Contact analysis: number of contacts within a cutoff
We calculate the number of salt bridges in an enzyme as it transitions from a closed to an open conformation.
Last updated: December 2022 with MDAnalysis 2.4.0-dev0
Minimum version of MDAnalysis: 0.17.0
import MDAnalysis as mda from MDAnalysis.tests.datafiles import PSF, DCD from MDAnalysis.analysis import contacts import numpy as np import pandas as pd import matplotlib.pyplot as plt %matplotlib inline
Quantifying the number of contacts over a trajectory can give insight into the formation and rearrangements of secondary and tertiary structure. This is closely related to native contacts analysis; where the fraction of native contacts refers to the fraction of contacts retained by a protein from the contacts in a reference frame, the number of contacts simply counts how many residues are within a certain cutoff for each frame. No reference is necessary. Please see the Fraction of native contacts for an introduction to native contacts analysis.
The test files we will be working with here feature adenylate kinase (AdK), a phosophotransferase enzyme. ([BDPW09]) The trajectory
DCD samples a transition from a closed to an open conformation.
u = mda.Universe(PSF, DCD)
/home/pbarletta/mambaforge/envs/guide/lib/python3.9/site-packages/MDAnalysis/coordinates/DCD.py:165: DeprecationWarning: DCDReader currently makes independent timesteps by copying self.ts while other readers update self.ts inplace. This behavior will be changed in 3.0 to be the same as other readers. Read more at https://github.com/MDAnalysis/mdanalysis/issues/3889 to learn if this change in behavior might affect you. warnings.warn("DCDReader currently makes independent timesteps"
Defining the groups for contact analysis
We define salt bridges as contacts between NH/NZ in ARG/LYS and OE*/OD* in ASP/GLU. It is not recommend to use this overly simplistic definition for real work that you want to publish.
sel_basic = "(resname ARG LYS) and (name NH* NZ)" sel_acidic = "(resname ASP GLU) and (name OE* OD*)" acidic = u.select_atoms(sel_acidic) basic = u.select_atoms(sel_basic)
Calculating number of contacts within a cutoff
Below, we define a function that calculates the number of contacts between
group_b within the
radius cutoff, for each frame in a trajectory.
def contacts_within_cutoff(u, group_a, group_b, radius=4.5): timeseries =  for ts in u.trajectory: # calculate distances between group_a and group_b dist = contacts.distance_array(group_a.positions, group_b.positions) # determine which distances <= radius n_contacts = contacts.contact_matrix(dist, radius).sum() timeseries.append([ts.frame, n_contacts]) return np.array(timeseries)
The results are returned as a numpy array. The first column is the frame, and the second is the number of contacts present in that frame.
ca = contacts_within_cutoff(u, acidic, basic, radius=4.5) ca.shape
ca_df = pd.DataFrame(ca, columns=['Frame', '# Contacts']) ca_df.head()
ca_df.plot(x='Frame') plt.ylabel('# salt bridges')
Text(0, 0.5, '# salt bridges')
 Oliver Beckstein, Elizabeth J. Denning, Juan R. Perilla, and Thomas B. Woolf. Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the Ensemble of Open↔Closed Transitions. Journal of Molecular Biology, 394(1):160–176, November 2009. 00107. URL: https://linkinghub.elsevier.com/retrieve/pii/S0022283609011164, doi:10.1016/j.jmb.2009.09.009.
 Richard J. Gowers, Max Linke, Jonathan Barnoud, Tyler J. E. Reddy, Manuel N. Melo, Sean L. Seyler, Jan Domański, David L. Dotson, Sébastien Buchoux, Ian M. Kenney, and Oliver Beckstein. MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations. Proceedings of the 15th Python in Science Conference, pages 98–105, 2016. 00152. URL: https://conference.scipy.org/proceedings/scipy2016/oliver_beckstein.html, doi:10.25080/Majora-629e541a-00e.
 Naveen Michaud-Agrawal, Elizabeth J. Denning, Thomas B. Woolf, and Oliver Beckstein. MDAnalysis: A toolkit for the analysis of molecular dynamics simulations. Journal of Computational Chemistry, 32(10):2319–2327, July 2011. 00778. URL: http://doi.wiley.com/10.1002/jcc.21787, doi:10.1002/jcc.21787.