Comparing interfacial dynamics in protein-protein complexes: an elastic network approach

BMC Structural Biology

Table 1 List of protein-protein interfaces investigated

				Chain Size (a.a.)			Interface		Semi-int.		NOXclass interface
PDB	Chains		Classification	1 ^st	2 ^nd	both	Å ²	a.a.	1 ^st	2 ^nd
Interfaces of Type I
1a03	A	B	calcium-binding protein	90	90	l80	307l	82	37	45	obligate
1gdh	A	B	oxidoreductase	320	320	640	6254	l48	74	74	obligate
1a05	A	B	oxidoreductase	357	357	7l4	5258	l25	62	63	obligate
1ag1	O	T	isomerase	249	249	498	3025	75	37	38	obligate
1hii	A	B	hydrolase	99	99	l98	3436	83	4l	42	obligate
1mdi	A	B	electron transport/peptide	l05	l3	ll8	l340	34	24	l0	non-obligate
2gsa	A	B	chlorophyll biosynthesis	427	427	854	9l78	233	ll8	ll5	obligate
1ger	A	B	oxidoreductase	448	448	896	6777	l72	86	86	obligate
Interfaces ofType II
1azy	A	B	glicosyltransferase	440	440	880	l744	42	2l	2l	non-biological
1a0a	A	B	transcription factor	63	63	l26	l860	44	22	22	obligate
1mv4	A	B	de novo protein	37	37	74	l833	43	2l	22	obligate
1a93	A	B	leucine zipper	32	32	64	l565	34	l7	l7	non-obligate
1a15	A	B	chemokine	67	67	l24	l480	38	l8	20	obligate
1q6a	A	B	circadian clock protein	l07	l07	2l4	l8l0	46	23	23	non-obligate
Interfaces ofType III
2fhw	B	A	signaling protein	27	24	5l	ll53	29	l5	l4	obligate
1jm7	A	B	antitumor	l03	97	200	2769	72	39	33	obligate
1tmz	A	B	tropomyosin	32	32	64	l586	35	l7	l8	obligate
1an2	A	C	DNA-binding protein	86	86	l72	257l	64	32	32	obligate
2sic	E	I	proteinase/inhibitor	275	l07	382	l6l7	45	3l	l4	non-obligate
1lfa	A	B	cell adhesion	l83	l83	365	628	2l	l0	ll	non-biological
1shc	A	B	signal transduction/peptide	l95	ll	206	l456	34	25	9	non-obligate
2a93	A	B	leucine zipper	32	32	64	l568	34	l6	l8	non-obligate

For each protein complex investigated in this work it is given: the PDB ID; the chains that form the considered interface; the classification, according to PRISM http://prism.ccbb.ku.edu.tr/prism/; the number of amino acids for the first and second chain listed, and the total number; the size of the interface in Å² and in number of amino acids involved; the number of interface amino acids in the first and second chain; the classification of the interface into biological obligate, biological non-obligate or non-biological, according to NOXclass [68].

ISSN: 1472-6807