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| 1 | +# Finding contacts within a protein chain: contact maps |
| 2 | + |
| 3 | +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 |
| 4 | + |
| 5 | +## Getting the contact map of a protein chain |
| 6 | + |
| 7 | +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): |
| 8 | + |
| 9 | +```java |
| 10 | + AtomCache cache = new AtomCache(); |
| 11 | + StructureIO.setAtomCache(cache); |
| 12 | + |
| 13 | + Structure structure = StructureIO.getStructure("1SMT"); |
| 14 | + |
| 15 | + Chain chain = structure.getChainByPDB("A"); |
| 16 | + |
| 17 | + // we want contacts between Calpha atoms only |
| 18 | + String[] atoms = {" CA "}; |
| 19 | + // the distance cutoff we use is 8A |
| 20 | + AtomContactSet contacts = StructureTools.getAtomsInContact(chain, atoms, 8.0); |
| 21 | + |
| 22 | + System.out.println("Total number of CA-CA contacts: "+contacts.size()); |
| 23 | + |
| 24 | + |
| 25 | +``` |
| 26 | + |
| 27 | +The algorithm to find the contacts uses geometric hashing without need to calculate a full distance matrix, thus it scales nicely. |
| 28 | + |
| 29 | +## Getting the contacts between two protein chains |
| 30 | + |
| 31 | +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): |
| 32 | + |
| 33 | +```java |
| 34 | + AtomCache cache = new AtomCache(); |
| 35 | + StructureIO.setAtomCache(cache); |
| 36 | + |
| 37 | + Structure structure = StructureIO.getStructure("1SMT"); |
| 38 | + |
| 39 | + AtomContactSet contacts = StructureTools.getAtomsInContact(structure.getChain(0), structure.getChain(1), 5, false); |
| 40 | + |
| 41 | + System.out.println("Total number of atom contacts: "+contacts.size()); |
| 42 | + |
| 43 | + // the list of atom contacts can be reduced to a list of contacts between groups: |
| 44 | + GroupContactSet groupContacts = new GroupContactSet(contacts); |
| 45 | +``` |
| 46 | + |
| 47 | + |
| 48 | +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. |
| 49 | + |
| 50 | + |
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