Table VIII.

Hydrophobicity of Amyloidogenic and Non-amyloidogenic Residues in Amyloidogenic Proteins and of Residues in Globular Proteins in General^a,b

	Amyloidogenic proteinsc
	Amyloidogenic residues	Non-amyloidogenic residues	All residues	Culled set of globular proteinsb
Secondary structured
All residues	0.600	0.372	0.380	0.366
Helical	0.638	0.409	0.418	0.356
Strand	0.800	0.625	0.634	0.616
Coil	0.356	0.159	0.165	0.218

¹Thirty amyloidogenic proteins represented by PDB models: 1A79, 1APS, 1ATI, 1B0G, 1BEB, 1CKT, 1GKG, 1HKQ, 1IRU, 1KCQ, 1LFH, 1QLX, 1REX, 1RW5, 1SOH, 1TTA, 1USG, 1W4R, 1WLA, 1X3B, 1XDA, 1XQ8, 2D4G, 2DPK, 2ES2, 2HNH, 2JD4, 2NTT, 2QJP and 3BN6. Hydrophobicity calculated using Perl program ‘stride_hydrophob’. Analysis comprised 589 amyloidogenic and 15654 non-amyloidogenic residues: 214 helical amyloidogenic, 188 strand amyloidogenic and 187 coil amyloidogenic residues; 5593 helical non-amyloidogenic, 4136 strand non-amyloidogenic and 5925 coil non-amyloidogenic residues.

²Culled set obtained from PISCES website: http://dunbrack.fccc.edu/PISCES.php (<20% SID, <1.6 Å resolution, <0.25 R factor).⁶² Hydrophobicity calculated using Perl program ‘stride_hydrophob’. Analysis comprised 586 PDB structures consisting of 200,754 amino acid residues.

³For AcP and medin, structures of homologous proteins were used (PDB IDs: 1APS and 3BN6, respectively), and the FASTA sequence from the UniProt entries, P14621 and Q08431, applies for hydrophobicity measurements.

⁴Secondary structure according to STRIDE: http://webclu.bio.wzw.tum.de/cgi-bin/stride/stridecgi.py.¹¹⁴