AppA Server

Structure 6bgt: Structure of Trastuzumab Fab mutant in complex with Her2 extracellular domain

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 = 20

Contact residues of heavy chain have 5 Hbonds, 60 hydrophobic, 63 vdW, 11 ionic interactions with antigen, and 3 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	VAL B 2	Framework	Strand	Intermediate	0	2	2	0	0
2	GLY B 26	CDR-H1	Strand	Exposed	0	0	0	0	0
3	PHE B 27	CDR-H1	Coil	Intermediate	0	4	6	0	0
4	ASN B 28	CDR-H1	Coil	Exposed	0	0	0	0	0
5	ASP B 31	CDR-H1	Coil	Exposed	0	0	0	0	0
6	TYR B 33	Framework	Strand	Intermediate	0	9	5	0	0
7	ARG B 50	Framework	Coil	Intermediate	4	0	7	8	2
8	TYR B 52	CDR-H2	Coil	Exposed	0	0	0	0	0
9	TYR B 57	CDR-H2	Strand	Exposed	0	15	11	0	1
10	THR B 58	Framework	Strand	Intermediate	0	0	0	0	0
11	ARG B 59	Framework	Strand	Exposed	0	0	4	3	0
12	ARG B 98	Framework	Strand	Intermediate	0	0	10	0	0
13	TRP B 99	CDR-H3	Strand	Intermediate	0	10	3	0	0
14	GLY B 100	CDR-H3	Strand	Buried	0	0	1	0	0
15	GLY B 101	CDR-H3	Coil	Exposed	0	0	0	0	0
16	ASP B 102	CDR-H3	Coil	Exposed	0	0	0	0	0
17	GLY B 103	CDR-H3	Coil	Exposed	1	0	4	0	0
18	PHE B 104	CDR-H3	Coil	Exposed	0	7	3	0	0
19	TYR B 105	CDR-H3	Coil	Exposed	0	13	7	0	0
20	TYR B 109	CDR-H3	Coil	Exposed	0	0	0	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 = 13

Contact residues of light chain have 4 Hbonds, 39 hydrophobic, 41 vdW, 0 ionic interactions with antigen, and 0 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	ASP A 28	CDR-L1	Coil	Exposed	0	0	0	0	0
2	ASN A 30	CDR-L1	Coil	Exposed	1	1	4	0	0
3	THR A 31	CDR-L1	Coil	Exposed	1	0	3	0	0
4	ALA A 32	CDR-L1	Strand	Intermediate	0	2	1	0	0
5	TYR A 49	Framework	Coil	Exposed	0	8	3	0	0
6	SER A 50	CDR-L2	Coil	Exposed	0	0	3	0	0
7	PHE A 53	CDR-L2	Coil	Exposed	0	15	5	0	0
8	TYR A 55	CDR-L2	Coil	Exposed	0	5	0	0	0
9	SER A 56	CDR-L2	Coil	Exposed	0	0	0	0	0
10	HIS A 91	CDR-L3	Strand	Exposed	0	0	7	0	0
11	TYR A 92	CDR-L3	Strand	Exposed	1	8	9	0	0
12	THR A 93	CDR-L3	Coil	Exposed	0	0	1	0	0
13	THR A 94	CDR-L3	Coil	Exposed	1	0	5	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 = 22

Contact residues of antigen have 9 Hbonds, 99 hydrophobic, 104 vdW, 11 ionic interactions with antibody, and 2 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	PRO C 557	Heavy	Coil	Exposed	0	10	7	0	0
2	GLU C 558	Heavy	Coil	Exposed	2	5	9	5	2
3	ASP C 560	Heavy & Light	Coil	Intermediate	3	0	8	6	0
4	GLN C 561	Heavy	Coil	Exposed	0	0	2	0	0
5	LYS C 569	Light	Coil	Exposed	1	2	2	0	0
6	ASP C 570	Heavy	Coil	Intermediate	0	1	2	0	0
7	PRO C 571	Heavy & Light	Coil	Exposed	0	8	7	0	0
8	PRO C 572	Heavy & Light	Coil	Exposed	0	3	13	0	0
9	PHE C 573	Heavy	Coil	Exposed	0	28	11	0	0
10	PRO C 579	Heavy	Coil	Intermediate	0	0	0	0	0
11	TYR C 588	Heavy	Coil	Exposed	0	6	19	0	0
12	MET C 589	Heavy & Light	Coil	Exposed	0	16	6	0	0
13	ILE C 591	Heavy	Coil	Exposed	0	1	2	0	0
14	LYS C 593	Heavy & Light	Strand	Intermediate	1	0	1	0	0
15	ASP C 596	Light	Strand	Exposed	0	0	0	0	0
16	GLU C 598	Light	Coil	Exposed	0	0	0	0	0
17	ALA C 600	Light	Strand	Exposed	0	1	3	0	0
18	CYS C 601	Light	Strand	Buried	0	0	0	0	0
19	GLN C 602	Light	Strand	Exposed	2	0	4	0	0
20	PRO C 603	Light	Strand	Exposed	0	15	8	0	0
21	CYS C 604	Light	Strand	Intermediate	0	0	0	0	0
22	PRO C 605	Light	Coil	Exposed	0	3	0	0	0


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

Number of interfacial waters = 1

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 C 816	3	0	2	0


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