Finding contacts between atoms in a protein: contact maps

Contacts are a useful tool to analyse protein structures. They simplify 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. For instance they can be useful for:

• development of structural alignment algorithms Holm 1993 Caprara 2004
• automatic domain identification Alexandrov 2003 Emmert-Streib 2007
• structural modelling by extraction of contact-based empirical potentials Benkert 2008
• structure prediction via contact prediction from sequence information Jones 2012

Getting the contact map of a protein chain

This code snippet will produce the set of contacts between all C alpha atoms for chain A of PDB entry 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 spatial hashing without need to calculate a full distance matrix, thus it scales nicely.

Getting the contacts between two protein chains

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:

		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 for a fully working demo of the examples above.

Navigation: Home | Book 3: The Structure Modules | Chapter 12 : Contacts Within a Chain and between Chains

Prev: Chapter 11 : Accessible Surface Areas

Next: Chapter 13 - Finding all Interfaces in Crystal: Crystal Contacts