4.7.1.2. HELANAL — analysis of protein helices

Author:

Lily Wang

Year:

2020

Copyright:

GNU Public License v3

New in version 2.0.0.

This module contains code to analyse protein helices using the HELANAL algorithm [Bansal2000, Sugeta1967].

The HELANAL algorithm quantifies the geometry of helices in proteins on the basis of their Cα atoms. It can determine local structural features such as the local helical twist and rise, virtual torsion angle, local helix origins and bending angles between successive local helix axes.

4.7.1.2.1. Example use

You can pass in a single selection:

import MDAnalysis as mda
from MDAnalysis.tests.datafiles import PSF, DCD
from MDAnalysis.analysis import helix_analysis as hel
u = mda.Universe(PSF, DCD)
helanal = hel.HELANAL(u, select='name CA and resnum 161-187')
helanal.run()

All computed properties are available in .results:

print(helanal.results.summary)

Alternatively, you can analyse several helices at once by passing in multiple selection strings:

helanal2 = hel.HELANAL(u, select=('name CA and resnum 100-160',
                                  'name CA and resnum 200-230'))

The helix_analysis() function will carry out helix analysis on atom positions, treating each row of coordinates as an alpha-carbon equivalent:

hel_xyz = hel.helix_analysis(u.atoms.positions, ref_axis=[0, 0, 1])

[Bansal2000]

Manju Bansal, Sandeep Kumart, and R. Velavan. Helanal: a program to characterize helix geometry in proteins. Journal of Biomolecular Structure and Dynamics, 17(5):811–819, 2000. PMID: 10798526. doi:10.1080/07391102.2000.10506570.

[Sugeta1967]

Hiromu Sugeta and Tatsuo Miyazawa. General method for calculating helical parameters of polymer chains from bond lengths, bond angles, and internal-rotation angles. Biopolymers, 5(7):673–679, 1967. doi:10.1002/bip.1967.360050708.