ABAC Database

Movie generated with PyMOL

A: d.9.1.1 (red/blue)

View d.9.1.1 in Scoppi
PDB: 1ml0 (Search literature with GoPubMed)
FA: Interleukin 8-like chemokines
SF: Interleukin 8-like chemokines
SP: Human (Homo sapiens)/Human (Homo sapiens)

B: b.116.1.1 (yellow)

View b.116.1.1 in Scoppi
PDB: 1ml0 (Search literature with GoPubMed)
FA: Viral chemokine binding protein m3
SF: Viral chemokine binding protein m3
SP: Murine herpesvirus 4, Muhv-4

C: d.9.1.1 (green)

View d.9.1.1 in Scoppi
PDB: 1b3a (Search literature with GoPubMed)
FA: Interleukin 8-like chemokines
SF: Interleukin 8-like chemokines
SP: Human (Homo sapiens)

	Center of mass, domain d.9.1.1
	Center of mass, domain b.116.1.1
	Center of mass of interface atoms, domain b.116.1.1
	Center of mass, domain d.9.1.1
	Center of mass of interface atoms, domain d.9.1.1

Geometric Parameters

RMSD A1-A2	0.79
Shared interface atoms	212 (70.0%)
Angle between green and yellow interface:	32.37
Angle between green and yellow domain:	60.06
Distance between center of mass of green and yellow interface (in Angstrom):	9.36
Distance between center of mass of green and yellow domain (in Angstrom)	36.54

Sequence Alignment of domain d.9.1.1

	Meaning
-----aVTCCYNFTnrkisvqrlasyrritssKcPKeavIfktivakEICadpkqkwvqdsidhldkqt PYSSDTTPCCFAYIarplprahikeyfy-tsgKCSnpavVfvtrknrQVCanpekkwvreyinslems- _..##:.:. #_._ : ::#

Aligned interface residues . : #	14 (66%)
Aligned, similar interface residues (with positive BLOSUM value) : #	9 (42%)
Raw BLOSUM-Score for the latter residues	46


Capital letters	Residue interacts with domain A
#	Identical interacting residues
:	Residues are similar and interact
.	Residues are not similar and interact
_	Only one residue interacts

Sequences of domain b.116.1.1 and d.9.1.1

hssgvstqsvdlsqikrgdeiqahcltpaetevtecagilkdvlsknlhelqglcnvknkmgvpwvsveelgqeiitgrl pfpsvggtpvndlvrvlvvaesntpeetpeeefyayvelqtelytfglsddnvvftsdymtvwmidipksyvdvgmltra tfleqwpgakvtvmipysstftwcgelgaiseesapqpslsarspvcknsarystskfcevdgctaetgmekmslltpfg gppqqakmntcpcYYKYSVSPLPAMdhliladlagldsltspvyvmaayfdsthenpvrpssklyhcalqmtshdgvwts tsseqcpirlvegqsqnvlqvrvaPTsmPnlvgvslmlegqqyrleyfgdh pYSSDTTPCCFAYIarplprahikeyfyTsgKCSnpavVfvtrknrQVCanpekkwvreyinslems



hssgvstqsvdlsqikrgdeiqahcltpaetevtecagilkdvlsknlhelqglcnvknkmgvpwvsveelgqeiitgrl 
pfpsvggtpvndlvrvlvvaesntpeetpeeefyayvelqtelytfglsddnvvftsdymtvwmidipksyvdvgmltra 
tfleqwpgakvtvmipysstftwcgelgaiseesapqpslsarspvcknsarystskfcevdgctaetgmekmslltpfg 
gppqqakmntcpcYYKYSVSPLPAMdhliladlagldsltspvyvmaayfdsthenpvrpssklyhcalqmtshdgvwts 
tsseqcpirlvegqsqnvlqvrvaPTsmPnlvgvslmlegqqyrleyfgdh 


pYSSDTTPCCFAYIarplprahikeyfyTsgKCSnpavVfvtrknrQVCanpekkwvreyinslems

Similarities between domain b.116.1.1 and d.9.1.1

Residue Pair	BLOSUM	Score	Avg.-Distance
Ser269-Ser4	4	9.46	0.95
Tyr268-Tyr3	7	8.83	1.90
Pro274-Pro9	7	8.25	2.06
Tyr266-Tyr3	7	7.77	0.70
Pro272-Thr7	-1	7.01	0.37
Ser271-Asp6	0	6.39	0.60
Val270-Ser5	-2	6.07	0.72
Leu273-Thr8	-1	4.89	1.17
Ala275-Cys10	0	1.97	1.03
Pro356-Lys33	-1	1.20	2.10
Met276-Thr30	-1	1.13	1.31
Met276-Cys34	-1	1.07	1.93
Lys267-Tyr3	-2	0.92	1.62
Pro360-Tyr3	-3	0.74	1.89
Ala275-Pro9	-1	0.77	2.23
Tyr266-Lys33	-2	0.58	1.25
Leu273-Lys33	-2	0.45	1.66
Ala275-Thr30	0	0.34	1.99
Thr357-Lys33	-1	0.01	2.97
Tyr265-Ser4	-2	0.03	2.92
Total Score		67.87

Symbol	Atom match between
	C-alpha atoms within 3 A
	C-beta atoms within 3 A
	backbone atoms within 3 A
	side chain atoms within 2 A

The score for each residue pair is simply its BLOSUM score (if positive) + the sum of atom pair scores. The latter are between 0 and 1, with 0 for 3A distance or above and 1 for exact coordinate matches, linearly interpolated.