Table 2.

Pairwise analysis of known chemokine structures

Molecule	SDF–1α	IL-8	NAP-2	PF-4	MGSA	MIP-1β	MCP-1	RANTES
SDF-1α	—	2.0/48	2.0/51	2.0/51	2.0/45	2.0/51	1.9/45	2.2/51
IL-8	27%	—	1.0/56	1.5/56	1.7/56	1.6/51	1.2/50	1.5/48
NAP-2	21%	46%	—	1.2/56	1.6/57	1.5/49	1.7/63	1.3/47
PF-4	19.4%	32%	51.4%	—	1.7/45	1.9/50	1.7/50	1.9/48
MGSA	22.3%	42%	57%	31.4%	—	1.6/41	1.6/47	1.6/48
MIP-1β	21%	22.2%	13.2%	12%	12%	—	1.3/50	1.3/52
MCP-1	16.4%	21%	17.1%	14%	11.4%	37%	—	1.4/54
RANTES	24%	24%	10%	11.4%	12.3%	50%	23.2%	—

The least squares superposition was done by using the Cα atoms of the four CXC chemokines IL-8 (18), NAP-2 (25), PF-4 (26), and MGSA (27), and the three CC chemokines MIP-1β (22), MCP-1 (23), and RANTES (24). The initial framework of residues used for the alignment consisted of Cys-9, Cys-34, Cys-50, and Trp-57 in SDF-1α and their counterparts in the other chemokines. The upper quadrant of the table lists the rms difference followed by the total number of aligned residues in the superposition for each pair of chemokines. Percentage sequence identities are shown in the bottom quadrant in bold lettering. The rms difference was calculated with the lsqman option in o (16).