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Figure 5 | BMC Structural Biology

Figure 5

From: Protein secondary structure assignment revisited: a detailed analysis of different assignment methods

Figure 5

Examples of disagreement between kaksi and stride. The divergent assignments are drawn in cartoon representation and highlighted in purple (helix and strand) and cyan (coil assigned by KAKSI). Images are generated with Molscript [46]. Average bending angles (AverBA) between local axes computed by HELANAL in long helices are reported, (a): hemoglobin I from the clam Lucina pectinata, PDB code:1b0b, resolution 1.43 Å. STRIDE assignment: α-helix from residues 4 to 35, AverBA = 15.4°. KAKSI assignment: two helices from 4 to 19, AverBA = 3.84° and 21 to 34, AverBA = 9.0°. (b): chain A of L(+)-mandelate dehydrogenase from Pseudomonas putida, PDB code: 1p4c, resolution 1.35 Å. STRIDE assignment: helix from 308 to 340, AverBA = 24.7°. KAKSI assignment: two helices from 308 to 315 and 320 to 341, AverBA = 4.3°. (c): chain B of C-phycocyanin from the thermophylic cyanobacterium Synechococcus elongatus, PDB code: 1jbo, resolution: 1.45 Å. STRIDE assignment: helix from residues 21 to 62, AverBA = 13.1°. KAKSI assignment: 3 helices from 21 to 33, AverBA = 4.5°, 35 to 46, AverBA = 3.0°, and 48 to 61, AverBA = 6.6°. (d): chain A from endo-xylanase from Clostridium stercorarium, PDB code: 1od3, resolution: 1 Å. STRIDE assignment: two β-strands from 61 to 82 and 116 to 135. KAKSI assignment: four β-strands from 61 to 69, 75 to 83, 115 to 122, and 128 to 136.

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