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Contact Analysis

Solvent accessibilities and antigen contacts were computed for all residues in the 26 antibody-antigen complex structures (Table 2.1). Figures 2.1 & 2.2 summarize this information for each of the six CDRs. The bar graphs show how many antibody structures have solvent accessible or antigen contacting residues at each sequence position. The line graphs compare contacts made by different antigen types (see Figure legends for details).

Table 2.1: Antibody crystal structures (complexed with antigen - total 26) - PDB July 1995

PDB code	name	antigen	antigen type	interface area (Å$^{2}$)	antigen size class	resolution/R-factor	topography
2mcp	McPC603	phosphatidyl choline	hapten	32.63	small	3.1Å /18.5%	moderately concave
1fig	1F7	TSA for chorismate mutase (catalytic)	hapten	54.97	small	3.0Å /22.0%	moderately concave
1dbb	DB3	progesterone	hapten	71.61	small	2.7Å /21.0%	concave
1eap	17E8	phosphonate TSA (catalytic)	hapten	76.46	small	2.5Å /18.6%	concave
4fab	4-4-20	fluorescein	hapten	81.89	small	2.7Å /21.5%	concave
1baf	AN02	DNP-spin-label	hapten	82.40	small	2.9Å /19.5%	planar
2cgr	2cgr	cyanophenyl diphenylmethyl guanidineacetic acid	hapten	87.73	small	2.2Å /21.4%	concave
1igj	26-10	digoxin	hapten	91.19	small	2.5Å /17.6%	concave
1ind	CHA255	indium(3+)-eotube	hapten	96.81	small	2.2Å /18.8%	moderately concave
1ibg	40-50	ouabain	hapten	101.47	small	2.7Å /20.9%	concave
1mfb	SE155-4	heptasaccharide	carbohydrate	118.88	medium	2.1Å /16.0%	concave
1acy	59.1	HIV-1 GP120 peptide	peptide	128.04	medium	3.0Å /21.0%	ridged
1fpt	C3	poliovirus type 1 peptide	peptide	128.18	medium	3.0Å /23.0%	ridged
1ggi	50.1	16aa peptide HIV-1 GP120	peptide	135.47	medium	2.8Å /18.8%	moderately concave
1him	17$/$9	8&9aa peptides from flu. HA	peptide	137.23	medium	2.9Å /20.0%	ridged
1cbv	BV04-01	ssDNA (Auto-antibody)	dna	139.19	medium	2.7Å /19.1%	ridged
2igf	B13I2	myohemerythrin residues 69-87	peptide	146.65	medium	2.8Å /22.0%	ridged
1tet	TE33	cholera toxin peptide 3	peptide	150.19	medium	2.3Å /14.8%	ridged
1ikf	1ikf	cyclosporin A	cyc-peptide	168.00	large	2.5Å /16.4%	ridged
1jhl	D11.15	pheasant egg lysozyme	protein	174.42	large	2.4Å /21.4%	planar
1jel	JE142	histidine containing protein	protein	191.50	large	2.8Å /19.3%	concave
1vfb	D1.3	hen egg lysozyme	protein	193.05	large	1.8Å /18.5%	planar
1mlc	D44.1	hen egg lysozyme	protein	198.26	large	2.1Å /18.4%	planar
3hfm	HyHEL-10	hen egg lysozyme	protein	223.56	large	3.0Å /24.6%	moderately concave
2hfl	HyHEL-5	hen egg lysozyme	protein	248.47	large	2.54Å /24.5%	moderately concave
1ncd	NC41	neuraminidase (N9 Whale)	protein	266.22	large	2.9Å /15.7%	planar

Table 2.2: Antibody crystal structures (Fab/Fv only - total 19) - PDB July 1995

PDB code	name	antigen	antigen type	resolution/R-factor	topography
1fai	R19.9	anti-arsonate (Xtal 2)	hapten	2.7Å /18.9%	concave
1lmk	L5MK16	anti-phosphatidylinositol scFv	hapten	2.6Å /20.0%	ridged
2gfb	CNJ206	catalytic (esterase)	hapten	3.0Å /21.3%	concave
6fab	36-71	anti-phenylarsonate	hapten	1.9Å /20.9%	moderately concave
1gig	HC19	influenza virus hemagglutinin	peptide	2.3Å /19.5%	concave
1bbj	B72.3	tumour marker (sialyl-Tn) (humanised)	carbohydrate	3.1Å /?	concave
2fbj	J539	anti-galactan	carbohydrate	1.95Å /19.4%	planar
1mam	YST9.1	lipopolysaccharide A antigen of Brucella abortus	carbohydrate	2.5Å /21.5%	concave
1bbd	8F5	anti-HRV2	protein	2.8Å /19.0%	ridged
1dfb	3D6	anti-HIV-GP41	protein	2.7Å /17.7%	concave
1fgv	H52	humanised anti-CD-18 (Some of H3 missing)	protein	1.9Å /18.0%	planar
1for	Fab17-IA	anti-human rhinovirus	protein	2.75Å /17.4%	concave
1fvc	Hu-4D5	ERBB2 receptor extracellular portion (hum.)	protein	2.2Å /18.3%	moderately concave
1rmf	R6.5	anti-ICAM-1	protein	2.8Å /18.8%	concave
1igc	MOPC21	bound to Streptococcus Protein G Domain III	unknown	2.6Å /16.8%	ridged
1igm	HuIgM	human IgM Fv	unknown	2.3Å /20.1%	planar
2fb4	Kol	myeloma Fab	unknown	1.9Å /18.9%	planar
7fab	New	unsure	unknown	2.0Å /16.9%	moderately concave
8fab	Hil	human myeloma	unknown	1.8Å /17.3%	moderately concave

(a) CDR-L1

(b) CDR-L2

(c) CDR-L3

Figure 2.1: Contact analysis for light chain antigen contacts. Unfilled bars: number of antibodies with residues at each sequence position. Grey bars: number of antibodies with accessible residues at sequence position. Black bars: number of antibodies making antigen contacts at each position (see Methods). Line graphs: $\overline{\rho}$ mean fractional burial by antigen type (see Methods). Thick solid lines: all antigens. Fine dashed lines: small antigens (see Table 2.1 column 6). Medium dashed lines: medium sized antigens. Thin solid lines: large antigens. Arrows mark the standard CDR definitions (see Table 2.3). Where these differ the dashed arrows denote the Kabat sequence variability definition; the solid arrows denote the Chothia loop definition. Arrows point towards the centre of combining site (see Figure 2.3).

(a) CDR-H1

(b) CDR-H2

(c) CDR-H3

Figure 2.2: Contact analysis for heavy chain antigen contacts. See legend to Figure 2.1. Note that in CDR-H2 the sequence variability definition extends to H65.

The two main CDR definitions (Table 2.3) are shown in Figures 2.1 & 2.2 with arrows pointing towards the centre of the combining site (Figure 2.3). All residue numbering follows the scheme of Chothia et al.chothia:d13,chothia:canon.

Table 2.3: CDR definitions - all residue numbering follows the scheme of Chothia et al.chothia:canon.

CDR	Kabat 1	Chothia 2	Contact range3
L1	L24 - L34	L24 - L34	L30 - L36
L2	L50 - L56	L50 - L56	L46 - L55
L3	L89 - L97	L89 - L97	L89 - L96
H1	H31 - H35	H26 - H32	H30 - H35
H2	H50 - H65	H52 - H56	H47 - H58
H3	H95 - H102	H95 - H102	H93 - H101

¹ sequence variability[Wu & Kabat, 1970]

² loop definition[Chothia et al., 1986,Chothia & Lesk, 1987]

³ start and end residues must satisfy $\overline{\rho} > 0.01$ and make at least one antigen contact (see Methods) in the set of complexes (see Table 2.1)

Figure 2.3: CDR arrangement. Contact CDR definitions (see Table 2.3) are shown in strong colours, residues defined by other CDR definitions are shown in grey.

Only two antigen contacts are made by residues not shown in Figures 2.1 & 2.2. These were L67 in antibody HyHEL-10 (3hfm, anti-lysozyme[Padlan et al., 1989]) and H64 in antibody NC41 (1ncd, anti-neuraminidase[Tulip et al., 1992]). Tables of the numeric data are available on the internet.