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# 3.7. HELANAL — analysis of protein helices

Author: | Benjamin Hall <benjamin.a.hall@ucl.ac.uk>, Oliver Beckstein
Year: | 2009, 2011
License: | GNU General Public License v2 (or higher)

The `MDAnalysis.analysis.helanal` module is a Python implementation of the HELANAL algorithm [Bansal2000] in helanal.f, which is also available through the HELANAL webserver.

Please cite the paper [Bansal2000] (and possibly [Kumar1996] and [Kumar1998]) in published work when using `helanal_trajectory` or `helanal_main`.

HELANAL quantifies the geometry of helices in proteins on the basis of their Cα atoms alone. It can extract the helices from the structure files and then characterises the overall geometry of each helix as being linear, curved or kinked, in terms of its local structural features, viz. local helical twist and rise, virtual torsion angle, local helix origins and bending angles between successive local helix axes. Even helices with large radius of curvature are unambiguously identified as being linear or curved. The program can also be used to differentiate a kinked helix and other motifs, such as helix-loop-helix or a helix-turn-helix (with a single residue linker) with the help of local bending angles. In addition to these, the program can also be used to characterise the helix start and end as well as other types of secondary structures.

## 3.7.1. Background

From the HELANAL home page:

HELANAL can be used to characterize the geometry of helices with a minimum 9 residues. The geometry of an alpha helix is characterized by computing local helix axes and local helix origins for four contiguous C-Alpha atoms, using the procedure of Sugeta and Miyazawa [Sugeta1967] and sliding this window over the length of the helix in steps of one C-Alpha atom.

The angles between successive local helix axes can identify local bends or kinks as well as occurrence of smooth curvature in the helix. A matrix, whose elements M(I, J) are the bending angles between local helix axes I and J, is obtained to get an idea about the overall geometry of the helix.

Unit twist and unit height of the alpha helix are also computed to analyze the uniformity of the helix. The local helix origins trace out the path described by the helix in three dimensional space. The local helix origins are reoriented in X-Y plane and the reoriented points are used to fit a circle as well as a line, by least squares method. Based on the relative goodness of line and circle fit to local helix origins, the helix is classified as being linear or curved. A helix is classified as being kinked, if at least one local bending angle in the middle of the helix is greater than 20 degrees.

## 3.7.2. References

[Sugeta1967] | Sugeta, H. and Miyazawa, T. 1967. General method for calculating helical parameters of polymer chains from bond lengths, bond angles and internal rotation angles. Biopolymers 5 673 - 679

[Kumar1996] | Kumar, S. and Bansal, M. 1996. Structural and sequence characteristics of long alpha-helices in globular proteins. Biophysical Journal 71(3):1574-1586.

[Kumar1998] | Kumar, S. and Bansal, M. 1998. Geometrical and sequence characteristics of alpha helices in globular proteins. Biophysical Journal 75(4):1935-1944.

[Bansal2000] | (1, 2) Bansal M, Kumar S, Velavan R. 2000. HELANAL - A program to characterise helix geometry in proteins. J Biomol Struct Dyn. 17(5):811-9. http://www.jbsdonline.com/c3003/c4003/HELANAL-A-Program-to-Characterize-Helix-Geometry-in-Proteins-p-811-820-p10020.html

## 3.7.3. Functions

`MDAnalysis.analysis.helanal.``helanal_trajectory`(universe, selection='name CA', start=None, end=None, begin=None, finish=None, matrix_filename='bending_matrix.dat', origin_pdbfile='origin.pdb', summary_filename='summary.txt', screw_filename='screw.xvg', tilt_filename='local_tilt.xvg', fitted_tilt_filename='fit_tilt.xvg', prefix='helanal_', ref_axis=None)

  Perform HELANAL helix analysis on all frames in universe.

  Note

  Only a single helix is analyzed. Use the selection to specify the helix, e.g. with “name CA and resid 1:20” or use start=1, stop=20.

  Arguments : | universe `Universe`
  Keywords : | selection selection string that selects Calpha atoms [“name CA”] start start residue end end residue begin start analysing for time >= begin; `None` starts from the beginning [`None`] finish stop analysis for time =< finish; `None` goes to the end of the trajectory [`None`] matrix_filename Output file- bending matrix [“bending_matrix.dat”] origin_pdbfile Output file- origin pdb file [“origin.pdb”] summary_filename Output file- all of the basic data [“summary.txt”] screw_filename Output file- local tilts of individual residues from 2 to n-1 [“screw.xvg”] tilt_filename Output file- tilt of line of best fit applied to origin axes [“local_tilt.xvg”] prefix Prefix to add to all output file names; set to `None` to disable [“helanal__“] ref_axis Calculate tilt angle relative to the axis; if `None` then [0,0,1] is chosen [`None`]

`MDAnalysis.analysis.helanal.``helanal_main`(pdbfile, selection='name CA', start=None, end=None, ref_axis=None, permissive=False)

  Simple HELANAL run on a single frame PDB/GRO.

  Note

  Only a single helix is analyzed. Use the selection to specify the helix, e.g. with “name CA and resid 1:20”.

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