Reference:-David Bacon and Wayne F. Anderson, "A Fast Algorithm for Rendering Space-Filling Molecule Pictures", Journal of Molecular Graphics, Vol. 6, No.4, pp.219-220, December 1988.
Amino acid Color name Example
ASP, GLU bright red  
CYS, MET yellow  
LYS, ARG blue  
SER, THR orange  
PHE, TYR mid blue  
ASN, GLN cyan  
GLY light grey  
LEU, VAL, ILE green  
ALA dark grey  
TRP pink  
HIS pale blue  
PRO flesh