An integrated approach to epitope analysis I: Dimensional reduction, visualization and prediction of MHC binding using amino acid principal components and regression approaches

Table 1 First three principal components of amino acid physical properties.

Amino acid	Principal Component 1	Amino acid	Principal Component 2	Amino acid	Principal Component 3
K	-6.68	W	-3.50	C	-3.84
R	-6.30	R	-2.93	H	-1.94
D	-6.04	Y	-2.06	M	-1.46
E	-5.70	F	-1.53	E	-1.46
N	-4.35	K	-1.32	R	-0.91
Q	-3.97	H	-1.00	V	-0.35
S	-2.65	Q	-0.47	D	-0.18
H	-2.55	M	-0.43	I	0.04
T	-1.42	P	-0.36	F	0.05
G	-0.76	L	-0.20	Q	0.15
P	-0.03	D	0.03	W	0.16
A	0.72	N	0.21	N	0.30
C	2.11	I	0.29	Y	0.37
Y	2.58	E	0.34	T	0.94
M	4.14	T	0.80	K	1.16
V	4.79	S	1.84	L	1.17
W	5.68	V	1.98	G	1.21
L	6.59	A	2.48	S	1.30
I	6.65	C	2.74	A	1.42
F	7.18	G	3.08	P	1.87

Principal component 1 is correlated with polarity or hydrophobicity, principal component 2 is correlated with size. The physical correlate of principal component 3 is not obvious but is generally considered to be electronic.