N U C P L O T manual

7. Missing bonds

There are several possible explanations:

a) Miscalculation of H-bond by HBPLUS

As mentioned in the introduction, NUCPLOT uses a list of bonds supplied by the HBPLUS program by default. In this case, HBPLUS sometimes gives incorrect results as, when the program encounters a ligand, residue or base it does not recognize, it may be unable to correctly calculate all the hydrogen bonds the interacting entity makes.

HBPLUS does allow the user to define ligands in a separate input file as described in section 2.6 of the HBPLUS Operating Manual. The file describes the nature of hydrogen bonds each atom in the ligand is able to make and therefore allows HBPLUS to correctly calculate the interactions to it.

A program called HBADD (see Appendix C) is supplied which aims to reduce the work involved in creating this input file for HBPLUS. The program looks for any HETATM records in a given PDB file and searches for its' structure in the Het Group Dictionary. HBADD relies on the atom names and connectivities of the ligand atoms in the PDB file matching those in the dictionary.

If there is a mismatch, you may have to edit the PDB file or create your own HBPLUS input file.

b) Expected bond falls outside the criteria

HBPLUS calculates hydrogen bonds in the following method. All possible hydrogen atom (H) positions are calculated for donor atoms (D) which satisfy specified geometrical criteria with acceptor atoms (A) in the vicinity. The criteria used are: the H-A distance is < 2.7Å, the D-A distance is < 3.35Å, the D-H-A angle is > 90° and the H-A-AA angle is > 90°, where AA is the atom attached to the acceptor.

For non-bonded contacts, all atoms within 3.9Å of each other are considered to be interacting by HBPLUS.

NUCPLOT uses an additional distance cut-off filter which is specified in the nucplot.par parameter file (more details). This is easier to alter than the input for HBPLUS and as long as the distance required is less than the cut-offs specified by HBPLUS, we recommend the use of this method.

c) Missing water contacts

NUCPLOT only considers hydrogen bonds between water molcules and nucleic acids. Non bonded contacts are not included to prevent overcrowding in the diagram.

d) Using the *.bond file

NUCPLOT can be instructed to read the interaction information from the *.bond file. The simplest way to make alterations to this file is to run NUCPLOT, see which bonds are missing, and add these manually to the file before re-running the program using NUCONLY. The file can also be edited to remove any unwanted interactions. See Section 5 for details on the nucplot.par file and Appendix B for an explanation of the *.bond file format.