Computational tools for the analysis of heteroatom groups and their neighbours in protein tertiary structure

A number of Protein Data Bank (PDB) entries contain heteroatoms defined as HETATM. These include the atomic co-ordinates mainly for heteroatom groups, such as cofactors, coenzymes, prosthetic groups, metal ions, sugars, drugs, peptides, heavy-atom derivatives, non-standard amino acid residues/nucleotides, water molecules and so on. In order to evaluate the different heteroatom (Het) groups and their distribution in protein tertiary structure, we have extracted these from all proteins in the PDB and provided the data in an easily accessible format at the following website. The data can be queried on the PDB code, protein name/description, Het Group code or Het Group name. Further, we have also developed a web-based software application that reports neighbouring atoms evaluated by a "user-defined" distance cut-off value (in Angstrom units), either between a specific Het Group or all Het Groups in a given PDB with amino acid residues and water molecules in the corresponding protein, or neighbours for only all the amino acid residues in the given PDB with respect to Het Groups and water molecules. Together, the database and software applications are useful to gather information that can be further analyzed in order to obtain insights into the preferred interactions of heteroatom groups in proteins, study their binding mode, design novel molecules or to annotate protein function.