PyIgClassify2: Canonical Clusters of Antibody CDR Loop Conformations

FCCC

PyIgClassify2: Classification of Antibody CDR Conformations

Dunbrack Lab

Summary info for CDR clusters

H1

Loop	# of Structures	% of Loop Length	Median PDB	Consensus Sequence	# of Unique Seq	% of Unique Seq	Gene	Loop Conformation	Median Angle	Consensus Sequence Logo
H1-13-1	7386	65.85	2H_1A3LH	aASGftFssYWmH	1519	56.51	heavy	BBBLBBAAABBBB	10
H1-13-3	115	1.03	1H_5IMKB	aASGrTFSsYaMG	42	1.56	heavy	BBBEAAAAABBBB	13
H1-13-4	233	2.08	3H_4KK8C	aaSGFtFsgYYWs	51	1.90	heavy	BBBLBBABLBBBB	13
H1-13-5	181	1.61	2H_7Z1AF	AASGSTFSIyAMG	44	1.64	heavy	BBBEBAAABABBB	15
H1-14-1	93	19.91	2H_5VPLD	TVtGYSITSDYaWN	27	23.48	heavy	BBBLBBAAABEBBB	8
H1-14-2	86	18.42	6H_6P60C	AVSGGSISSSYyWS	28	24.35	heavy	BBBLBBAABBBBBB	11
H1-15-1	172	32.64	2H_1TJGH	tFSGFSLsTSgMgvG	48	26.82	heavy	BBBLBBAABBLBBBB	9
H1-15-2	132	25.05	2H_6OELH	TVSGdSiSssdyYWg	40	22.35	heavy	BBBLBBAABAABBBB	12

L1

Loop	# of Structures	% of Loop Length	Median PDB	Consensus Sequence	# of Unique Seq	% of Unique Seq	Gene	Loop Conformation	Median Angle	Consensus Sequence Logo
L1-8-1	23	54.76	1L_7A0YD	SGSsYNYG	9	50.00	lambda	BLBABBBB	12
L1-10-1	252	58.74	1K_1YQVL	SASSSVSYMH	58	75.33	kappa	BBABBBABBB	8
L1-11-1	2554	51.21	3K_4NHHK	RASQSISsylA	402	43.32	kappa	BBABBAEABBB	7
L1-11-2	771	15.46	1K_6I1OL	RASQDISNYLA	166	17.89	kappa	BBABBALLBBB	7
L1-11-3	211	4.23	3L_6A3WH	gGDniGDKsVH	61	6.57	lambda	BBBLAAABBBB	8
L1-11-4	196	3.93	2L_7MF7D	SGDALPKKYAY	57	6.14	lambda	BBAAAAABBBB	10
L1-12-1	399	44.58	1K_6XE1L	RASQSvsSsYLA	77	42.31	kappa	BBABBBBAAABB	8
L1-12-2	174	19.44	1K_1RHHA	RASQSVssNYLA	27	14.84	kappa	BBABBBBLLBBB	6
L1-13-1	431	52.37	1L_4BUHA	SGSSSNIGsNyVS	88	48.89	lambda	BBBAAAAAABBBB	8
L1-13-2	105	12.76	2L_4YNYD	TRSSGSIaSnYVQ	16	8.89	lambda	BBABEBAAABBBB	7
L1-13-3	59	7.17	1K_5I8KL	QSSQSVyNNNrLa	18	10.00	kappa	BBABBBBLLABBB	6
L1-14-1	225	23.41	1L_1NC2A	RSSTGAVTtsNYAN	25	13.16	lambda	BBAAEBBBAAALBB	9
L1-14-2	292	30.39	2L_7E7YD	TGTSSDVGgYNYVS	65	34.21	lambda	BBBAAAAAABABBB	9
L1-14-3	94	9.78	1L_7N4JL	TGSSSNIGAgyDVH	20	10.53	lambda	BBBAAAAAALBBBB	9
L1-15-1	327	55.99	2K_2XQYL	RASeSVDYyGdSYMH	76	55.07	kappa	BBABBABBLLBBBBB	8
L1-16-1	904	79.44	1K_2D03L	RSSQSlVHSNGNTYLE	172	69.92	kappa	BBABBABBAALBBBBB	8
L1-17-1	438	70.65	1K_6ANAL	KSSQSLLySsNQKNYLA	99	69.72	kappa	BBABBABBAAALBBBBB	7

H2

Loop	# of Structures	% of Loop Length	Median PDB	Consensus Sequence	# of Unique Seq	% of Unique Seq	Gene	Loop Conformation	Median Angle	Consensus Sequence Logo
H2-9-1	2133	81.47	4H_7RK1D	yISySGsTY	534	77.17	heavy	BBBAALBBB	10
H2-10-1	3989	44.28	5H_6FFJA	WInPgnGdTn	986	43.00	heavy	BBBAAALBBB	11
H2-10-2	2325	25.81	2H_4ZYKH	aIsSDGSstY	572	24.95	heavy	BBBAALABBB	10
H2-10-3	214	2.38	2H_6B3KH	eIYPGsGsTN	67	2.92	heavy	BBBBEALBBB	13
H2-10-4	253	2.81	2H_7W56E	gISSGGgytY	25	1.09	heavy	BBBBLLABBB	9
H2-10-6	243	2.70	2H_6ZHDE	wInPsGGsTY	71	3.10	heavy	BBBABLLBBB	11
H2-11-1	29	22.66	2H_7O4YH	RTYYRSKwYND	11	22.00	heavy	BBBBBLBBBBB	7
H2-12-1	459	85.63	2H_2R1YB	rIrnKanGyTTE	90	69.77	heavy	BBBBAAALLBBB	9

L2

Loop	# of Structures	% of Loop Length	Median PDB	Consensus Sequence	# of Unique Seq	% of Unique Seq	Gene	Loop Conformation	Median Angle	Consensus Sequence Logo
L2-8-1	8065	76.82	4K_6KR0D	YdASnRAs	971	66.05	kappa lambda	BLLABBBB	8
L2-8-4	352	3.35	2L_5WCCL	YgaSNrpS	87	5.92	kappa lambda	BEAABBBB	17
L2-12-2	45	59.21	1L_5EORL	KlNSDGShTKGD	11	50.00	lambda	BBBAALBBBBBB	7

H3

Loop	# of Structures	% of Loop Length	Median PDB	Consensus Sequence	# of Unique Seq	% of Unique Seq	Gene	Loop Conformation	Median Angle	Consensus Sequence Logo
H3-5-2	36	38.71	21H_4WHTQ	TrRDY	6	23.08	heavy	BAEAB	8
H3-6-1	45	30.61	2H_3U0WH	ARGfDY	15	32.61	heavy	BBEAAB	11
H3-6-2	28	19.05	2H_4TRPH	ARGfDY	12	26.09	heavy	BBLLAB	11
H3-7-1	74	33.33	2H_2DQCH	ARwdGDY	14	23.73	heavy	BBAALAB	7
H3-8-2	38	14.13	3H_5NH3H	ARGRYFDY	14	18.92	heavy	BBEAALAB	8
H3-9-2	44	9.19	3H_6DWAB	aRgyyAfDY	20	11.49	heavy	BBBAABBAB	16
H3-10-1	85	14.89	5H_1PG7H	ARdGyGaFDy	27	13.99	heavy	BBBBLLBBAB	13
H3-10-2	50	8.76	3H_4YNYA	ARhrgnYFDY	19	9.85	heavy	BBBBEABBAB	16
H3-11-1	123	13.04	2H_1PZ5B	AREgysGaFDY	43	14.98	heavy	BBBBAALBBAB	15
H3-12-1	132	9.09	3H_1A4KB	ARGdgYygaFDY	42	10.83	heavy	BBBBAAALBBAB	15
H3-12-3	42	2.89	2H_7LY0H	ARGvyGtyYFDY	14	3.61	heavy	BBBBBLBABBAB	15
H3-13-2	95	8.42	4H_4GW5D	ARGgSdYsyWFdY	12	3.97	heavy	BBBABAABABBAB	7
H3-14-2	64	4.51	5H_7SHZC	ARELYyGGMwyFDv	13	3.99	heavy	BBBBBBLLBBBBAB	11

L3

Loop	# of Structures	% of Loop Length	Median PDB	Consensus Sequence	# of Unique Seq	% of Unique Seq	Gene	Loop Conformation	Median Angle	Consensus Sequence Logo
L3-5-1	217	91.18	1K_4OLYL	QqyEf	27	84.38	kappa lambda	BBEAB	9
L3-8-1	321	46.93	1K_3O2DL	QQYYnLwT	71	34.98	kappa	BBAABEBB	8
L3-8-3	127	18.57	3P_5O1RL	QQYySsPT	39	19.21	kappa	BBAABBBB	8
L3-8-4	53	7.75	2L_7CQDM	qQYDsSpT	19	9.36	kappa lambda	BBBAABBB	18
L3-9-1	169	2.46	1L_7REWB	QqwDsshWV	52	3.46	kappa lambda	BBBBLLBBB	12
L3-9-2	530	7.72	5K_4XBGK	QQYYStPyT	148	9.85	kappa	BBAABABBB	11
L3-9-3	148	2.16	2K_6N35L	QSYdsSSvV	30	2.00	kappa lambda	BBBBAABBB	16
L3-9-4	206	3.00	1L_5XCTB	ALWYSsHWV	28	1.86	kappa lambda	BBBBEABBB	8
L3-9-cis7-1	4616	67.26	2K_6HX4M	qQyySyPyT	897	59.72	kappa	BBAABBbBB	9
L3-9-cis7-2	59	0.86	1K_5DFWH	QHFWgTPrT	21	1.40	kappa	BBABEBbBB	13
L3-10-1	197	17.37	1L_6CBJL	sSYtSSSTWV	45	13.12	kappa lambda	BBBBAALBBB	14
L3-10-2	61	5.38	2L_7E7YD	CSYAGSsTwV	21	6.12	kappa lambda	BBBAELLBBB	7
L3-10-3	42	3.70	2L_5FGBB	QVWDSSSDvV	19	5.54	kappa lambda	BBBBAAAEBB	15
L3-10-cis78-1	51	4.50	2K_3EYFC	QQRthWPPlT	21	6.12	kappa	BBAABBbbBB	7
L3-11-1	449	42.32	1L_7RP2I	QaWDSSLsgvV	123	41.55	kappa lambda	BBBBAAALBBB	10
L3-11-2	59	5.56	1L_7LY0L	QStDSSGTywV	21	7.10	lambda	BBBBAALABBB	14
L3-13-2	12	13.79	2K_4MA3L	LGsYDCSSADClA	5	19.23	kappa	BBBBBAAABBABB	8

H4

Loop	# of Structures	% of Loop Length	Median PDB	Consensus Sequence	# of Unique Seq	% of Unique Seq	Gene	Loop Conformation	Median Angle	Consensus Sequence Logo
H4-6-1	76	82.61	5H_6BA5B	KTSTTV	9	60.00	heavy	BBAABB	8
H4-7-1	63	86.30	4H_4ZTOI	ktSSTTV	7	70.00	heavy	BABAABB	7
H4-8-1	10892	90.39	2H_4FQLH	RDtSKntA	907	74.90	heavy	BBAAALBB	9

L4

Loop	# of Structures	% of Loop Length	Median PDB	Consensus Sequence	# of Unique Seq	% of Unique Seq	Gene	Loop Conformation	Median Angle	Consensus Sequence Logo
L4-6-1	6368	62.04	2K_5I76C	GSGTDF	97	27.56	kappa lambda	EBEABB	9
L4-6-2	2531	24.66	1L_3MUGA	kSGttA	120	34.09	kappa lambda	BBEABB	12
L4-6-3	364	3.55	1K_6MV5L	GSGTDF	30	8.52	kappa lambda	EBAABB	13
L4-8-1	171	86.80	2L_6W4YB	KDASsNsG	11	78.57	lambda	BBAAALBB	8

Site developed by the Antibody Team at the lab of Roland Dunbrack. Last updated on Oct. 13, 2022

Contact Us | ProtCID | ProtCAD | Dunbrack Laboratory | Fox Chase Cancer Center