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Figure 1 | Theoretical Biology and Medical Modelling

Figure 1

From: IMGT/Collier-de-Perles: a two-dimensional visualization tool for amino acid domain sequences

Figure 1

Amino acid properties and the IMGT Collier de Perles 2D hydropathy plot. (A): The 11 IMGT physicochemical classes of the 20 common amino acids [1]. (B): IMGT Colliers de Perles of a V domain of an IG or antibody. IMGT Collier de Perles on one layer, obtained by the IMGT/Collier-de-Perles online tool [14] at the IMGT Home page, http://www.imgt.org. Four options are shown for the V domain of the heavy domain (VH) of trastuzumab, a therapeutic antibody: ‘50% hydrophobic positions’ (with that option, an amino acid at a given position is colored in blue if an hydrophobic amino acid is found at that position in 50% or more of the sequences used for establishing the statistical profile [17], ‘IGH 80% hydropathy classes’, ‘IGH 80% volume classes’, ‘IGH 80% physicochemical classes’. The CDR-IMGT lengths are [8.8.13]. The five conserved amino acid positions of a V domain 23, 41, 89, 104 and 118 (1st-CYS C23, CONSERVED-TRP W41, hydrophobic 89, 2nd-CYS C104, J-PHE or J-TRP 118, here W118) appear with red and bold letters. The six anchors (positions 26 and 39, 55 and 66, 104 and 118) which belong to the framework regions (FR-IMGT) and support the complementarity determining regions (CDR-IMGT) are in squares. (C): IMGT Collier de Perles on 2 layers and with hydrogen bonds (green lines) of the trastuzumab VH , provided by IMGT/3Dstructure-DB [26, 34] (PDB code 1n8z). These hydrogen bonds are from the experimental 3D structures and are displayed by the IMGT/Collier-de-Perles tool integrated in IMGT/3Dstructure-DB [26, 34]. The 3D structure representation of a V domain with its strands and loops, based on the IMGT Collier de Perles delimitations [21, 22, 25], is also shown.

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