta. It stems from the fact that the occurrence of contact sites in class beta is higher than in class alpha. Furthermore, the change of cutoff and separation parameters affects Wc values for all amino acids in the same way. With the increase of the cutoff values, the Wc values grow for all amino acids. The difference between bar heights for two adjoining amino acids on the x-axis remains the same. However, similarly to what was observed in the previous paragraph, the change of the separation has lower impact on contact sites occurrence than a change of the cutoff.Fig. 4

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biomedical Engineering and Instrumentation, Wroclaw University of Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wroclaw, Poland, pawel.p.wozniak@pwr.edu.pl.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus