. Author manuscript; available in PMC: 2010 Jul 1.

Published in final edited form as: Proteins. 2009 Jul;76(1):13–29. doi: 10.1002/prot.22315

Table (IV).

Per amino acid agreements for the two-state scenario

		PDB				PDB
			TM	SOL	avg		TM	SOL	avg
*pred*		*UHS*				*Guy*
	TM		70 ± 10	25 ± 7			81	49
	*SOL*		30 ± 10	75 ± 7			19	51
					73 ± 2				66
*pred*		*GES*				*PM_1D*
	TM		66	23			86	53
	*SOL*		34	77			14	47
					71				66
*pred*		*Janin*				*PM_3D*
	TM		72	32			83	52
	*SOL*		28	67			17	48
					70				66
*pred*		KD				HW
	TM		76	39			89	59
	*SOL*		24	61			11	41
					68				65
*pred*		WW				EW
	TM		48	13			88	60
	*SOL*		52	87			12	40
					67				64
*pred*		*HWvH*
	TM		11	1
	*SOL*		89	99
					55

The table shows the percentage per amino acid agreements for the two-state scenario between the prediction and the PDB for the hydrophobicity scales from the literature and the UHS. (TM) membrane bilayer; (SOL) soluble phase (SOL); (avg) average value of agreement between TM and SOL. The values are computed for a window size of 15 residues for averaging. The first four scales on the left show similar performances for the TM and the SOL, whereas the other scales exhibit an uneven distribution.