Issue April 2000

category image Volume 17
No. 5 (p 769-932)
April 2000
ISSN 0739-1102

HELANAL: A Program to Characterize Helix Geometry in Proteins (p. 811-820)

A detailed analysis of structural and position dependent characteristic features of helices will give a better understanding of the secondary structure formation in globular proteins. Here we describe an algorithm that quantifies the geometry of helices in proteins on the basis of their Cα atoms alone. The Fortran program HELANAL can extract the helices from the PDB 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.

Manju Bansal*
Sandeep Kumar1
R. Velavan

Molecular Biophysics Unit
Indian Institute of Science
Bangalore ? 560 012, India
1Present Address:
Laboratory of Experimental and Computational Biology
Bldg. 469, Rm. 151
NCI-FCRDC
Frederick MD 21702, USA
*mb@mbu.iisc.ernet.in

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