If we have a PDB structrure, how can we find residues physically interacting with each other in space? I know that we must find the distance between residues and if the distance is less than 5-6 Angstrom, we say that residues are physically interacting. But how can we find the distance between all residues and how can we finally determine the distances between all residues? Is there a software or webserver for that?
$\begingroup$ These interaction may be already annotated in the PDB, see Connectivity Section and Connectivity Annotation Section in the PDB spec. $\endgroup$– marcinJun 16, 2017 at 14:47
$\begingroup$ One thing you're going to have to define for yourself is what you mean by "distance between residues". Do you mean closest atom pair? Closest heavyatom pair? Distance between C-alphas? The exact mechanism is probably going to be similar, regardless, but the details and the results will differ based on the definition. $\endgroup$– R.M.Jun 16, 2017 at 21:18
$\begingroup$ I mean the distance between C-alphas $\endgroup$– SaraJun 16, 2017 at 21:33
$\begingroup$ Is the Ring 2.0 webserver (protein.bio.unipd.it/ring) good enough for this purpose? $\endgroup$– SaraJun 17, 2017 at 10:56
$\begingroup$ If anyone is interested in speed benchmarks of distance calculations using various software, there are some at github.com/jgreener64/pdb-benchmarks. There are also example scripts for each software in that repository. $\endgroup$– jgreenerSep 10, 2019 at 21:29
If you need to process multiple files, you could use Biopython to parse a PDB structure.
from Bio.PDB import PDBParser # create parser parser = PDBParser() # read structure from file structure = parser.get_structure('PHA-L', '1fat.pdb') model = structure chain = model['A'] # this example uses only the first residue of a single chain. # it is easy to extend this to multiple chains and residues. for residue1 in chain: for residue2 in chain: if residue1 != residue2: # compute distance between CA atoms try: distance = residue1['CA'] - residue2['CA'] except KeyError: ## no CA atom, e.g. for H_NAG continue if distance < 6: print(residue1, residue2, distance) # stop after first residue break
If you need to look at one structure, using a viewer perhaps would be easier. You could try PyMOL: (how to measure distance). There are other PDB viewers, some of which can work even through a browser.
$\begingroup$ Dear lakov, I installed Anaconda and Biopython packages and run the above code in PyCharm 5.0 and got the following error: $\endgroup$ Jun 16, 2017 at 16:27
$\begingroup$ Traceback (most recent call last): File "C:/Users/VN7-592/PycharmProjects/untitled/sara.py", line 7, in <module> structure = parser.get_structure('PHA-L', '1FAT.pdb') $\endgroup$ Jun 16, 2017 at 16:29
$\begingroup$ File "C:\Users\VN7-592\Desktop\Anaconda\lib\site-packages\Bio\PDB\PDBParser.py", line 81, in get_structure with as_handle(file, mode='rU') as handle: File "C:\Users\VN7-592\Desktop\Anaconda\lib\contextlib.py", line 17, in enter return self.gen.next() File "C:\Users\VN7-592\Desktop\Anaconda\lib\site-packages\Bio\File.py", line 88, in as_handle with open(handleish, mode, **kwargs) as fp: IOError: [Errno 2] No such file or directory: '1FAT.pdb' $\endgroup$ Jun 16, 2017 at 16:29
1$\begingroup$ You don't have the 1FAT.pdb file in the working directory, or your operating system is case sensitive. $\endgroup$– AjasjaJun 16, 2017 at 20:01
$\begingroup$ But this gives only intermolecular distances? BioPython ignores crystal symmetry? In general, to check for contacts between residues X and Y one would need to calculate distance between X and the nearest symmetrical image of Y. $\endgroup$ Jun 17, 2017 at 19:36
Could you use CCP4's NCONT program? There's a GUI and a command line interface, whatever suits. You can specify which chains you want to target and interact with and set a cut off for distance. The bonus here is once you're in you have a nice suite of other structural tools to use.
If you're just doing it once, the GUI is friendly enough to work things out, if you're doing a batch then you can run it across several files via the command line.
$\begingroup$ I have downloaded the program but I haven't been able to work with it yet. I'm trying to run it $\endgroup$ Jun 17, 2017 at 2:03
$\begingroup$ @Sara what is it you're having a problem with? $\endgroup$– TW93Jun 17, 2017 at 18:24
$\begingroup$ It doesn't run with an error. The program says choose a project name and even when I have chosen a project name, again says choose a project name and stops running $\endgroup$ Jun 18, 2017 at 8:03
As part of a project me and some teammates did a script that outputs visual maps of distances between residues. It uses Biopython.
The module contact_map.py does what you are looking for. As an example, if you want to find the residues whose CA are below 5 you can run the following command:
python3 contact_map.py pdb1cd8.ent -a CA -CA 5
This will produce three files:
distance_map_pdb1cd8_CA.png # Heatmap of the distance between the residues contact_map_pdb1cd8_CA.png # Black/White heatmap: If it is at that min distance contact_map.log # The actions taken
If you don't have downloaded already the pdb structue you can use the main module:
python3 cozmic.py real 1cd8 -a CA -CA 5
$\begingroup$ How it calculates distances? Inside the asymmetric unit only, or as the shortest distance between the two residues in the crystal (or in biological assembly)? $\endgroup$ Jun 20, 2017 at 16:28
$\begingroup$ @marcin It calculates the distance between the C alpha (or beta if you chose so) between each residue in the file. $\endgroup$– llrsJun 21, 2017 at 7:29
$\begingroup$ Usually, the file == asymmetric unit. If you'd like to find all contacts in biological assembly or in crystal you'd need to take the symmetry into account. $\endgroup$ Jun 21, 2017 at 8:12
$\begingroup$ Thanks for the tips, maybe you want to contribute to the modules. $\endgroup$– llrsJun 21, 2017 at 8:53
You can use MDtraj. The package is easy to install using Anaconda.
You can get the interacting residues using the following snippet (taken from http://mdtraj.org/1.6.2/examples/native-contact.html)
heavy_pairs = np.array( [(i,j) for (i,j) in combinations(heavy, 2) if abs(native.topology.atom(i).residue.index - \ native.topology.atom(j).residue.index) > 3]) # compute the distances between these pairs in the native state heavy_pairs_distances = md.compute_distances(native, heavy_pairs) # and get the pairs s.t. the distance is less than NATIVE_CUTOFF native_contacts = heavy_pairs[heavy_pairs_distances < NATIVE_CUTOFF] print("Number of native contacts", len(native_contacts))
Distance between C-alphas can also be found using the BioStructures.jl package in Julia:
using BioStructures struc = read("1AKE.pdb", PDB) calphas = collectatoms(struc['A'], calphaselector) dm = DistanceMap(calphas)
dm[5, 10] gives
Other variations also work, see the docs.