Amino acid colour schemes


The Clustal default colour scheme is:
G, P, S, T Orange
H, K, R Red
F, W, Y Blue
I, L, M, V Green


The colour scheme in Lesk, Introduction to Bioinformatics, uses 5 groups (note Histidine):
Small nonpolar G, A, S, T Orange
Hydrophobic C, V, I, L, P, F, Y, M, WGreen
Polar N, Q, H Magenta
Negatively charged D, E Red
Positively charged K, R Blue


The colour scheme used by Multiple Alignment Editor:
A, G Light green
C Green
D, E, N, Q Dark green
I, L, M, V Blue
F, W, Y Lilac
H Dark blue
K, R Orange
P Pink
S, T Red


Polar positive H, K, R Blue
Polar negative D, E Red
Polar neutral S, T, N, Q Green
Non-polar aliphaticA, V, L, I, M White
Non-polar aromatic F, W, Y Magenta
P, G Brown
C Yellow
Special characters B, Z, X, -Grey


See this site, Shapely table, for amino acid colours in Shapely scheme.