A non-redundant dataset of inter-residue lysine-lysine solvent accessible surface distances in homo-oligomeric protein complexes

Aljaž Gaber

doi:10.1016/j.dib.2019.104834

A non-redundant dataset of inter-residue lysine-lysine solvent accessible surface distances in homo-oligomeric protein complexes

Data Brief. 2019 Nov 18:28:104834. doi: 10.1016/j.dib.2019.104834. eCollection 2020 Feb.

Author

Aljaž Gaber¹

Affiliation

¹ Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana SI 1000, Slovenia.

Abstract

This article contains inter-residue solvent accessible surface distances between lysines in a comprehensive dataset homo-oligomeric protein complex structures, downloaded from 3D Complex database. Solvent Accessible Surface Distances were calculated with Jwalk algorithm. To avoid unnecessary redundancy due to symmetry, we calculated only distances originating from the first subunit of each protein complex. Redundancy was further reduced by including only the shortest of the two possible inter-subunit alternatives in the final non-redundant dataset. For each protein complexes we also calculated weight ob subunits, number of lysines radius of gyration and average distances. This data can be used for structural analyses of homo-oligomeric protein complexes and for further optimization of distance-based restraints, such as those based on data obtained from chemical cross-linking coupled with mass spectrometry.

Keywords: Chemical cross-linking; Homo-oligomers; Solvent accessible surface distances.