Note: Released Jul. 28, 2020
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.
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
at a threshold of 3.5 Å. 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).
each amino acid in the contact table the "Codon" column gives the codon's
nucleotide values and position in the
sequence. Amino acids that could not be aligned to the reference, for example
insertions or deletions engineered to facilitate protein expression, are
flagged by "-".
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.
be converted from binary to ASCII text by our command-line tool bigBedToBed.
Instructions for downloading this command can be found on our
The tool can also be used to obtain features within a given range without downloading the file,
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.
Track created by Alastair Fyfe, UCSC, mentored by David Haussler.