The program Probe allows one to evaluate atomic packing, either within or between molecules. It generates “contact dots” where atoms are in close contact. Probe reads atomic coordinates from protein databank (PDB) format files and writes dot-lists for inclusion in a kinemage file. Alternatively, the packing information can be quantified and displayed in a table listing scores for van der Waals interactions, H-bonds and atomic overlaps ("clashes"). Essentially the inverse of the Connolly algorithm, the approach is to place a very small probe (typically of radius 0.25A) at points along the van der Waals surface of a selected set of atoms and determine if this probe also contacts atoms within a second "target" set. Probe provides a flexible method for selecting the source and target atoms along with command line flags for altering the probe radius and dot density. In addition, Probe can generate contact surfaces within a set of atoms ("self dots") and even "surface dots" where there are no nearby atoms. For a detailed description see Word, et al. (1999), “Visualizing and Quantifying Molecular Goodness-of-Fit: Small-probe Contact Dots with Explicit Hydrogen Atoms” J. Mol. Biol. 285, 1709-1731. (https://doi.org/10.1006/jmbi.1998.2400)
Meaningful analysis of molecular contact surfaces requires that ALL atoms are considered. Before using Probe, use the companion program Reduce to add hydrogens to the coordinate file. Reduce-modified PDBs can be generated on your computer or via our MolProbity web service. The animated image above shows a ternary system of 2 histidines and an asparagine in cellulase (1CEM); the structure of which is improved by contact analysis with our automatic tools (MolProbity). In the red-colored state, the three side chain positions show numerous clashes (pink & red spikes) when H's are added (Reduce) and contacts are visualized by Probe and Mage. Flipping the sidechains as recommended by Reduce yields the green-state with less clashing.
KiNG and Mage are both capable of updating contact dots interactively as the displayed model is changed. The implementation and use of interactive contact dots is more straightforward in KiNG and is recommended.