* Color scheme for logos of proteins (for the MakeLogo program).
* The colors are based on the divisions discussed on the usenet
* and given to me by Irit Orr. Modification according to division of Joel
* Sussman. The differences from Sussman's division are -
* Met in a group by itself (not with Pro), Ala with hydrophobic (not with Gly),
* Tyr with aromatics (not with Asn and Gln), His with Arg and Lys (not by
* itself), and charged aa separated to positive and negative.
* Shmuel Pietrokovski. June 94'
* 
* Red for acidic amino acids; Glu, Asp
D 1 0 0
d 1 0 0
E 1 0 0
e 1 0 0
*
*Blue for basic amino acids; Lys, Arg, His
K 0 0 1 
k 0 0 1 
R 0 0 1 
r 0 0 1 
H 0 0 1 
h 0 0 1 
*
*White for polar OH/SH amino acids; Ser, Thr, Cys
* White would not be seen onthe background so it is light grey
C 0.8 0.8 0.8
c 0.8 0.8 0.8
S 0.8 0.8 0.8
s 0.8 0.8 0.8
T 0.8 0.8 0.8
t 0.8 0.8 0.8
*
*Green for amide amino acids; Asn and Gln
N 0 0.8 0.4
n 0 0.8 0.4
Q 0 0.8 0.4
q 0 0.8 0.4
*
*Yellow (sulphur) for Metionine
M 1 0.9 0
m 1 0.9 0
*
*Black for hydrophobic amino acids; Ala, Val, Leu, Ile
*(Black is the opposite of white and so if white is for hydrophilic
*hydroxyl amino acids black is a natural for hydrophobic ones)
*A
*a
*V
*v
*L
*l
*I
*i
*
*Orange for aromatic amino acids; Tyr, Phe, Trp
*(since "orange" sounds a little like "aromatic" and
*oranges are aromatic (if that suits you better))
Y 1 0.6 0
y 1 0.6 0
F 1 0.6 0
f 1 0.6 0
W 1 0.6 0
w 1 0.6 0
*
*Purple for proline; Pro
*(since both have "prl" in them)
P 0.7 0 1
p 0.7 0 1
*
*Grey for glycine; Gly
*(since both start with "g" and grey is sort of blah-like glycine)
G 0.5 0.5 0.5
g 0.5 0.5 0.5
*
*All other letters light blue so they would stand out
B 0 1 1
b 0 1 1
J 0 1 1
j 0 1 1
O 0 1 1
o 0 1 1
U 0 1 1
u 0 1 1
X 0 1 1
x 0 1 1
Z 0 1 1
z 0 1 1
