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Structure 1bj1: VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH A NEUTRALIZING ANTIBODY

Heavy chain: blue color; Light chain: violet color; Antigen: salmon color; Interfacial waters: red balls; Contact residues: shown in sticks

Number of contact residues of heavy chain = 21

Contact residues of heavy chain have 10 Hbonds, 53 hydrophobic, 134 vdW, 2 ionic interactions with antigen, and 1 Hbonds with interfacial waters

No.	Contact Residues of Heavy Chain	Region Chothia	Secondary Structure	Solvent Accessibility	Number of Hbonds with Antigen	Number of Hydrophobic Interactions	Number of VdW Interactions	Number of Ionic Interactions	Number of Hbonds with Interfacial Waters
1	THR H 30	CDR-H1	Coil	Exposed	0	0	2	0	0
2	ASN H 31	CDR-H1	Coil	Exposed	0	5	9	0	0
3	TYR H 32	CDR-H1	Strand	Intermediate	0	8	6	0	0
4	GLY H 33	Framework	Strand	Intermediate	1	0	4	0	0
5	TRP H 47	Framework	Strand	Exposed	0	0	0	0	0
6	TRP H 50	Framework	Strand	Intermediate	1	2	11	0	0
7	ASN H 52	CDR-H2	Strand	Exposed	0	1	8	0	1
8	THR H 53	CDR-H2	Strand	Buried	1	0	2	0	0
9	TYR H 54	CDR-H2	Coil	Exposed	0	18	5	0	0
10	THR H 55	CDR-H2	Coil	Exposed	0	1	0	0	0
11	THR H 59	Framework	Strand	Exposed	0	1	1	0	0
12	TYR H 99	CDR-H3	Strand	Intermediate	1	1	5	0	0
13	PRO H 100	CDR-H3	Strand	Buried	1	0	3	0	0
14	HIS H 101	CDR-H3	Coil	Exposed	0	0	5	2	0
15	TYR H 102	CDR-H3	Coil	Exposed	3	6	35	0	0
16	TYR H 103	CDR-H3	Coil	Exposed	0	4	6	0	0
17	GLY H 104	CDR-H3	Coil	Exposed	1	0	3	0	0
18	SER H 105	CDR-H3	Coil	Exposed	0	0	1	0	0
19	SER H 106	CDR-H3	Coil	Exposed	1	0	9	0	0
20	HIS H 107	CDR-H3	Coil	Exposed	0	0	0	0	0
21	TRP H 108	CDR-H3	Coil	Exposed	0	6	19	0	0


Interactions of contact residues of heavy chain		Structure of contact residues of heavy chain		Detailed contact residues of heavy chain

Number of contact residues of light chain = 5

Contact residues of light chain have 0 Hbonds, 7 hydrophobic, 5 vdW, 0 ionic interactions with antigen, and 2 Hbonds with interfacial waters

No.	Contact Residues of Light Chain	Region Chothia	Secondary Structure	Solvent Accessibility	Number of Hbonds with Antigen	Number of Hydrophobic Interactions	Number of VdW Interactions	Number of Ionic Interactions	Number of Hbonds with Interfacial Waters
1	TYR L 91	CDR-L3	Strand	Intermediate	0	0	0	0	1
2	SER L 92	CDR-L3	Strand	Intermediate	0	0	0	0	0
3	THR L 93	CDR-L3	Coil	Exposed	0	0	0	0	0
4	VAL L 94	CDR-L3	Coil	Exposed	0	3	2	0	1
5	TRP L 96	CDR-L3	Coil	Exposed	0	4	3	0	0


Interactions of contact residues of light chain		Structure of contact residues of light chain		Detailed contact residues of light chain

Number of contact residues of antigen = 17

Contact residues of antigen have 10 Hbonds, 60 hydrophobic, 139 vdW, 2 ionic interactions with antibody, and 3 Hbonds with interfacial waters

No.	Contact Residues of Antigen	Interact with Antibody Chain	Secondary Structure	Solvent Accessibility	Number of Hbonds with Antibody	Number of Hydrophobic Interactions	Number of VdW Interactions	Number of Ionic Interactions	Number of Hbonds with Interfacial Waters
1	TYR W 45	Heavy	Coil	Intermediate	0	2	1	0	0
2	LYS W 48	Heavy	Coil	Exposed	0	5	3	0	0
3	GLN W 79	Heavy	Strand	Exposed	0	0	0	0	0
4	ILE W 80	Heavy	Strand	Buried	1	0	2	0	0
5	MET W 81	Heavy	Strand	Intermediate	0	12	4	0	0
6	ARG W 82	Heavy	Strand	Intermediate	0	4	16	0	0
7	ILE W 83	Heavy	Strand	Intermediate	0	2	2	0	0
8	LYS W 84	Heavy	Strand	Intermediate	0	2	1	0	0
9	HIS W 86	Heavy & Light	Coil	Exposed	1	2	4	0	1
10	GLN W 87	Heavy & Light	Coil	Exposed	1	7	10	0	2
11	GLY W 88	Heavy	Strand	Exposed	0	0	15	0	0
12	GLN W 89	Heavy	Strand	Exposed	2	4	19	0	0
13	HIS W 90	Heavy	Strand	Exposed	2	6	22	0	0
14	ILE W 91	Heavy	Strand	Exposed	1	8	14	0	0
15	GLY W 92	Heavy	Strand	Exposed	0	0	14	0	0
16	GLU W 93	Heavy	Strand	Exposed	2	4	10	2	0
17	MET W 94	Heavy	Strand	Intermediate	0	2	2	0	0


Interactions of contact residues of antigen		Structure of contact residues of antigen		Detailed contact residues of antigen

Number of interfacial waters = 4

No.	Interfacial Waters	Number of Hbonds with Heavy Chain	Number of Hbonds with Light Chain	Number of Hbonds with Antigen	Number of Hbonds with Other Interfacial Waters
1	HOH H 421	1	0	0	1
2	HOH W 116	0	0	1	1
3	HOH L 246	0	1	1	0
4	HOH W 118	0	1	1	0


Hbonds of interfacial water molecules		Structure of interfacial water molecules		[back to top]