Analysis of interatomic Contacts of Structural Units in PDB entry:
8YKD

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 8YKD entry

There are 6 chains in PDB entry 8YKD (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	LEU 22	LEU 394
B	LEU 4	ASN 340
G	SER 8	ARG 62
N	GLN 1	SER 127
R	ALA 619	ARG 883
S	VAL 2	LEU 247

There are 30 helices in PDB entry 8YKD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	23	50	Right-handed alpha
Helix 2	AA2	A	62	74	Right-handed alpha
Helix 3	AA3	A	244	249	Right-handed 310
Helix 4	AA4	A	265	279	Right-handed alpha
Helix 5	AA5	A	293	304	Right-handed alpha
Helix 6	AA6	A	307	312	Right-handed alpha
Helix 7	AA7	A	331	350	Right-handed alpha
Helix 8	AA8	A	370	391	Right-handed alpha
Helix 9	AA9	B	5	26	Right-handed alpha
Helix 10	AB1	B	29	34	Right-handed alpha
Helix 11	AB2	G	9	24	Right-handed alpha
Helix 12	AB3	G	29	44	Right-handed alpha
Helix 13	AB4	N	28	32	Right-handed 310
Helix 14	AB5	N	62	65	Right-handed 310
Helix 15	AB6	R	620	645	Right-handed alpha
Helix 16	AB7	R	646	649	Right-handed 310
Helix 17	AB8	R	651	677	Right-handed alpha
Helix 18	AB9	R	682	713	Right-handed alpha
Helix 19	AC1	R	725	749	Right-handed alpha
Helix 20	AC2	R	750	753	Right-handed 310
Helix 21	AC3	R	782	809	Right-handed alpha
Helix 22	AC4	R	824	835	Right-handed alpha
Helix 23	AC5	R	836	839	Right-handed 310
Helix 24	AC6	R	840	845	Right-handed alpha
Helix 25	AC7	R	849	859	Right-handed alpha
Helix 26	AC8	R	862	872	Right-handed alpha
Helix 27	AC9	R	875	882	Right-handed alpha
Helix 28	AD1	S	62	65	Right-handed 310
Helix 29	AD2	S	87	91	Right-handed 310
Helix 30	AD3	S	220	224	Right-handed 310

There are 15 sheets in PDB entry 8YKD. 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,

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	217	224	first strand
Strand 2	A	227	234	anti-parallel
Strand 3	A	52	55	parallel
Strand 4	A	253	259	parallel
Strand 5	A	286	292	parallel
Strand 6	A	359	363	parallel

Back to list of sheets
Back to top of page

There are 4 strands in AA2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	47	52	first strand
Strand 2	B	335	339	anti-parallel
Strand 3	B	327	330	anti-parallel
Strand 4	B	317	320	anti-parallel

Back to list of sheets
Back to top of page

There are 4 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	58	63	first strand
Strand 2	B	69	74	anti-parallel
Strand 3	B	78	83	anti-parallel
Strand 4	B	89	94	anti-parallel

Back to list of sheets
Back to top of page

There are 4 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	100	105	first strand
Strand 2	B	111	116	anti-parallel
Strand 3	B	120	125	anti-parallel
Strand 4	B	134	140	anti-parallel

Back to list of sheets
Back to top of page

There are 4 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	146	151	first strand
Strand 2	B	156	161	anti-parallel
Strand 3	B	165	170	anti-parallel
Strand 4	B	176	181	anti-parallel

Back to list of sheets
Back to top of page

There are 4 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	187	192	first strand
Strand 2	B	198	203	anti-parallel
Strand 3	B	207	212	anti-parallel
Strand 4	B	217	223	anti-parallel

Back to list of sheets
Back to top of page

There are 4 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	229	234	first strand
Strand 2	B	240	245	anti-parallel
Strand 3	B	250	254	anti-parallel
Strand 4	B	260	264	anti-parallel

Back to list of sheets
Back to top of page

There are 4 strands in AA8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	273	277	first strand
Strand 2	B	284	289	anti-parallel
Strand 3	B	294	298	anti-parallel
Strand 4	B	304	308	anti-parallel

Back to list of sheets
Back to top of page

There are 4 strands in AA9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	N	3	6	first strand
Strand 2	N	18	25	anti-parallel
Strand 3	N	78	83	anti-parallel
Strand 4	N	69	73	anti-parallel

Back to list of sheets
Back to top of page

There are 6 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	N	11	12	first strand
Strand 2	N	122	126	parallel
Strand 3	N	92	98	anti-parallel
Strand 4	N	34	39	anti-parallel
Strand 5	N	45	51	anti-parallel
Strand 6	N	59	60	anti-parallel

Back to list of sheets
Back to top of page

There are 4 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	S	3	7	first strand
Strand 2	S	19	25	anti-parallel
Strand 3	S	78	83	anti-parallel
Strand 4	S	68	73	anti-parallel

Back to list of sheets
Back to top of page

There are 6 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	S	11	12	first strand
Strand 2	S	115	119	parallel
Strand 3	S	92	98	anti-parallel
Strand 4	S	34	39	anti-parallel
Strand 5	S	45	51	anti-parallel
Strand 6	S	58	60	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	S	11	12	first strand
Strand 2	S	115	119	parallel
Strand 3	S	92	98	anti-parallel
Strand 4	S	110	111	anti-parallel

Back to list of sheets
Back to top of page

There are 4 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	S	140	141	first strand
Strand 2	S	155	161	anti-parallel
Strand 3	S	211	216	anti-parallel
Strand 4	S	203	207	anti-parallel

Back to list of sheets
Back to top of page

There are 5 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	S	194	195	first strand
Strand 2	S	185	190	anti-parallel
Strand 3	S	176	179	anti-parallel
Strand 4	S	226	228	anti-parallel
Strand 5	S	243	244	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: 8YKD

Analysis of interatomic Contacts of Structural Units in PDB entry:
8YKD