HELANAL, a program to characterize alpha helix geometry in protein and peptide structures.

In proteins, alpha helices usually do not follow a perfectly straight helix axis. Most often the alpha helices curve, bend and kink as they wind their way in and out of the protein core. Recently, it has been shown that amino acid sequence information in protein not only specifies whether or not a given stretch of amino acids will from an alpha helix, but also geometry, length and location of the helix in the protein globule. HELANAL is a program to characterize overall geometry of an alpha helix from its C-alpha atom coordinates. This program can be very useful in analysis of protein secondary structure, modeling of membrane proteins, analysis of molecular dynamics runs of alpha helices or alpha helical proteins, designed peptides containing alpha helical motifs, etc. For a detailed explanation of the algorithm used in this program, please refer to my 1996 and 1998 papers in the biophysical journal. My thesis, entitled "Geometry and sequence correlation studies on alpha helices in globular proteins" submitted to Indian Institute of Science, Bangalore, India - 56602, is another excellent source of reference.

Brief description of HELANAL algorithm

The program can be used to characterize the geometry of helices with a minimum 9 residues. 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,1967 (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.) 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 atleast one local bending angle in the middle of the helix is greater than 20 degrees.

If you wish to download this program along with sample I/O files, here are the links.

• Reprint 1
• Reprint 2
• README
• example.inp
• coiled.coil
• pdb2zta.ent
• pdb1rib.ent
• pdb1bge.ent
• pdb1lis.ent
• helanal.f
• RUN.ANS
• example.prm
• example.tab
• angle.out
• axes.out
• helca.out
• nh.out
• origin.out

I would greatly appreciate a citation of my work, in case you publish your results obtained by using HELANAL. Please cite one or all of the following papers:

Kumar, S. and Bansal, M. 1996. Structural and sequence characteristics of long alpha-helices in globular proteins. Biophysical Journal, 71, 3, 1574-1586.

Kumar, S. and Bansal, M. 1998. Geometrical and sequence characteristics of alpha helices in globular proteins. Biophysical Journal, 75, 4, 1935-1944.

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.