. Author manuscript; available in PMC: 2015 Oct 1.

Published in final edited form as: Biochim Biophys Acta. 2014 Jul 10;1844(10):1729–1740. doi: 10.1016/j.bbapap.2014.07.002

Table 2.

Contact residues during Eph-ephrin recognition at different time frame^*. The common anchoring residues are highlighted in bold fonts.

EphA4-ephrinA2

Opened EphA4								Closed EphA4

Snapshot 1 (27 ps)		Snapshot 2 (39 ps)		Snapshot 3 (48 ps)		Snapshot 4 (63 ps)		Snapshot 1 (49 ps)		Snapshot 2 (53 ps)		Snapshot 3 (61 ps)		Snapshot 4 (73 ps)

Eph	Ephrin	Eph	Ephrin	Eph	Ephrin	Eph	Ephrin	Eph	Ephrin	Eph	Ephrin	Eph	Ephrin	Eph	Ephrin

CYS73	PRO135	CYS73	PRO135	CYS73	PRO135	GLN71	ARG111			CYS73	PRO135	CYS73	PRO135	ILE59	ARG111
	PHE136	THR104	PHE136	THR104	PHE136	CYS73	PRO135			THR104	PHE136	THR104	PHE136	CYS73	PRO135
	SER137	LEU105	SER137	LEU105	SER137	THR104	PHE136			LEU105	SER137	LEU105	SER137	THR104	PHE136
		ARG106	LEU138	ARG106	LEU138	LEU105	SER137			ARG106	LEU138	ARG106	LEU138	LEU105	SER137
		ARG162		ARG162		ARG106	LEU138			CYS191		ARG162		ARG106	LEU138
		CYS191		CYS191		ARG162				ILE192		CYS191		ARG162
		ILE192		ILE192		CYS191				ALA193		ILE192		CYS191
		ALA193		ALA193		ILE192 ALA193						ALA193		ILE192 ALA193

EphA4-ephrinB2

Opened EphA4								Closed EphA4

Snapshot 1 (39 ps)		Snapshot 2 (54 ps)		Snapshot 3 (64 ps)		Snapshot 4 (150 ps)		Snapshot 1 (56 ps)		Snapshot 2 (60 ps)		Snapshot 3 (62 ps)		Snapshot 4 (66 ps)

Eph	Ephrin	Eph	Ephrin	Eph	Ephrin	Eph	Ephrin	Eph	Ephrin	Eph	Ephrin	Eph	Ephrin	Eph	Ephrin

		ILE59	PRO119	ILE59	ILE108	ILE59	THR96			ILE59	THR96	ILE59	THR96	ILE59	THR96
		THR104	ASN120	THR104	LYS109	GLN71	LEU97				LEU97	THR104	LEU97	THR104	LEU97
		LEU105	LEU121	LEU105	PHE110	CYS73	ASP107				ASP107	LEU105	ASP107	LEU105	ASP107
		ARG106	TRP122	ARG106	THR111	THR104	ILE108				ILE108	ARG106	ILE108	ARG106	ILE108
		CYS191	GLY123	CYS191	PRO119	LEU105	LYS109				LYS109	CYS191	LYS109	ARG162	LYS109
		ILE192		ILE192	ASN120	ARG106	PHE110				LEU121	ILE192	PHE110	CYS191	PHE110
		ALA193		ALA193	LEU121	CYS191	THR111				TRP122	ALA193	THR111	ILE192	THR111
					TRP122	ILE192	ILE112				GLY123		PRO119	ALA193	ILE112
					GLY123	ALA193	LYS113						ASN120		LYS113
							PRO119						LEU121		PRO119
							ASN120						TRP122		ASN120
							LEU121						GLY123		LEU121
							TRP122								TRP122
							GLY123								GLY123

The snapshots were taken when a complex structure reaches different RMSD stages: snapshot 1: RMSD = 0.45 nm; snapshot2: RMSD = 0.35; snapshot3: RMSD = 0.25; snapshot4: RMSD = 0.15.