. Author manuscript; available in PMC: 2016 May 15.

Published in final edited form as: ACS Chem Biol. 2015 Feb 23;10(5):1278–1289. doi: 10.1021/cb5010367

Table 1. A-site Binding Analysis^a.

Position 2		Position 1
		Positive		Polar					Negative	Aromati			Non-Polar
		R	K	H	N	C	S	T	D	W	Y	F	βA	V	L	P
	N/A	105	125	39	54	76	52	15	14	62	33	33	51	36	35	40
Positive	R	0	-	97	0	107	1	12	2	99	0	0	0	0	0	0
Polar	H	107	-	33	8	94	17	41	7	74	57	61	67	35	65	41
	N	11	-	53	13	80	0	0	0	0	0	0	0	2	0	0
	C	103	-	21	1	39	9	37	0	85	29	0	46	67	0	22
	S	70	112	77	2	78	41	9	0	111	7	40	28	44	36	42
	T	84	94	53	48	45	44	38	3	93	58	48	49	47	41	42
Negative	D	26	-	17	0	59	2	3	0	49	9	6	9	6	4	1
Aromatic	W	120	-	68	73	4	42	78	29	44	99	35	39	63	113	47
	Y	92	16	64	19	111	31	60	0	122	12	44	28	54	48	27
	F	56	-	9	32	83	2	26	0	67	35	41	21	28	23	34
Non-Polar	βA	0	-	0	29	61	0	0	0	102	0	37	7	30	6	0
	V	89	81	65	70	132	50	37	16	66	61	50	46	48	35	45
	L	69	-	58	14	29	49	41	0	116	24	26	47	16	40	44
	P	90	-	75	37	40	36	27	12	96	34	19	37	46	38	39
Color coding ^* =			+2	+1	0	-1	-2	Zwitter

The compounds were analyzed based on the charge on individual amino acids.

The numbers are the percentage displacement of F-neo from an A-site/F-neo complex by peptidic neomycin as shown in Figure 1C for each DPA numbered compound as a function of each amino acid(s) conjugated. The third row gives the one-letter code of the amino acid on the conjugate position 1 (firstly conjugated to neomycin). The second column gives the one-letter code of the amino acid on conjugate position 2 (secondly conjugated to neomycin). Results are color coded as total charges of the amino acids on peptidic neomycin.

Total charges of the amino acids on peptidic neomycin under physiological pH. Zwitter indicates that the peptidic neomycin contains an amino acid with a positively charged side chain and an amino acid with a negatively charged side chain.

Table 1. A-site Binding Analysisa.

Table 1. A-site Binding Analysis^a.