Modeling the bound conformation of Pemphigus Vulgaris-associated peptides to MHC Class II DR and DQ Alleles

Immunome Research

Table 2 Preferred core residues for PV associated alleles. Best fitting nonameric core residues in the binding groove are underlined.

No.	Residues	Allele	Core peptide sequences	No.	Residues	Allele	Core peptide sequences
I	96–112	DRB1*0402	-	V	342–356	DRB1*0402	SVKLSIAVKNKAEFH
		DQB1*0503	PFGIFVVDKNTGDINIT			DQB1*0503	SVKLSIAVKNKAEFH
			PFGIFVVDKNTGDINIT	VI	380–394	DRB1*0402	GIAFRPASKTFTVQK
II	191–205	DRB1*0402	NSKIAFKIVSQEPAG			DQB1*0503	---
		DQB1*0503	---	VII	763–777	DRB1*0402	SGTMRTRHSTGGTNK
III	206–220	DRB1*0402	TPMFLLSRNTGEVRT			DQB1*0503	---
		DQB1*0503	TPMFLLSRNTGEVRT	VIII	810–824	DRB1*0402	NDCLLIYDNEGADAT
IV	252–266	DRB1*0402	ECNIKVKDVNDNFPM			DQB1*0503	NDCLLIYDNEGADAT
		DQB1*0503	ECNIKVKDVNDNFPM	IX	963–977	DRB1*0402	ERVICPISSVPGNLA
			ECNIKVKDVNDNFPM			DQB1*0503	ERVICPISSVPGNLA