Table 4. Clusters predicted by computer algorithm. Cluster # Amino acids Cluster # Amino acids ECD#1 ECD#2 ECD#3 ECD#4 ECD#5 ECD#6 98–100, 113, 135, 138, 162 86–90, 155–157, 159–160 336–338, 359, 361, 363–366, 369–370 1, 26, 29, 445, 466–471 474–475, 477, 480–482 249, 252, 259–263, 265 FL#1 FL#2 FL#3 FL#4 FL#5 FL#6 doi:10.1371/journal.pone.0005309.t004 137–138, 164–169 172–173, 175–176, 179 336–338, 359, 361–363, 365–367, 370, 372– 373 32, 35–36, 50–51, 53–57, 59, 73, 75–76, 84, 467–468 284–286, 289,291, 295–299, 311–312 323, 326–328, 331 Epitope Mapping with Mimotopes Cluster # TUBO#1 Amino acids 246, 248–249, 252, 260–264 Figure 4. Three-dimensional modeling of predicted epitopes and non-conserved amino acids. A. Epitopes predicted by the DiscoTope method. Immunodominant epitopes are coloured in red, epitopes of lower immunogenicity are shown in yellow. B. Map reveals surface exposed amino acids on the rat HER-2 extracellular domain that differ from the corresponding residues on mouse HER-2. Amino acid are coloured according to RasMol amino acid colour code: red = Glu and Asp, blue = Arg and Lys, brown = Pro, orange = Ser and Thr, Cyan = Asn and Gln, violet = Trp and Phe, purple = His. doi:10.1371/journal.pone.0005309.g004 PLoS ONE | www.plosone.org 9 April 2009 | Volume 4 | Issue 4 | e5309