9
$\begingroup$

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?

$\endgroup$
5
  • $\begingroup$ These interaction may be already annotated in the PDB, see Connectivity Section and Connectivity Annotation Section in the PDB spec. $\endgroup$
    – marcin
    Jun 16 '17 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 '17 at 21:18
  • $\begingroup$ I mean the distance between C-alphas $\endgroup$
    – Sara
    Jun 16 '17 at 21:33
  • $\begingroup$ Is the Ring 2.0 webserver (protein.bio.unipd.it/ring) good enough for this purpose? $\endgroup$
    – Sara
    Jun 17 '17 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. $\endgroup$
    – jgreener
    Sep 10 '19 at 21:29
9
$\begingroup$

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[0]
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.

$\endgroup$
5
  • $\begingroup$ Dear lakov, I installed Anaconda and Biopython packages and run the above code in PyCharm 5.0 and got the following error: $\endgroup$
    – Sara
    Jun 16 '17 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') $\endgroup$
    – Sara
    Jun 16 '17 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' $\endgroup$
    – Sara
    Jun 16 '17 at 16:29
  • 1
    $\begingroup$ You don't have the 1FAT.pdb file in the working directory, or your operating system is case sensitive. $\endgroup$
    – Ajasja
    Jun 16 '17 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. $\endgroup$
    – marcin
    Jun 17 '17 at 19:36
4
$\begingroup$

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.

Download

$\endgroup$
3
  • $\begingroup$ I have downloaded the program but I haven't been able to work with it yet. I'm trying to run it $\endgroup$
    – Sara
    Jun 17 '17 at 2:03
  • $\begingroup$ @Sara what is it you're having a problem with? $\endgroup$
    – TW93
    Jun 17 '17 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 $\endgroup$
    – Sara
    Jun 18 '17 at 8:03
1
$\begingroup$

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 
$\endgroup$
6
  • $\begingroup$ 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)? $\endgroup$
    – marcin
    Jun 20 '17 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. $\endgroup$
    – llrs
    Jun 21 '17 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. $\endgroup$
    – marcin
    Jun 21 '17 at 8:12
  • $\begingroup$ Thanks for the tips, maybe you want to contribute to the modules. $\endgroup$
    – llrs
    Jun 21 '17 at 8:53
  • $\begingroup$ I'm working now on a project that in the future may be competitive to Bio.PDB, but probably not this year yet :-) $\endgroup$
    – marcin
    Jun 21 '17 at 18:52
0
$\begingroup$

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[0], heavy_pairs)[0]
# 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))
$\endgroup$
0
$\begingroup$

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)

Then dm[5, 10] gives 12.19677604943208 etc.

Other variations also work, see the docs.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.