BMC Bioinformatics

Table 3 Description of Protein Blocks in short loops. For each position (indexed from -4 to + 4) of the 16 protein blocks (PBs), the highest amino acid over-representations (Z-score > 4) and under-representations (Z-score < -4) are labeled by the symbols (+) and (-), respectively. The new over- and under-representations specific to the short loops are displayed in bold and italics respectively. For analysis purpose, a five-residue PB (numbered from -2 to +2) is encompassed in a longer fragment of length 9 (numbered from -4 to +4).

From: Use of a structural alphabet for analysis of short loops connecting repetitive structures

PB		-4	-3	-2	-1	0	1	2	3	4
a	+			N	G	V		V
	-				IVLAPT	P	G	G
b	+	F	V			D		P
	-
c	+		G	G		VL	IVP	IVP
	-		IV	IVL	PG	GD	GE	GD
d	+
	-
e	+		V	V	V			G	G	G
	-							VL
f	+	G	F	V	IVL	STD	P	SDE	G
	-			G	GD	K	G	VLPG
g	+						P	G
	-
h	+			V			G
	-
i	+				P	G	K
	-
j	+					G
	-
k	+			I	STD	P	DE		A	E
	-				VLAR	G	PG	P
l	+			PSTD	P	DE		LA	E	A
	-			VLA		PG		GD
m	+
	-
n	+			LA				G
	-				G		G	VLA
o	+		LA		A E		G		P	V
	-				G	PG	VLAPT	G
p	+	A		AE		G	M	P	V
	-			G	PG	AP		G

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ISSN: 1471-2105

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