PDB Ligand Contacts Track Settings
 
Potential contact residues in PDB structures of viral proteins   (All Genes and Gene Predictions tracks)

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Data last updated: 2020-07-19 10:48:09


new Note: Released Jul. 28, 2020

Description

This track shows potential contact residues for ligands, inferred from structures in the PDB database by Alastair Fyfe, UCSC.

Display Conventions and Configuration

Genomic locations of contact residues are highlighted with thick blocks, that look identical to exons. Contact residues of the same PDB structure are connected by thin intron lines.

To display the 3D structure viewer with these contact residues highlighted, follow the outlink at the top of the details page of any feature.

Methods

PDB SEQRES protein sequences were aligned to the genome with tblastn. Ligands were determined manually, all amino acids closer than 3.5 Angstroms were obtained as described below. The positions of these close amino acids on the genome were determined using the tblastn alignment and are highlighted on the genome with exon blocks.

The find nearby amino acids, inter-atom distances were calculated with the libraries GEMMI and Clipper at a threshold of 3.5 . Distances between atoms whose proximity is due to crystal packing or symmetry are listed but cannot be inspected in the viewer. These contacts are flagged by a check in the "Symm?" column. They include atoms in adjacent unit cells and atoms brought into proximity by application of a symmetry transformation to the asymmetric unit (ASU), but not atoms related by non-crystallographic symmetry (NCS).

For each amino acid in the contact table the "Codon" column gives the codon's nucleotide values and position in the NC_045512.2 reference sequence. Amino acids that could not be aligned to the reference, for example insertions or deletions engineered to facilitate protein expression, are flagged by "-".

Data Access

The raw data can be explored interactively with the Table Browser or combined with other datasets in the Data Integrator tool. For automated analysis, the genome annotation is stored in a bigBed file that can be downloaded from the download server.

Annotations can be converted from binary to ASCII text by our command-line tool bigBedToBed. Instructions for downloading this command can be found on our utilities page. The tool can also be used to obtain features within a given range without downloading the file, for example:

bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/wuhCor1/bbi/contacts.bb -chrom=NC_045512v2 -start=0 -end=29902 stdout

Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.

Credits

Track created by Alastair Fyfe, UCSC, mentored by David Haussler.