Analysis of interatomic Contacts of Structural Units in PDB entry:
3JD5

Contacts of Structural Units (CSU) are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332).
This page provides analyses of contacts formed by:

chains
helices
sheets
residues

For analysis of ligand-protein contacts, use:

LPC software

3D structure can be seen in additional window with STING software for 3JD5 entry

There are 33 chains in PDB entry 3JD5 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	A 4	U 955
B	ARG 47	GLN 263
C	LYS 36	ILE 167
E	SER 88	THR 430
F	MET 1	LYS 124
G	SER 35	TRP 242
I	THR 70	ARG 396
J	PRO 61	VAL 188
K	SER 62	LEU 197
L	ALA 31	LYS 139
N	TYR 28	TRP 128
O	GLU 63	LYS 235
P	LYS 10	THR 125
Q	MET 1	PRO 109
R	SER 47	GLU 143
U	MET 1	GLY 86
a	LYS 65	ILE 353
b	MET 1	VAL 135
c	PRO 2	ALA 169
d	ARG 27	HIS 202
e	SER 37	ALA 401
f	VAL 78	GLU 175
g	GLU 60	LEU 397
h	PRO 284	SER 386
i	LEU 4	ARG 101
j	MET 1	THR 213
k	ARG 51	MET 325
m	MET 1	SER 118
n	ARG 128	LYS 199
o	GLU 56	SER 641
p	TYR 51	LYS 237
s	UNK 2360	UNK 2375
z	UNK 692	UNK 708

There are210 helices in PDB entry 3JD5. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	B	71	76	Right-handed alpha
Helix 2	2	B	106	127	Right-handed alpha
Helix 3	3	B	140	152	Right-handed alpha
Helix 4	4	B	195	202	Right-handed alpha
Helix 5	5	B	217	221	Right-handed 310
Helix 6	6	B	231	261	Right-handed alpha
Helix 7	7	C	58	62	Right-handed 310
Helix 8	8	C	83	100	Right-handed alpha
Helix 9	9	C	128	147	Right-handed alpha
Helix 10	10	E	94	97	Right-handed 310
Helix 11	11	E	98	103	Right-handed alpha
Helix 12	12	E	162	186	Right-handed alpha
Helix 13	13	E	265	278	Right-handed alpha
Helix 14	14	E	317	326	Right-handed alpha
Helix 15	15	E	342	355	Right-handed alpha
Helix 16	16	E	358	367	Right-handed alpha
Helix 17	17	E	407	416	Right-handed alpha
Helix 18	18	F	15	31	Right-handed alpha
Helix 19	19	F	74	84	Right-handed alpha
Helix 20	20	G	48	53	Right-handed alpha
Helix 21	21	G	57	70	Right-handed alpha
Helix 22	22	G	88	96	Right-handed alpha
Helix 23	23	G	97	99	Right-handed 310
Helix 24	24	G	103	129	Right-handed alpha
Helix 25	25	G	132	137	Right-handed alpha
Helix 26	26	G	140	151	Right-handed alpha
Helix 27	27	G	175	189	Right-handed alpha
Helix 28	28	G	190	193	Right-handed 310
Helix 29	29	G	200	214	Right-handed alpha
Helix 30	30	G	217	231	Right-handed alpha
Helix 31	31	G	233	237	Right-handed 310
Helix 32	32	I	71	91	Right-handed alpha
Helix 33	33	I	101	112	Right-handed alpha
Helix 34	34	I	127	132	Right-handed alpha
Helix 35	35	I	150	154	Right-handed 310
Helix 36	36	I	157	172	Right-handed alpha
Helix 37	37	I	201	210	Right-handed alpha
Helix 38	38	I	214	229	Right-handed alpha
Helix 39	39	I	240	245	Right-handed 310
Helix 40	40	I	300	304	Right-handed alpha
Helix 41	41	I	306	311	Right-handed alpha
Helix 42	42	I	314	319	Right-handed alpha
Helix 43	43	I	338	352	Right-handed alpha
Helix 44	44	I	353	356	Right-handed 310
Helix 45	45	I	357	366	Right-handed alpha
Helix 46	46	J	85	103	Right-handed alpha
Helix 47	47	J	149	163	Right-handed alpha
Helix 48	48	K	123	127	Right-handed 310
Helix 49	49	K	128	144	Right-handed alpha
Helix 50	50	K	161	171	Right-handed alpha
Helix 51	51	L	33	38	Right-handed alpha
Helix 52	52	N	32	47	Right-handed alpha
Helix 53	53	N	49	54	Right-handed alpha
Helix 54	54	N	55	58	Right-handed 310
Helix 55	55	N	66	77	Right-handed alpha
Helix 56	56	N	83	87	Right-handed 310
Helix 57	57	N	107	115	Right-handed alpha
Helix 58	58	O	85	92	Right-handed alpha
Helix 59	59	O	99	112	Right-handed alpha
Helix 60	60	O	125	145	Right-handed alpha
Helix 61	61	O	148	171	Right-handed alpha
Helix 62	62	O	173	185	Right-handed alpha
Helix 63	63	O	201	234	Right-handed alpha
Helix 64	64	P	69	78	Right-handed alpha
Helix 65	65	P	84	95	Right-handed alpha
Helix 66	66	P	100	125	Right-handed alpha
Helix 67	67	R	77	82	Right-handed alpha
Helix 68	68	R	94	99	Right-handed alpha
Helix 69	69	R	103	117	Right-handed alpha
Helix 70	70	U	19	33	Right-handed alpha
Helix 71	71	U	35	42	Right-handed alpha
Helix 72	72	U	47	75	Right-handed alpha
Helix 73	73	U	76	80	Right-handed 310
Helix 74	74	a	71	81	Right-handed alpha
Helix 75	75	a	106	125	Right-handed alpha
Helix 76	76	a	146	150	Right-handed 310
Helix 77	77	a	184	196	Right-handed alpha
Helix 78	78	a	213	219	Right-handed alpha
Helix 79	79	a	226	234	Right-handed alpha
Helix 80	80	a	239	256	Right-handed alpha
Helix 81	81	a	258	262	Right-handed 310
Helix 82	82	a	266	277	Right-handed alpha
Helix 83	83	a	283	290	Right-handed alpha
Helix 84	84	a	293	298	Right-handed alpha
Helix 85	85	a	298	307	Right-handed alpha
Helix 86	86	a	311	320	Right-handed alpha
Helix 87	87	a	326	334	Right-handed alpha
Helix 88	88	a	340	353	Right-handed alpha
Helix 89	89	b	13	22	Right-handed alpha
Helix 90	90	b	31	38	Right-handed alpha
Helix 91	91	b	65	76	Right-handed alpha
Helix 92	92	b	94	105	Right-handed alpha
Helix 93	93	b	113	127	Right-handed alpha
Helix 94	94	c	14	19	Right-handed alpha
Helix 95	95	c	41	49	Right-handed alpha
Helix 96	96	c	52	57	Right-handed alpha
Helix 97	97	c	94	106	Right-handed alpha
Helix 98	98	c	109	124	Right-handed alpha
Helix 99	99	c	156	159	Right-handed 310
Helix 100	100	c	160	167	Right-handed alpha
Helix 101	101	d	49	54	Right-handed alpha
Helix 102	102	d	54	87	Right-handed alpha
Helix 103	103	d	88	164	Right-handed alpha
Helix 104	104	d	169	173	Right-handed 310
Helix 105	105	d	175	183	Right-handed alpha
Helix 106	106	e	49	63	Right-handed alpha
Helix 107	107	e	69	77	Right-handed alpha
Helix 108	108	e	82	96	Right-handed alpha
Helix 109	109	e	107	115	Right-handed alpha
Helix 110	110	e	124	132	Right-handed alpha
Helix 111	111	e	142	153	Right-handed alpha
Helix 112	112	e	160	168	Right-handed alpha
Helix 113	113	e	177	192	Right-handed alpha
Helix 114	114	e	199	204	Right-handed alpha
Helix 115	115	e	217	238	Right-handed alpha
Helix 116	116	e	259	266	Right-handed alpha
Helix 117	117	e	332	343	Right-handed alpha
Helix 118	118	e	355	363	Right-handed alpha
Helix 119	119	e	372	401	Right-handed alpha
Helix 120	120	f	80	85	Right-handed alpha
Helix 121	121	f	88	94	Right-handed alpha
Helix 122	122	g	71	76	Right-handed alpha
Helix 123	123	g	83	94	Right-handed alpha
Helix 124	124	g	102	112	Right-handed alpha
Helix 125	125	g	136	144	Right-handed alpha
Helix 126	126	g	145	147	Right-handed 310
Helix 127	127	g	156	161	Right-handed 310
Helix 128	128	g	179	191	Right-handed alpha
Helix 129	129	g	194	199	Right-handed alpha
Helix 130	130	g	221	231	Right-handed alpha
Helix 131	131	g	234	250	Right-handed alpha
Helix 132	132	g	264	268	Right-handed 310
Helix 133	133	g	282	285	Right-handed 310
Helix 134	134	g	286	291	Right-handed alpha
Helix 135	135	g	292	297	Right-handed alpha
Helix 136	136	g	323	329	Right-handed alpha
Helix 137	137	g	333	337	Right-handed 310
Helix 138	138	g	348	351	Right-handed 310
Helix 139	139	g	352	362	Right-handed alpha
Helix 140	140	g	372	382	Right-handed alpha
Helix 141	141	g	386	397	Right-handed alpha
Helix 142	142	h	287	299	Right-handed alpha
Helix 143	143	h	313	317	Right-handed 310
Helix 144	144	h	325	329	Right-handed 310
Helix 145	145	h	336	351	Right-handed alpha
Helix 146	146	h	356	374	Right-handed alpha
Helix 147	147	h	375	380	Right-handed alpha
Helix 148	148	i	6	19	Right-handed alpha
Helix 149	149	i	30	39	Right-handed alpha
Helix 150	150	i	54	57	Right-handed 310
Helix 151	151	i	58	68	Right-handed alpha
Helix 152	152	i	75	87	Right-handed alpha
Helix 153	153	j	14	27	Right-handed alpha
Helix 154	154	j	29	34	Right-handed alpha
Helix 155	155	j	51	55	Right-handed 310
Helix 156	156	j	64	71	Right-handed 310
Helix 157	157	j	84	87	Right-handed 310
Helix 158	158	j	167	182	Right-handed alpha
Helix 159	159	k	105	110	Right-handed alpha
Helix 160	160	k	117	125	Right-handed alpha
Helix 161	161	k	126	130	Right-handed 310
Helix 162	162	k	141	149	Right-handed alpha
Helix 163	163	k	185	197	Right-handed alpha
Helix 164	164	k	216	234	Right-handed alpha
Helix 165	165	k	258	275	Right-handed alpha
Helix 166	166	k	282	288	Right-handed alpha
Helix 167	167	k	288	296	Right-handed alpha
Helix 168	168	k	298	303	Right-handed alpha
Helix 169	169	k	307	320	Right-handed alpha
Helix 170	170	m	46	53	Right-handed alpha
Helix 171	171	m	67	88	Right-handed alpha
Helix 172	172	m	102	111	Right-handed 310
Helix 173	173	n	129	150	Right-handed alpha
Helix 174	174	n	151	178	Right-handed alpha
Helix 175	175	o	69	78	Right-handed alpha
Helix 176	176	o	99	122	Right-handed alpha
Helix 177	177	o	124	128	Right-handed 310
Helix 178	178	o	146	155	Right-handed alpha
Helix 179	179	o	162	172	Right-handed alpha
Helix 180	180	o	221	231	Right-handed alpha
Helix 181	181	o	238	249	Right-handed alpha
Helix 182	182	o	256	268	Right-handed alpha
Helix 183	183	o	273	284	Right-handed alpha
Helix 184	184	o	291	299	Right-handed alpha
Helix 185	185	o	312	325	Right-handed alpha
Helix 186	186	o	332	341	Right-handed alpha
Helix 187	187	o	354	361	Right-handed alpha
Helix 188	188	o	375	383	Right-handed alpha
Helix 189	189	o	387	398	Right-handed alpha
Helix 190	190	o	418	430	Right-handed alpha
Helix 191	191	o	434	440	Right-handed alpha
Helix 192	192	o	460	467	Right-handed alpha
Helix 193	193	o	473	485	Right-handed alpha
Helix 194	194	o	492	506	Right-handed alpha
Helix 195	195	o	511	522	Right-handed alpha
Helix 196	196	o	525	529	Right-handed 310
Helix 197	197	o	530	537	Right-handed alpha
Helix 198	198	o	547	557	Right-handed alpha
Helix 199	199	o	581	589	Right-handed alpha
Helix 200	200	o	592	602	Right-handed alpha
Helix 201	201	o	626	639	Right-handed alpha
Helix 202	202	p	55	60	Right-handed alpha
Helix 203	203	p	62	68	Right-handed alpha
Helix 204	204	p	120	125	Right-handed alpha
Helix 205	205	p	136	141	Right-handed alpha
Helix 206	206	p	143	158	Right-handed alpha
Helix 207	207	p	200	204	Right-handed 310
Helix 208	208	p	209	220	Right-handed alpha
Helix 209	209	s	2361	2374	Right-handed alpha
Helix 210	210	z	699	707	Right-handed alpha

There are 29 sheets in PDB entry 3JD5. Click on sheet of interest to get list of strands forming it: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, AA, AB, AC,

There are 2 strands in A sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	95	99	first strand
Strand 2	B	102	105	anti-parallel

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There are 5 strands in B sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	154	156	first strand
Strand 2	B	131	134	parallel
Strand 3	B	181	184	parallel
Strand 4	B	208	212	parallel
Strand 5	B	225	226	parallel

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There are 4 strands in C sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	70	71	first strand
Strand 2	C	110	113	parallel
Strand 3	C	116	120	anti-parallel
Strand 4	C	151	154	parallel

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There are 2 strands in D sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	139	140	first strand
Strand 2	E	158	159	anti-parallel

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There are 4 strands in E sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	221	231	first strand
Strand 2	E	237	246	anti-parallel
Strand 3	E	253	258	anti-parallel
Strand 4	E	279	281	anti-parallel

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There are 3 strands in F sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	295	297	first strand
Strand 2	E	302	306	anti-parallel
Strand 3	E	333	335	anti-parallel

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There are 2 strands in G sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	369	372	first strand
Strand 2	a	102	105	anti-parallel

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There are 4 strands in H sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	36	41	first strand
Strand 2	F	64	68	anti-parallel
Strand 3	F	4	8	anti-parallel
Strand 4	F	93	95	anti-parallel

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There are 2 strands in I sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	45	46	first strand
Strand 2	F	60	61	anti-parallel

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There are 2 strands in J sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	158	163	first strand
Strand 2	G	166	171	anti-parallel

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There are 6 strands in K sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	260	261	first strand
Strand 2	I	268	271	anti-parallel
Strand 3	I	284	286	anti-parallel
Strand 4	I	328	330	anti-parallel
Strand 5	I	293	295	parallel
Strand 6	I	298	299	anti-parallel

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There are 2 strands in L sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	274	275	first strand
Strand 2	I	280	281	anti-parallel

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There are 5 strands in M sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	72	73	first strand
Strand 2	J	170	178	anti-parallel
Strand 3	J	75	80	anti-parallel
Strand 4	J	141	146	anti-parallel
Strand 5	J	107	108	anti-parallel

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There are 5 strands in N sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	72	73	first strand
Strand 2	J	170	178	anti-parallel
Strand 3	k	151	159	anti-parallel
Strand 4	k	174	178	anti-parallel
Strand 5	k	206	209	anti-parallel

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There are 2 strands in O sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	114	116	first strand
Strand 2	J	136	138	anti-parallel

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There are 6 strands in P sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	113	114	first strand
Strand 2	K	98	103	anti-parallel
Strand 3	K	88	93	anti-parallel
Strand 4	K	149	155	parallel
Strand 5	K	174	180	parallel
Strand 6	U	11	12	anti-parallel

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There are 5 strands in Q sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	90	92	first strand
Strand 2	L	80	84	anti-parallel
Strand 3	L	57	66	anti-parallel
Strand 4	L	107	111	anti-parallel
Strand 5	L	124	125	anti-parallel

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There are 9 strands in R sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	P	82	83	first strand
Strand 2	P	18	23	parallel
Strand 3	P	32	37	anti-parallel
Strand 4	P	49	54	anti-parallel
Strand 5	P	64	68	anti-parallel
Strand 6	a	155	159	parallel
Strand 7	a	172	175	anti-parallel
Strand 8	a	179	182	anti-parallel
Strand 9	a	140	142	anti-parallel

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There are 5 strands in S sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	Q	43	50	first strand
Strand 2	Q	27	34	anti-parallel
Strand 3	Q	12	17	anti-parallel
Strand 4	Q	63	68	anti-parallel
Strand 5	Q	79	86	anti-parallel

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There are 2 strands in T sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	Q	91	92	first strand
Strand 2	Q	99	100	anti-parallel

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There are 4 strands in U sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	c	63	68	first strand
Strand 2	c	29	34	parallel
Strand 3	c	75	79	anti-parallel
Strand 4	c	88	89	anti-parallel

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There are 3 strands in V sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	f	99	102	first strand
Strand 2	f	141	147	anti-parallel
Strand 3	f	167	173	anti-parallel

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There are 3 strands in W sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	f	104	105	first strand
Strand 2	f	112	116	anti-parallel
Strand 3	f	123	126	anti-parallel

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There are 5 strands in X sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	g	150	154	first strand
Strand 2	g	257	262	parallel
Strand 3	g	304	308	parallel
Strand 4	g	122	126	parallel
Strand 5	g	340	343	parallel

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There are 2 strands in Y sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	g	168	170	first strand
Strand 2	g	176	178	anti-parallel

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There are 2 strands in Z sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	g	202	203	first strand
Strand 2	g	219	220	anti-parallel

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There are 2 strands in AA sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	g	207	208	first strand
Strand 2	g	214	215	anti-parallel

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There are 2 strands in AB sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	j	79	82	first strand
Strand 2	j	139	142	anti-parallel

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There are 3 strands in AC sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	j	94	102	first strand
Strand 2	j	112	120	anti-parallel
Strand 3	j	123	130	anti-parallel

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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il

Analysis of interatomic Contacts of Structural Units in PDB entry: 3JD5

Analysis of interatomic Contacts of Structural Units in PDB entry:
3JD5