Analysis of interatomic Contacts of Structural Units in PDB entry:
8KD4

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 8KD4 entry

There are 16 chains in PDB entry 8KD4 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
D	GLY 11	MET 401
F	GLY 11	TYR 373
O	LYS 37	ARG 134
P	LEU 22	PHE 100
Q	ARG 11	PRO 117
R	LYS 28	SER 120
S	LYS 37	GLU 133
T	LEU 22	PHE 100
U	ARG 11	PRO 117
V	THR 29	THR 119
X	G -88	G 75
Y	C -75	C 88
A	ASP 17	ASP 423
B	GLU 664	LEU 1324
E	LYS 33	VAL 561
G	LYS 320	GLN 570

There are104 helices in PDB entry 8KD4. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	D	98	113	Right-handed alpha
Helix 2	AA2	D	225	241	Right-handed alpha
Helix 3	AA3	D	253	269	Right-handed alpha
Helix 4	AA4	D	273	293	Right-handed alpha
Helix 5	AA5	D	301	317	Right-handed alpha
Helix 6	AA6	D	321	325	Right-handed 310
Helix 7	AA7	D	327	344	Right-handed alpha
Helix 8	AA8	D	348	369	Right-handed alpha
Helix 9	AA9	D	391	399	Right-handed alpha
Helix 10	AB1	F	98	112	Right-handed alpha
Helix 11	AB2	F	229	239	Right-handed alpha
Helix 12	AB3	F	253	260	Right-handed alpha
Helix 13	AB4	F	260	265	Right-handed alpha
Helix 14	AB5	F	275	290	Right-handed alpha
Helix 15	AB6	F	299	314	Right-handed alpha
Helix 16	AB7	F	328	343	Right-handed alpha
Helix 17	AB8	F	348	367	Right-handed alpha
Helix 18	AB9	O	44	55	Right-handed alpha
Helix 19	AC1	O	63	76	Right-handed alpha
Helix 20	AC2	O	85	114	Right-handed alpha
Helix 21	AC3	O	120	132	Right-handed alpha
Helix 22	AC4	P	25	29	Right-handed 310
Helix 23	AC5	P	30	41	Right-handed alpha
Helix 24	AC6	P	49	76	Right-handed alpha
Helix 25	AC7	P	82	92	Right-handed alpha
Helix 26	AC8	Q	16	21	Right-handed alpha
Helix 27	AC9	Q	26	37	Right-handed alpha
Helix 28	AD1	Q	45	73	Right-handed alpha
Helix 29	AD2	Q	79	90	Right-handed alpha
Helix 30	AD3	Q	90	97	Right-handed alpha
Helix 31	AD4	R	34	46	Right-handed alpha
Helix 32	AD5	R	52	81	Right-handed alpha
Helix 33	AD6	R	87	99	Right-handed alpha
Helix 34	AD7	R	101	120	Right-handed alpha
Helix 35	AD8	S	44	56	Right-handed alpha
Helix 36	AD9	S	63	79	Right-handed alpha
Helix 37	AE1	S	85	114	Right-handed alpha
Helix 38	AE2	S	120	132	Right-handed alpha
Helix 39	AE3	T	25	29	Right-handed 310
Helix 40	AE4	T	30	41	Right-handed alpha
Helix 41	AE5	T	49	76	Right-handed alpha
Helix 42	AE6	T	82	92	Right-handed alpha
Helix 43	AE7	U	16	21	Right-handed alpha
Helix 44	AE8	U	26	37	Right-handed alpha
Helix 45	AE9	U	45	73	Right-handed alpha
Helix 46	AF1	U	79	90	Right-handed alpha
Helix 47	AF2	U	90	97	Right-handed alpha
Helix 48	AF3	V	34	46	Right-handed alpha
Helix 49	AF4	V	52	81	Right-handed alpha
Helix 50	AF5	V	87	99	Right-handed alpha
Helix 51	AF6	V	101	119	Right-handed alpha
Helix 52	AF7	A	28	32	Right-handed 310
Helix 53	AF8	A	42	55	Right-handed alpha
Helix 54	AF9	A	56	61	Right-handed 310
Helix 55	AG1	A	79	89	Right-handed alpha
Helix 56	AG2	A	90	94	Right-handed 310
Helix 57	AG3	A	98	104	Right-handed alpha
Helix 58	AG4	A	115	137	Right-handed alpha
Helix 59	AG5	A	164	175	Right-handed alpha
Helix 60	AG6	A	190	197	Right-handed alpha
Helix 61	AG7	A	226	230	Right-handed 310
Helix 62	AG8	A	243	262	Right-handed alpha
Helix 63	AG9	A	287	300	Right-handed alpha
Helix 64	AH1	A	315	330	Right-handed alpha
Helix 65	AH2	A	343	347	Right-handed 310
Helix 66	AH3	A	365	381	Right-handed alpha
Helix 67	AH4	A	404	408	Right-handed 310
Helix 68	AH5	B	665	677	Right-handed alpha
Helix 69	AH6	B	678	694	Right-handed alpha
Helix 70	AH7	B	698	710	Right-handed alpha
Helix 71	AH8	B	713	725	Right-handed alpha
Helix 72	AH9	B	771	778	Right-handed alpha
Helix 73	AI1	B	785	791	Right-handed alpha
Helix 74	AI2	B	801	840	Right-handed alpha
Helix 75	AI3	B	842	848	Right-handed alpha
Helix 76	AI4	B	861	871	Right-handed alpha
Helix 77	AI5	B	872	886	Right-handed alpha
Helix 78	AI6	B	890	929	Right-handed alpha
Helix 79	AI7	B	934	943	Right-handed alpha
Helix 80	AI8	B	944	967	Right-handed alpha
Helix 81	AI9	B	982	997	Right-handed alpha
Helix 82	AJ1	B	1003	1022	Right-handed alpha
Helix 83	AJ2	B	1141	1164	Right-handed alpha
Helix 84	AJ3	B	1164	1174	Right-handed alpha
Helix 85	AJ4	B	1178	1185	Right-handed alpha
Helix 86	AJ5	B	1202	1216	Right-handed alpha
Helix 87	AJ6	B	1221	1230	Right-handed alpha
Helix 88	AJ7	B	1236	1240	Right-handed 310
Helix 89	AJ8	B	1241	1259	Right-handed alpha
Helix 90	AJ9	B	1259	1273	Right-handed alpha
Helix 91	AK1	B	1282	1294	Right-handed alpha
Helix 92	AK2	B	1307	1309	Right-handed 310
Helix 93	AK3	E	292	296	Right-handed 310
Helix 94	AK4	E	303	308	Right-handed alpha
Helix 95	AK5	E	321	330	Right-handed alpha
Helix 96	AK6	E	333	345	Right-handed alpha
Helix 97	AK7	E	354	360	Right-handed alpha
Helix 98	AK8	E	382	387	Right-handed alpha
Helix 99	AK9	E	402	407	Right-handed 310
Helix 100	AL1	E	430	434	Right-handed 310
Helix 101	AL2	E	543	559	Right-handed alpha
Helix 102	AL3	G	322	326	Right-handed 310
Helix 103	AL4	G	337	342	Right-handed alpha
Helix 104	AL5	G	541	569	Right-handed alpha

There are 17 sheets in PDB entry 8KD4. 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,

There are 2 strands in AA1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	244	246	first strand
Strand 2	D	387	389	anti-parallel

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There are 2 strands in AA2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	O	83	84	first strand
Strand 2	P	80	81	parallel

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There are 2 strands in AA3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	O	118	119	first strand
Strand 2	P	45	46	parallel

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There are 2 strands in AA4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	P	96	98	first strand
Strand 2	U	100	102	parallel

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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	Q	42	43	first strand
Strand 2	R	85	86	parallel

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There are 2 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	Q	77	78	first strand
Strand 2	R	50	51	parallel

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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	Q	100	102	first strand
Strand 2	T	96	98	parallel

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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	S	83	84	first strand
Strand 2	T	80	81	parallel

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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	S	118	119	first strand
Strand 2	T	45	46	parallel

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There are 2 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	U	42	43	first strand
Strand 2	V	85	86	parallel

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There are 2 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	U	77	78	first strand
Strand 2	V	50	51	parallel

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There are 8 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	62	64	first strand
Strand 2	A	21	24	parallel
Strand 3	A	141	144	parallel
Strand 4	A	305	311	parallel
Strand 5	A	266	272	parallel
Strand 6	A	180	184	parallel
Strand 7	A	203	210	parallel
Strand 8	A	233	238	parallel

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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	B	977	978	first strand
Strand 2	B	1311	1316	anti-parallel
Strand 3	B	1301	1305	anti-parallel
Strand 4	B	1136	1140	anti-parallel

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There are 2 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	272	274	first strand
Strand 2	E	281	283	anti-parallel

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There are 2 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	365	366	first strand
Strand 2	E	372	373	anti-parallel

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There are 2 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	437	438	first strand
Strand 2	E	447	448	anti-parallel

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There are 2 strands in AB8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	521	522	first strand
Strand 2	E	541	542	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: 8KD4

Analysis of interatomic Contacts of Structural Units in PDB entry:
8KD4