. Author manuscript; available in PMC: 2011 Aug 24.

Published in final edited form as: J Mol Graph Model. 2010 Apr 24;29(1):46–53. doi: 10.1016/j.jmgm.2010.04.005

Table 1.

Interactions between VEEV nsP2 protease and peptide substrates.

	nsP12	Substrate nsP23	nsP34	Enzyme	nsP12	Contact nsP23	nsP34
				Ala⁴⁷⁴		+	+
				Asn⁴⁷⁵	+	+	+
P1’	Gly⁵³⁶	Ala¹³³⁰	Tyr¹⁸⁶⁷	Cys⁴⁷⁷	+	+	+
				Lys⁴⁸⁰			±^‡
				His⁵⁴⁶	±	±	±
				Asn⁴⁷⁵	+	+	+
				Cys⁴⁷⁷	+	±	+
				Trp⁴⁷⁸	±
P1	Ala⁵³⁵	Cys¹³²⁹	Ala¹⁸⁶⁶	Ala⁵⁰⁹	+	+	+
				Asn⁵⁴⁵	±		±
				His⁵⁴⁶	+	+	+
				Leu⁶⁶⁵	+	+	+
				Cys⁴⁷⁷	+		+
				Trp⁴⁷⁸		+
P2	Gly⁵³⁴	Gly¹³²⁸	Gly¹⁸⁶⁵	Ala⁵⁰⁹	+	+	+
				His⁵¹⁰	±	±	±
				Trp⁵⁴⁷	+	+	+
				His⁵¹⁰	+	+	+
				Ile⁵⁴²	+		+
P3	Ala⁵³³	Ala¹³²⁷	Ala¹⁸⁶⁴	Trp⁵⁴⁷	+	+	+
				Ile⁶⁹⁸	+	+	+
				Met⁷⁰²	+	+	+
				Ser⁵¹¹	±	±	±
				Glu⁵¹³	±
P4	Glu⁵³²	Glu¹³²⁶	Asp¹⁸⁶³	Trp⁵⁴⁷	+	+	+
				Met⁷⁰²			+
				Lys⁷⁰⁶	±	±	±

+ VDW contact

± hydrogen bond

^{±^‡}

Indicates probable cation-π interaction

Contacts were determined using the Contact of Structural Units (CSU) server[15] and LIGPLOT[14] with a 4.0 Å cut-off distance.