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A program to characterize overall geometry of an alpha helix

The program can be used to characterize the geometry of helices with a minimum 9 residues. Geometry of an alpha helix is characterised by computing local helix axes and local helix origins for four contiguous C-Alpha atoms, using the procedure of Sugeta and Miyazawa,1967 (Sugeta, H. & 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.) 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 analyse 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. There is a homepage for Helanal .

In the core, helanal has been compiled for the SGI's Linux and the Dec's:

type: **setup helanal& **in a directory where you have write
permission.

Sample I/O files can be found in /eve/dist/helanal/example

For each run of HELANAL the following output files are created.

RUN.ANS contains the questions and their answers during a run of HELANAL.

HELCA.OUT contains Coordinates of the C-alpha atoms.

HELINFO.OUT file is created only when the HELIX records in the PDB files are used for information on helix start/end residues and contains these helix records.

AXES.OUT contains the local helix axes fitted to 4 consecutive C-alpha atoms along with a matrix M(I, J) whose elements are the angles between local helix axes I and J.

ANGLE.OUT contains the angle between successive local helix axes. It also gives mean bending angle and Maximum bending angle for the helix.

ORIGIN.OUT contains the local helix origins for the helix along with statistics obtained by fitting least square plane, circle and line to the local helix origins.

NH.OUT contains unit height and unit twist for every turn of the helix as well as average unit height and average unit twist for the whole helix.

***.PRM contains summary of various parameters obtained by HELANAL.

***.TAB presents the results in tabular form along with the overall geometry assignment for the helices.

Acknowledgements:

Please cite the following reference if you use the program:

Bansal, M., Kumar, S. and Velavan, R. 2000. HELANAL - A program to characterise helix geometry in proteins. Journal of Biomolecular Structure and Dynamics, 17, 5, 811 - 819.

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