Fig. 3

Characteristics of Eph LBD and Ephrin RBD domains. a Multiple sequence alignment of animal representatives of the Eph-receptor extracellular Ligand Binding Domain (LBD). Alignment depicts only the conserved blocks and residue number is not continuous. For complete alignment see Additional file 1: Figure S2. Secondary structure elements shown above the alignment are based on the LBD domain (Chain-A) of EphA2-EphrinA1 structural complex (3CZU) [30]. The “A-M” nomenclature shown above the alignment was adapted from [37] The three regions highlighted in pink (residues: 35–41; 52–70; 151–168) form the interaction interface between the Eph’s LBD and Ephrin’s RBD; the residues previously characterised to be involved in the interaction between these domains are shown in red. Such interface residues that are substituted with similar amino acid properties across alignment are marked in blue. b Multiple sequence alignment of the Ephrin ligand Receptor Binding Domain (RBD) in representatives of animals and choanoflagellates. Alignment depicts only the conserved blocks and residue number is not continuous. For complete alignment see Additional file 1: Figure S3. Secondary structure elements shown above the alignment are based on the RBD domain (Chain-B) of EphA2-EphrinA1 structural complex (3CZU). The “A-K” nomenclature shown above the alignment was adapted from [37]. The four regions highlighted in light green (residues: 19–21; 44–46; 89–90; 102–120) form the interaction interface between the Ephrin’s RBD and Eph’s LBD; residues previously characterised to be involved in the interaction between these domains are shown in red. Such interface residues that are substituted with similar amino acid properties across alignment are highlighted in blue. These interface residues were screened or identified based on all available vertebrate Eph-Ephrin structural complexes (see Additional file 1: Table S4 for comprehensive screen of interface residues and corresponding literature). The inset on the right (from top to bottom) shows structural renderings of: 1) EphA2-LBD (regions forming the interface with the Ephrin-A1-RBD are colored dark pink); 2) interaction interface regions of EphA2-LBD and Ephrin-A1-RBD (interface regions are shown as dots); Ephrin-A1-RBD (regions forming interface with EphA2-LBD are colored light green). See Additional file 1, Figure S2 and S3 for full-length alignments shown in panels A and B, respectively. For both the alignments, the colouring is based on 30% consensus threshold using the following scheme: nonpolar residues (AGVLIPFMW) shaded yellow, uncharged/charged polar (NQSTYDEHRK) shaded light blue, negatively charged (DE) shaded light purple, positively charged (HKR) shaded light green, aromatic (FHWY) residues shaded light brown and cysteines forming disulphide bridges shaded orange