1 DEFINING α-HELIX GEOMETRY BY C α ATOM TRACE vs (φ-ψ) TORSION ANGLES: A COMPARATIVE ANALYSIS ASHISH SHELAR*, PRASUN KUMAR*, MANJU BANSAL Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560 012, India * Both authors contributed equally A regular secondary structure is described by a well defined set of values for the backbone dihedral angles (φ, ψ and ω) in a polypeptide chain. However in real protein structures small local variations give rise to distortions from the ideal structures, which can lead to considerable variation in higher order organization. Protein structure analysis and accurate assignment of various structural elements, especially their terminii, are important first step in protein structure prediction and design. Various algorithms are available for assigning secondary structure elements in proteins but some lacunae still exist. In this study, results of a recently developed in-house program ASSP have been compared with those from STRIDE, in identification of α-helical regions in both globular and membrane proteins. It is found that, while a combination of hydrogen bond patterns and backbone torsional angles (φ-ψ) are generally used to define secondary structure elements, the geometry of the C α atom trace by itself is sufficient to define the parameters of helical structures in proteins. It is also possible to differentiate the various helical structures by their C α trace and identify the deviations occurring both at mid-positions as well as at the terminii of α-helices, which often lead to occurrence of 310 and π-helical fragments in both globular and membrane proteins. 1. Introduction The most general description of ‘helix’ is a smooth 3D curve that lies on a conical or cylindrical surface. Helices which constitute the major secondary structure elements in proteins take up this structure due to repeating values of the backbone torsion angles (φ, ψ and ω) accompanied by regular hydrogen bond patterns between the backbone NH and CO groups of amino acids. Numerous secondary structure assignment algorithms which use atomic coordinate data have been developed and can be broadly classified into three categories: (i) algorithms based on backbone torsion angles and hydrogen bond patterns (ii) algorithms based on 3D geometry (iii) hybrid methods, which use both (i) and (ii). Programs like DSSP 1 , STRIDE 2 and PROSS 3 fall into the first category, DEFINE-S 4 , P-CURVE 5 come under second category whereas KAKSI 6 , PALSSE 7 etc. fall under the third category. All these algorithms identify the main body of the α-helix, however they often differ in their definition of helix terminii. Even in the main body, sometimes differences occur in the assignment because of small local deviations from the uniform helical character, arising due to solvent induced distortions 8 , peptide bond distortions 9,10 or presence of Proline 11-13 , Serine and Threonine residues 14,15 . Blundell et.al. 8 carried out the first survey on the irregularities in helices and concluded that a majority of the helices are curved, which has been confirmed by subsequent studies 16 . α-helices also show distinct preferences for amino acids at their N and