This script finds interface residues between two proteins or chains, using the following concept. First, we take the area of the complex. Then, we split the complex into two pieces, one for each chain. Next, we calculate the chain-only surface area. Lastly, we take the difference between the comeplex-based areas and the chain-only-based areas. If that value is greater than your supplied cutoff, then we call it an interface residue.
interfaceResidue complexName[, cA=firstChainName[, cB=secondChainName[, cutoff=dAsaCutoff[, selName=selectionNameToReturn ]]]]
- The name of the complex. cA and cB must be within in this complex
- The name of the first chain to investigate
- The name of the 2nd chain to investigate
- The dASA cutoff, in sqaure Angstroms
- Name of the selection to return.
For each residue in the newly defined interface, this script returns the model (cA or cB) name, the residue number and the change in area. To get that information use interfaceResidues in the api form as:
myInterfaceResidues = interfaceResidue(complexName[, cA=firstChainName[, cB=secondChainName[, cutoff=dAsaCutoff[, selName=selectionNameToReturn ]]]])
and the result,
will have all the value for you.
For these two examples, make sure you've run the script first.
This just finds the residues b/t chain A and chain B
fetch 1h4g, async=0 interfaceResidues 1h4g
More Complex Example
fetch 1qox, async=0 foundResidues = interfaceResidues("1qox", cA="c. I", cB="c. J", cutoff=0.75, selName="foundIn1QOX")
from pymol import cmd, stored def interfaceResidues(cmpx, cA='c. A', cB='c. B', cutoff=1.0, selName="interface"): """ interfaceResidues -- finds 'interface' residues between two chains in a complex. PARAMS cmpx The complex containing cA and cB cA The first chain in which we search for residues at an interface with cB cB The second chain in which we search for residues at an interface with cA cutoff The difference in area OVER which residues are considered interface residues. Residues whose dASA from the complex to a single chain is greater than this cutoff are kept. Zero keeps all residues. selName The name of the selection to return. RETURNS * A selection of interface residues is created and named depending on what you passed into selName * An array of values is returned where each value is: ( modelName, residueNumber, dASA ) NOTES If you have two chains that are not from the same PDB that you want to complex together, use the create command like: create myComplex, pdb1WithChainA or pdb2withChainX then pass myComplex to this script like: interfaceResidues myComlpex, c. A, c. X This script calculates the area of the complex as a whole. Then, it separates the two chains that you pass in through the arguments cA and cB, alone. Once it has this, it calculates the difference and any residues ABOVE the cutoff are called interface residues. AUTHOR: Jason Vertrees, 2009. """ # Save user's settings, before setting dot_solvent oldDS = cmd.get("dot_solvent") cmd.set("dot_solvent", 1) # set some string names for temporary objects/selections tempC, selName1 = "tempComplex", selName+"1" chA, chB = "chA", "chB" # operate on a new object & turn off the original cmd.create(tempC, cmpx) cmd.disable(cmpx) # remove cruft and inrrelevant chains cmd.remove(tempC + " and not (polymer and (%s or %s))" % (cA, cB)) # get the area of the complete complex cmd.get_area(tempC, load_b=1) # copy the areas from the loaded b to the q, field. cmd.alter(tempC, 'q=b') # extract the two chains and calc. the new area # note: the q fields are copied to the new objects # chA and chB cmd.extract(chA, tempC + " and (" + cA + ")") cmd.extract(chB, tempC + " and (" + cB + ")") cmd.get_area(chA, load_b=1) cmd.get_area(chB, load_b=1) # update the chain-only objects w/the difference cmd.alter( "%s or %s" % (chA,chB), "b=b-q" ) # The calculations are done. Now, all we need to # do is to determine which residues are over the cutoff # and save them. stored.r, rVal, seen = , ,  cmd.iterate('%s or %s' % (chA, chB), 'stored.r.append((model,resi,b))') cmd.enable(cmpx) cmd.select(selName1, 'none') for (model,resi,diff) in stored.r: key=resi+"-"+model if abs(diff)>=float(cutoff): if key in seen: continue else: seen.append(key) rVal.append( (model,resi,diff) ) # expand the selection here; I chose to iterate over stored.r instead of # creating one large selection b/c if there are too many residues PyMOL # might crash on a very large selection. This is pretty much guaranteed # not to kill PyMOL; but, it might take a little longer to run. cmd.select( selName1, selName1 + " or (%s and i. %s)" % (model,resi)) # this is how you transfer a selection to another object. cmd.select(selName, cmpx + " in " + selName1) # clean up after ourselves cmd.delete(selName1) cmd.delete(chA) cmd.delete(chB) cmd.delete(tempC) # show the selection cmd.enable(selName) # reset users settings cmd.set("dot_solvent", oldDS) return rVal cmd.extend("interfaceResidues", interfaceResidues)