Topologies

Tables B.2, B.3 and B.4 give text descriptions for every topology referred to in the text, taken from the February 1997 version of CATH. Some entries are highlighted in bold; these are topologies frequently referred to in the text and/or are superfolds[Orengo et al., 1994].

Unfortunately, the current version of CATH on the Web is not the same as the one used here. It has undergone some significant revisions, resulting in many domains having CATH numbers different to those used here. The search facility on the CATH Web pages allows the current classifications to be retrieved for any domains used in this work.

**Table B.1:** CATH architectures
CATH code	Architecture description
Mainly- $\alpha$ class
1.10	Non-bundle
1.20	Bundle
1.30	Few secondary structures
Mainly- $\beta$ class
2.10	Ribbon
2.20	Single sheet
2.30	Roll
2.40	Barrel
2.50	Clam
2.60	Sandwich
2.70	Distorted sandwich
2.80	Trefoil
2.90	Orthogonal prism
2.100	Aligned prism
2.110	4 Propellor
2.120	6 Propellor
2.130	7 Propellor
2.140	8 Propellor
2.150	2 Solenoid
2.160	3 Solenoid
2.170	Complex
Mixed- $\alpha \beta$ class
3.10	Roll
3.20	Barrel
3.30	2-Layer sandwich
3.40	3-Layer $\alpha\beta\alpha$ sandwich
3.50	3-Layer $\beta\beta\alpha$ sandwich
3.60	4-Layer sandwich
3.70	Box
3.80	Horseshoe
3.90	Complex
3.100	Few secondary structures
Irregular class (Few secondary structures)
4.10	Irregular

**Table B.2:** Descriptions for selected mainly- $\alpha$ CATH topologies
CATH code	Topology description
1.10.270	Glutathione S-Transferase, subunit A, domain 2
1.10.320	Cytochrome P450 ERYF, domain 3
1.10.390	Neutral Protease Domain 2
1.10.400	GI Alpha 1, domain 2-like
1.10.430	Interferon Gamma, subunit A
1.10.490	Globin-like
1.10.500	Beta-Lactamase, domain 2
1.10.530	Lysozyme
1.10.550	Cytochrome P450 ERYF, domain 2
1.10.560	GROEL, domain 1
1.20.120	Four Helix Bundle (Hemerythrin (Met), subunit A)
1.20.140	Butyryl-COA Dehydrogenase, subunit A, domain 3
1.20.160	Granulocyte Colony-Stimulating Factor (Form II RCG-CSFII), subunit A

**Table B.3:** Descriptions for selected mainly- $\beta$ CATH topologies
CATH code	Topology description
2.10.90	Cystine Knot Cytokines, subunit B
2.30.40	Urease, subunit C, domain 1
2.40.100	Cyclophilin
2.40.110	Butyryl-COA Dehydrogenase, subunit A, domain 2
2.40.130	Lipocalin (Streptavidin, subunit A)
2.40.80	Elongation Factor TU, domain 3
2.40.90	Nitrate Reductase (C-Terminal Fragment), domain 1
2.60.40	Immunoglobulin-like
2.60.90	Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)
2.60.140	Jelly Roll
2.60.150	Delta-Endotoxin, domain 2
2.70.70	Glucose Permease (Domain IIA)
2.70.90	Xylanase
2.110.10	Hemopexin
2.170.10	Pepsin Hydrolase, subunit A, domain 1

**Table B.4:** Descriptions for selected mixed- $\alpha \beta$ CATH topologies
CATH code	Topology description
3.10.10	HIV Type 1 Reverse Transcriptase, subunit A, domain 1
3.10.70	Grea Transcript Cleavage Factor, domain 2
3.10.100	Mannose-Binding Protein A, subunit A
3.10.110	Ubiquitin Conjugating Enzyme
3.10.160	Papain, domain 1
3.10.200	Carbonic Anhydrase II
3.10.210	Biotin Carboxylase, subunit A, domain 3
3.20.40	TIM Barrel
3.30.160	Human Macrophage Inflammatory Protein 1 Beta, subunit A
3.30.190	Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
3.30.280	Urease, subunit A
3.30.340	Alpha-Beta Plaits
3.30.390	Enolase-like, domain 1
3.30.420	Human HIV Type 1 Reverse Transcriptase, subunit A, domain 4
3.30.550	Holo-D-Glyceraldehyde-3-Phosphate Dehydrogenase, domain 2
3.40.40	Heat-Shock Protein, domain 1
3.40.50	Nitrogenase Molybdenum-Iron Protein, subunit A, domain 3
3.40.100	Phosphofructokinase, subunit A, domain 2
3.40.110	Phosphoglycerate Kinase, domain 1
3.40.170	Transketolase, subunit A, domain 3
3.40.180	Ribonuclease H Domain of HIV-1 Reverse Transcriptase
3.40.190	D-Maltodextrin-Binding Protein, domain 2
3.40.270	Tryptophan Synthase, subunit B, domain 1
3.40.320	D-Alanine-D-Alanine Ligase, domain 1
3.40.330	Doubly wound
3.40.360	Succinyl-COA Synthetase, subunit B, domain 1
3.40.390	Collagenase (Catalytic Domain)
3.40.400	Phosphate-Binding Protein, domain 1
3.40.430	Dihydrofolate Reductase, subunit A
3.40.470	Uracil-DNA Glycosylase, subunit E
3.40.480	Phosphoglycerate Kinase, domain 2
3.40.490	GMP Synthetase, subunit A, domain 1
3.40.500	Pyruvate Oxidase, subunit A, domain 3
3.40.520	Tryptophan Synthase, subunit B, domain 2
3.40.560	Rec A Protein, domain 1
3.40.610	Deoxyribonuclease I, subunit A, domain 1
3.40.640	Aspartate Aminotransferase, domain 2
3.90.90	Lysozyme
3.90.230	Creatine Amidinohydrolase