Analysis of interatomic Contacts of Structural Units in PDB entry:
8KD2

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 8KD2 entry

There are 16 chains in PDB entry 8KD2 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	SER 16	VAL 426
B	GLU 664	LEU 1322
D	ILE 220	MET 401
E	LYS 33	VAL 561
F	GLY 273	GLU 360
G	LYS 321	ASP 553
O	PRO 38	GLU 133
P	LEU 22	PHE 100
Q	ARG 11	PRO 117
R	THR 29	THR 119
S	PRO 38	GLU 133
T	ASP 24	PHE 100
U	ARG 11	PRO 117
V	THR 29	SER 120
X	G -81	C 92
Y	G -92	C 81

There are 92 helices in PDB entry 8KD2. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	26	30	Right-handed 310
Helix 2	AA2	A	42	55	Right-handed alpha
Helix 3	AA3	A	57	61	Right-handed 310
Helix 4	AA4	A	70	75	Right-handed alpha
Helix 5	AA5	A	79	89	Right-handed alpha
Helix 6	AA6	A	97	104	Right-handed alpha
Helix 7	AA7	A	115	137	Right-handed alpha
Helix 8	AA8	A	164	173	Right-handed alpha
Helix 9	AA9	A	190	197	Right-handed alpha
Helix 10	AB1	A	226	230	Right-handed 310
Helix 11	AB2	A	243	262	Right-handed alpha
Helix 12	AB3	A	272	276	Right-handed 310
Helix 13	AB4	A	287	300	Right-handed alpha
Helix 14	AB5	A	314	330	Right-handed alpha
Helix 15	AB6	A	365	381	Right-handed alpha
Helix 16	AB7	B	667	676	Right-handed alpha
Helix 17	AB8	B	678	694	Right-handed alpha
Helix 18	AB9	B	698	710	Right-handed alpha
Helix 19	AC1	B	714	723	Right-handed alpha
Helix 20	AC2	B	785	790	Right-handed alpha
Helix 21	AC3	B	801	840	Right-handed alpha
Helix 22	AC4	B	843	848	Right-handed alpha
Helix 23	AC5	B	861	871	Right-handed alpha
Helix 24	AC6	B	872	886	Right-handed alpha
Helix 25	AC7	B	890	929	Right-handed alpha
Helix 26	AC8	B	934	943	Right-handed alpha
Helix 27	AC9	B	944	957	Right-handed alpha
Helix 28	AD1	B	958	960	Right-handed 310
Helix 29	AD2	B	982	998	Right-handed alpha
Helix 30	AD3	B	1003	1022	Right-handed alpha
Helix 31	AD4	B	1142	1164	Right-handed alpha
Helix 32	AD5	B	1164	1174	Right-handed alpha
Helix 33	AD6	B	1179	1183	Right-handed 310
Helix 34	AD7	B	1202	1217	Right-handed alpha
Helix 35	AD8	B	1220	1233	Right-handed alpha
Helix 36	AD9	B	1236	1240	Right-handed 310
Helix 37	AE1	B	1241	1259	Right-handed alpha
Helix 38	AE2	B	1260	1274	Right-handed alpha
Helix 39	AE3	B	1284	1292	Right-handed alpha
Helix 40	AE4	D	225	240	Right-handed alpha
Helix 41	AE5	D	253	265	Right-handed alpha
Helix 42	AE6	D	273	292	Right-handed alpha
Helix 43	AE7	D	292	297	Right-handed alpha
Helix 44	AE8	D	302	316	Right-handed alpha
Helix 45	AE9	D	327	337	Right-handed alpha
Helix 46	AF1	D	337	343	Right-handed alpha
Helix 47	AF2	D	348	369	Right-handed alpha
Helix 48	AF3	D	369	374	Right-handed alpha
Helix 49	AF4	D	391	399	Right-handed alpha
Helix 50	AF5	E	306	311	Right-handed alpha
Helix 51	AF6	E	321	330	Right-handed alpha
Helix 52	AF7	E	333	335	Right-handed 310
Helix 53	AF8	E	336	342	Right-handed alpha
Helix 54	AF9	E	357	361	Right-handed 310
Helix 55	AG1	E	400	407	Right-handed alpha
Helix 56	AG2	E	430	434	Right-handed 310
Helix 57	AG3	E	544	561	Right-handed alpha
Helix 58	AG4	F	348	351	Right-handed 310
Helix 59	AG5	F	352	360	Right-handed alpha
Helix 60	AG6	G	322	330	Right-handed alpha
Helix 61	AG7	O	44	57	Right-handed alpha
Helix 62	AG8	O	63	76	Right-handed alpha
Helix 63	AG9	O	85	114	Right-handed alpha
Helix 64	AH1	O	120	131	Right-handed alpha
Helix 65	AH2	P	24	29	Right-handed 310
Helix 66	AH3	P	30	41	Right-handed alpha
Helix 67	AH4	P	49	76	Right-handed alpha
Helix 68	AH5	P	82	93	Right-handed alpha
Helix 69	AH6	Q	26	37	Right-handed alpha
Helix 70	AH7	Q	45	73	Right-handed alpha
Helix 71	AH8	Q	79	90	Right-handed alpha
Helix 72	AH9	Q	90	97	Right-handed alpha
Helix 73	AI1	R	34	46	Right-handed alpha
Helix 74	AI2	R	52	81	Right-handed alpha
Helix 75	AI3	R	87	99	Right-handed alpha
Helix 76	AI4	R	100	119	Right-handed alpha
Helix 77	AI5	S	44	57	Right-handed alpha
Helix 78	AI6	S	63	79	Right-handed alpha
Helix 79	AI7	S	85	114	Right-handed alpha
Helix 80	AI8	S	120	132	Right-handed alpha
Helix 81	AI9	T	30	41	Right-handed alpha
Helix 82	AJ1	T	49	76	Right-handed alpha
Helix 83	AJ2	T	82	92	Right-handed alpha
Helix 84	AJ3	U	16	22	Right-handed alpha
Helix 85	AJ4	U	26	37	Right-handed alpha
Helix 86	AJ5	U	45	74	Right-handed alpha
Helix 87	AJ6	U	79	90	Right-handed alpha
Helix 88	AJ7	U	90	97	Right-handed alpha
Helix 89	AJ8	V	34	46	Right-handed alpha
Helix 90	AJ9	V	52	81	Right-handed alpha
Helix 91	AK1	V	87	98	Right-handed alpha
Helix 92	AK2	V	101	120	Right-handed alpha

There are 16 sheets in PDB entry 8KD2. 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,

There are 8 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	63	64	first strand
Strand 2	A	21	24	parallel
Strand 3	A	141	144	parallel
Strand 4	A	305	308	parallel
Strand 5	A	266	270	parallel
Strand 6	A	180	184	parallel
Strand 7	A	203	210	parallel
Strand 8	A	235	238	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	B	756	757	first strand
Strand 2	B	782	783	anti-parallel

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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	1136	1141	first strand
Strand 2	B	1300	1305	anti-parallel
Strand 3	B	1313	1316	anti-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	D	244	246	first strand
Strand 2	D	387	389	anti-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	E	437	439	first strand
Strand 2	E	446	448	anti-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	E	475	476	first strand
Strand 2	E	490	491	anti-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	E	521	523	first strand
Strand 2	E	541	543	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	O	83	84	first strand
Strand 2	P	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	O	118	119	first strand
Strand 2	P	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	P	96	98	first strand
Strand 2	U	100	102	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	Q	42	43	first strand
Strand 2	R	85	86	parallel

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There are 2 strands in AB3 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 AB4 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 AB5 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 AB6 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 AB7 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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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il

Analysis of interatomic Contacts of Structural Units in PDB entry: 8KD2

Analysis of interatomic Contacts of Structural Units in PDB entry:
8KD2