Fig. 4.

Representatives of the five fold classes in our test set. The arc repressor mutant, subunit A fold (CATH 1.10.10) is a common orthogonal helix bundle, found for example in the DNA-binding domain of the human telomeric protein HTRF1 (CATH code 1ba500). The immunoglobulin-like fold (CATH 2.60.40) is a β sandwich, found in many immunoglobulin-like proteins, such as the rat CD4 protein (CATH code 1cid02). The TIM barrel (CATH 3.20.30) is a very common α/β fold, shown in narbonin, a plant seed protein (CATH code 1nar00). The α/β plait fold (CATH 3.30.70) is a two-layer sandwich, shown here in MERP, a mercury binding protein (CATH code 2hqi00). The Rossmann fold (CATH 3.40.50) is a very common 3-layer sandwich fold in the mixed α/β class, found for example in the glycyl-tRNA synthetase from thermus thermophilus (CATH code 1atiB2). For each protein we show the cartoon representation of its structure (top) and the 3D trace of its sequence (bottom). Regions corresponding to helices and strands are shown in red and blue, respectively. All images were generated using PYMOL (http://www.pymol.org).