Contacts are a useful tool to analyse protein structures. It simplifies the 3-Dimensional view of the structures into a 2-Dimensional set of contacts between its atoms or its residues. The representation of the contacts in a matrix is known as the contact map. Many protein structure analysis and prediction efforts are done by using contacts, see for instance

This code snippet will produce the set of contacts between all C alpha atoms for chain A of PDB entry [1SMT](http://www.rcsb.org/pdb/explore.do?structureId=1SMT):

AtomCache cache = new AtomCache();

StructureIO.setAtomCache(cache);

Structure structure = StructureIO.getStructure("1SMT");

Chain chain = structure.getChainByPDB("A");

// we want contacts between Calpha atoms only

String[] atoms = {" CA "};

// the distance cutoff we use is 8A

AtomContactSet contacts = StructureTools.getAtomsInContact(chain, atoms, 8.0);

System.out.println("Total number of CA-CA contacts: "+contacts.size());

The algorithm to find the contacts uses geometric hashing without need to calculate a full distance matrix, thus it scales nicely.

One can also find the contacting atoms between two protein chains. For instance the following code finds the contacts between the first 2 chains of PDB entry [1SMT](http://www.rcsb.org/pdb/explore.do?structureId=1SMT):

AtomCache cache = new AtomCache();

StructureIO.setAtomCache(cache);

Structure structure = StructureIO.getStructure("1SMT");

AtomContactSet contacts = StructureTools.getAtomsInContact(structure.getChain(0), structure.getChain(1), 5, false);

System.out.println("Total number of atom contacts: "+contacts.size());

// the list of atom contacts can be reduced to a list of contacts between groups:

GroupContactSet groupContacts = new GroupContactSet(contacts);

See [DemoContacts](https://github.com/biojava/biojava/blob/master/biojava3-structure/src/main/java/demo/DemoContacts.java) for a fully working demo of the example above.