Figure 4.

Parameters for assignment of helix and β-strand property to individual residues. Cα distance and Cα torsion angle were calculated for defining helices (fig. a) and β-strands (fig. b). The distance between residues i, i+3 (shown joined by a blue line) and torsion angle between residues i, i+1, i+2, i+3 (shown as angle between two colored planes; yellow plane between residues i, i+1, i+2 and orange plane between residues i+1, i+2, i+3) are used to assign loose-helix, strict-helix and loose-strand secondary structure property to individual residues. 4c: Distance between i, i+3 Cα residues from helix and β-strand definitions obtained from DSSP [8] output. Distances were binned in 0.2 Å intervals. Cutoff distance c1 (8.1 Å) is the maximum distance allowed for assigning loose-helix property to a residue. Cutoff c1 is also the minimum distance allowed for assigning loose-strand property to a residue. Residues at i and i+3 positions are allowed in the same SSE template (SSET) only if the cutoff distance c1 passes. Cutoff c2 (6.4 Å) is the maximum i, i+3 Cα distance for strict helix definition. 4d: Torsion angle between i, i+1, i+2, i+3 Cα atoms for helix and β-strand definitions obtained from DSSP output. Angles are binned in 5° intervals. A loose-helix definition is assigned to a residue only if the torsion angle for the residue falls between c1 (-35°) and c2 (115°). A loose-strand is assigned only if the torsion angle is -180° to c1 or c2 to 180°. c3 is the optimal torsion angle for helices and is used to define strict-helix residues if the torsion angle is within a 2 sigma deviation from c3.

Majumdar et al. BMC Bioinformatics 2005 6:202   doi:10.1186/1471-2105-6-202
Download authors' original image