InterfaceResidues

Overview

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.

Usage

interfaceResidue complexName[, cA=firstChainName[, cB=secondChainName[, cutoff=dAsaCutoff[, selName=selectionNameToReturn ]]]]

where,

complexName

The name of the complex. cA and cB must be within in this complex

cA

The name of the first chain to investigate

cB

The name of the 2nd chain to investigate

cutoff

The dASA cutoff, in sqaure Angstroms

selName

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,

myInterfaceResidues

will have all the value for you.

Examples

For these two examples, make sure you've run the script first.

Simple Example

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")

The Code

from pymol import 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)