Analysis of interatomic Contacts of Structural Units in PDB entry:
4PD4

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 4PD4 entry

There are 11 chains in PDB entry 4PD4 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	ALA 27	TRP 457
B	LEU 17	LEU 368
C	MET 1	LYS 385
D	MET 62	LYS 309
E	LYS 31	GLY 215
F	VAL 74	LYS 147
G	PRO 2	LYS 127
H	GLY 2	VAL 94
I	SER 2	ALA 58
J	GLU 1	PRO 127
K	ASP 1	LYS 107

There are 87 helices in PDB entry 4PD4. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	68	77	Right-handed alpha
Helix 2	AA2	A	79	89	Right-handed alpha
Helix 3	AA3	A	113	125	Right-handed alpha
Helix 4	AA4	A	136	141	Right-handed alpha
Helix 5	AA5	A	143	148	Right-handed alpha
Helix 6	AA6	A	150	155	Right-handed alpha
Helix 7	AA7	A	155	169	Right-handed alpha
Helix 8	AA8	A	172	176	Right-handed 310
Helix 9	AA9	A	189	201	Right-handed alpha
Helix 10	AB1	A	215	224	Right-handed alpha
Helix 11	AB2	A	274	286	Right-handed alpha
Helix 12	AB3	A	292	297	Right-handed alpha
Helix 13	AB4	A	301	307	Right-handed alpha
Helix 14	AB5	A	339	357	Right-handed alpha
Helix 15	AB6	A	359	379	Right-handed alpha
Helix 16	AB7	A	382	397	Right-handed alpha
Helix 17	AB8	A	402	413	Right-handed alpha
Helix 18	AB9	A	414	426	Right-handed alpha
Helix 19	AC1	A	444	449	Right-handed alpha
Helix 20	AC2	A	450	453	Right-handed 310
Helix 21	AC3	B	38	42	Right-handed 310
Helix 22	AC4	B	46	53	Right-handed alpha
Helix 23	AC5	B	63	75	Right-handed alpha
Helix 24	AC6	B	97	112	Right-handed alpha
Helix 25	AC7	B	115	135	Right-handed alpha
Helix 26	AC8	B	137	150	Right-handed alpha
Helix 27	AC9	B	169	180	Right-handed alpha
Helix 28	AD1	B	181	183	Right-handed 310
Helix 29	AD2	B	193	204	Right-handed alpha
Helix 30	AD3	B	205	209	Right-handed 310
Helix 31	AD4	B	249	261	Right-handed alpha
Helix 32	AD5	B	265	270	Right-handed 310
Helix 33	AD6	B	293	300	Right-handed alpha
Helix 34	AD7	B	303	311	Right-handed alpha
Helix 35	AD8	B	315	318	Right-handed 310
Helix 36	AD9	B	319	327	Right-handed alpha
Helix 37	AE1	B	358	362	Right-handed 310
Helix 38	AE2	B	364	368	Right-handed 310
Helix 39	AE3	C	2	7	Right-handed alpha
Helix 40	AE4	C	9	15	Right-handed alpha
Helix 41	AE5	C	31	52	Right-handed alpha
Helix 42	AE6	C	57	71	Right-handed alpha
Helix 43	AE7	C	74	103	Right-handed alpha
Helix 44	AE8	C	110	134	Right-handed alpha
Helix 45	AE9	C	137	150	Right-handed alpha
Helix 46	AF1	C	157	165	Right-handed alpha
Helix 47	AF2	C	172	203	Right-handed alpha
Helix 48	AF3	C	223	247	Right-handed alpha
Helix 49	AF4	C	253	258	Right-handed 310
Helix 50	AF5	C	275	284	Right-handed alpha
Helix 51	AF6	C	287	301	Right-handed alpha
Helix 52	AF7	C	304	309	Right-handed alpha
Helix 53	AF8	C	315	318	Right-handed 310
Helix 54	AF9	C	319	342	Right-handed alpha
Helix 55	AG1	C	347	365	Right-handed alpha
Helix 56	AG2	C	365	381	Right-handed alpha
Helix 57	AG3	D	63	68	Right-handed alpha
Helix 58	AG4	D	86	100	Right-handed alpha
Helix 59	AG5	D	101	104	Right-handed 310
Helix 60	AG6	D	111	116	Right-handed alpha
Helix 61	AG7	D	121	131	Right-handed alpha
Helix 62	AG8	D	161	168	Right-handed alpha
Helix 63	AG9	D	187	196	Right-handed alpha
Helix 64	AH1	D	246	260	Right-handed alpha
Helix 65	AH2	D	262	297	Right-handed alpha
Helix 66	AH3	E	50	81	Right-handed alpha
Helix 67	AH4	E	122	130	Right-handed alpha
Helix 68	AH5	E	142	147	Right-handed alpha
Helix 69	AH6	F	78	87	Right-handed alpha
Helix 70	AH7	F	88	111	Right-handed alpha
Helix 71	AH8	F	113	117	Right-handed 310
Helix 72	AH9	F	123	139	Right-handed alpha
Helix 73	AI1	F	141	146	Right-handed 310
Helix 74	AI2	G	4	18	Right-handed alpha
Helix 75	AI3	G	18	36	Right-handed alpha
Helix 76	AI4	G	37	42	Right-handed 310
Helix 77	AI5	G	44	49	Right-handed alpha
Helix 78	AI6	G	53	59	Right-handed alpha
Helix 79	AI7	G	64	84	Right-handed alpha
Helix 80	AI8	G	103	123	Right-handed alpha
Helix 81	AI9	H	49	80	Right-handed alpha
Helix 82	AJ1	H	81	84	Right-handed 310
Helix 83	AJ2	H	85	93	Right-handed alpha
Helix 84	AJ3	I	3	12	Right-handed alpha
Helix 85	AJ4	I	17	44	Right-handed alpha
Helix 86	AJ5	I	48	56	Right-handed alpha
Helix 87	AJ6	J	87	91	Right-handed 310

There are 18 sheets in PDB entry 4PD4. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8, AA9, AB1, AB2, AB3, AB4, AB5, AB6, AB7, AB8, AB9,

There are 6 strands in AA1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	30	33	first strand
Strand 2	A	37	42	anti-parallel
Strand 3	A	206	212	parallel
Strand 4	A	49	55	anti-parallel
Strand 5	A	102	108	anti-parallel
Strand 6	A	92	97	anti-parallel

Back to list of sheets
Back to top of page

There are 7 strands in AA2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	287	289	first strand
Strand 2	A	314	321	anti-parallel
Strand 3	A	326	334	anti-parallel
Strand 4	A	259	266	anti-parallel
Strand 5	A	432	437	anti-parallel
Strand 6	A	247	252	parallel
Strand 7	H	26	29	anti-parallel

Back to list of sheets
Back to top of page

There are 3 strands in AA3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	18	19	first strand
Strand 2	B	185	187	parallel
Strand 3	B	33	35	anti-parallel

Back to list of sheets
Back to top of page

There are 3 strands in AA4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	28	30	first strand
Strand 2	B	91	94	anti-parallel
Strand 3	B	77	78	anti-parallel

Back to list of sheets
Back to top of page

There are 2 strands in AA5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	81	82	first strand
Strand 2	B	87	88	anti-parallel

Back to list of sheets
Back to top of page

There are 5 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	228	232	first strand
Strand 2	B	352	357	parallel
Strand 3	B	237	242	anti-parallel
Strand 4	B	283	291	anti-parallel
Strand 5	B	273	278	anti-parallel

Back to list of sheets
Back to top of page

There are 2 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	312	313	first strand
Strand 2	B	345	346	anti-parallel

Back to list of sheets
Back to top of page

There are 2 strands in AA8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	21	23	first strand
Strand 2	C	218	220	anti-parallel

Back to list of sheets
Back to top of page

There are 2 strands in AA9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	213	214	first strand
Strand 2	D	222	223	anti-parallel

Back to list of sheets
Back to top of page

There are 3 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	95	97	first strand
Strand 2	E	211	213	anti-parallel
Strand 3	E	206	208	anti-parallel

Back to list of sheets
Back to top of page

There are 3 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	106	111	first strand
Strand 2	E	114	120	anti-parallel
Strand 3	E	152	156	anti-parallel

Back to list of sheets
Back to top of page

There are 3 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	167	170	first strand
Strand 2	E	174	178	anti-parallel
Strand 3	E	183	186	anti-parallel

Back to list of sheets
Back to top of page

There are 4 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	3	9	first strand
Strand 2	J	17	25	anti-parallel
Strand 3	J	78	80	anti-parallel
Strand 4	J	71	73	anti-parallel

Back to list of sheets
Back to top of page

There are 3 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	3	9	first strand
Strand 2	J	17	25	anti-parallel
Strand 3	J	83	84	anti-parallel

Back to list of sheets
Back to top of page

There are 6 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	11	12	first strand
Strand 2	J	116	120	parallel
Strand 3	J	92	100	anti-parallel
Strand 4	J	34	40	anti-parallel
Strand 5	J	46	53	anti-parallel
Strand 6	J	58	60	anti-parallel

Back to list of sheets
Back to top of page

There are 4 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	11	12	first strand
Strand 2	J	116	120	parallel
Strand 3	J	92	100	anti-parallel
Strand 4	J	108	112	anti-parallel

Back to list of sheets
Back to top of page

There are 3 strands in AB8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	22	24	first strand
Strand 2	K	70	72	anti-parallel
Strand 3	K	66	67	anti-parallel

Back to list of sheets
Back to top of page

There are 4 strands in AB9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	53	54	first strand
Strand 2	K	44	49	anti-parallel
Strand 3	K	33	38	anti-parallel
Strand 4	K	88	90	anti-parallel

Back to list of sheets
Back to top of page

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

Analysis of interatomic Contacts of Structural Units in PDB entry: 4PD4

Analysis of interatomic Contacts of Structural Units in PDB entry:
4PD4