Ramachandran plot of dynein motor domainΒΆ

This script creates a Ramachandran plot of the motor domain of dynein (PDB: 3VKH). The protein mainly consists of alpha-helices, as the plot clearly indicates.

Ramachandran plot of dynein motor domain
# Code source: Patrick Kunzmann
# License: BSD 3 clause

from tempfile import gettempdir
import biotite.structure as struc
import biotite.structure.io as strucio
import biotite.database.rcsb as rcsb
import matplotlib.pyplot as plt
import numpy as np
from matplotlib import colors
import scipy.stats as sts

# Download and parse file
file = rcsb.fetch("3vkh", "cif", gettempdir())
atom_array = strucio.load_structure(file)
# Calculate backbone dihedral angles
# from one of the two identical chains in the asymmetric unit
phi, psi, omega = struc.dihedral_backbone(
    atom_array[atom_array.chain_id == "A"]
# Conversion from radians into degree
phi *= 180/np.pi
psi *= 180/np.pi
# Remove invalid values (NaN) at first and last position
phi= phi[1:-1]
psi= psi[1:-1]

# Plot density
figure = plt.figure()
ax = figure.add_subplot(111)
h, xed, yed, image = ax.hist2d(phi, psi, bins=(200, 200),
                cmap="RdYlGn_r", cmin=1)
cbar = figure.colorbar(image, orientation="vertical")
ax.set_xlim(-180, 175)
ax.set_ylim(-180, 175)
ax.set_title("Ramachandran plot of dynein motor domain")

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