Table (II).

Chart summarizing the different hydrophobicity scales and their applicability

scale	ref	year	derivation*	α/β	2-state/3-state	characteristics/applicability
Hopp & Woods	1	1981	exp	n/a	2	• hydrophilicity scale for antigenic sites on the protein surface; • derived from the values of Levitt44; • some values were adjusted to fit immunochemical data of 12 proteins; • for the proteins only the primary sequence was available!; • window used is 6 residues ≈ length of antigenic determinant
Goldman, Engelman, Steitz	2	1986	exp	α	2	• hydrophobicity scale for single trans-membrane helices; • semi-theoretical approach based on energetic considerations of residues undergoing hydrogen bonds in helices derived from experimental data in the literature; • hydrophobicity scale as a sum of hydrophilic and hydrophobic components
Wimley & White	3,4	1996	exp	α	2 + 3	• derived by measuring the partitioning energies of host-guest penta-peptides; • whole residue scale that considers the polar peptide bond; • interface: POPC vesicle interface; bilayer: n-octanol; • for unfolded peptides in all 3 phases (solution, interface, bilayer)
Hessa et al.	23,24	2005/2007	exp	α	2 / pot	• designed TM helix within the Lep protein that is inserted via the Sec61 translocon; • TM helix is 19-residue helix with amino acid in question incorporated in the center; • measured fraction of singly vs. doubly glycosylated Lep molecules to derive the scale; • therefore applicable to folded MPs; • scale has been extended to position-dependent free energy scale (2007)
Eisenberg & Weiss	45	1982	cons	n/a	2	• normalized consensus scale of five different scales
Kyte & Doolittle	10	1982	cons	n/a	2	• normalized consensus scale based on experimental observations of different scales; • refinement by studying hydropathy plots of proteins of known X-ray structure;
Guy	18	1985	cons	n/a	2	• based on experimental and statistical results from several studies; • considers solvent accessibility according to accessible layers of amino acids in globular proteins
Janin	7	1979	KB	n/a	2	• derived from X-ray structures of 22 soluble proteins; • looked at molar fraction of buried and accessible residues
Punta & Maritan	8	2003	KB	α	2	• derived two membrane propensity scales from two TM helix databases using a simple perceptron algorithm; • databases contained 118/228 TM helices; • sequence identity of the proteins was 30%
Beuming & Weinstein	25	2004	KB	α	n/a	• calculated surface propensities of amino acids (probability of finding a residue on the surface of a TM protein); • based on surface fractions of residues; • considered 28 α-helical MPs
Senes et al.	9	2007	KB	α	2 / pot	• calculated membrane depth-dependent potential for amino acid side-chains; • considered 24 α-helical MPs
UHS		2008	KB	α/β	2 + 3	• derived from 60 known structures of folded MPs; • considers folded structures both in solution and membrane bilayer; • both α, β, and α/β structures were taken into account with approximately equal distribution of helices and strands; • considers only depth in membrane bilayer and no accessibility or secondary structure
MHS		2008	KB	α	2 + 3	• derived from 16 known structures of folded MPs from mammalian organisms; • only α-helical structures could be taken into account; • considers folded structures both in solution and membrane bilayer; • considers only depth in membrane bilayer and no accessibility or secondary structure

^*exp: experimental; cons: consensus; KB: knowledge-based; pot: potential