Analysis of interatomic Contacts of Structural Units in PDB entry:
5D39

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 5D39 entry

There are 12 chains in PDB entry 5D39 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	GLN 125	GLY 640
A	VAL 642	GLU 651
B	GLN 125	GLY 640
B	VAL 642	GLU 651
C	GLN 125	GLY 640
C	VAL 642	GLU 651
D	GLN 125	GLY 640
D	VAL 642	GLU 651
N	T 1	T 21
M	A 1	A 21
E	A 1	A 21
F	T 1	T 21

There are 80 helices in PDB entry 5D39. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	125	148	Right-handed alpha
Helix 2	AA2	A	149	151	Right-handed 310
Helix 3	AA3	A	181	187	Right-handed alpha
Helix 4	AA4	A	189	212	Right-handed alpha
Helix 5	AA5	A	221	244	Right-handed alpha
Helix 6	AA6	A	250	271	Right-handed alpha
Helix 7	AA7	A	297	302	Right-handed alpha
Helix 8	AA8	A	318	323	Right-handed alpha
Helix 9	AA9	A	378	382	Right-handed 310
Helix 10	AB1	A	415	417	Right-handed 310
Helix 11	AB2	A	418	433	Right-handed alpha
Helix 12	AB3	A	448	464	Right-handed alpha
Helix 13	AB4	A	470	483	Right-handed alpha
Helix 14	AB5	A	499	504	Right-handed alpha
Helix 15	AB6	A	513	529	Right-handed alpha
Helix 16	AB7	A	529	535	Right-handed alpha
Helix 17	AB8	A	543	553	Right-handed alpha
Helix 18	AB9	A	593	600	Right-handed alpha
Helix 19	AC1	A	601	609	Right-handed alpha
Helix 20	AC2	A	621	626	Right-handed alpha
Helix 21	AC3	A	627	629	Right-handed 310
Helix 22	AC4	B	126	148	Right-handed alpha
Helix 23	AC5	B	149	151	Right-handed 310
Helix 24	AC6	B	182	187	Right-handed alpha
Helix 25	AC7	B	189	213	Right-handed alpha
Helix 26	AC8	B	221	244	Right-handed alpha
Helix 27	AC9	B	250	271	Right-handed alpha
Helix 28	AD1	B	318	322	Right-handed alpha
Helix 29	AD2	B	378	382	Right-handed 310
Helix 30	AD3	B	415	417	Right-handed 310
Helix 31	AD4	B	418	433	Right-handed alpha
Helix 32	AD5	B	448	464	Right-handed alpha
Helix 33	AD6	B	470	483	Right-handed alpha
Helix 34	AD7	B	499	504	Right-handed alpha
Helix 35	AD8	B	513	529	Right-handed alpha
Helix 36	AD9	B	529	535	Right-handed alpha
Helix 37	AE1	B	543	553	Right-handed alpha
Helix 38	AE2	B	593	600	Right-handed alpha
Helix 39	AE3	B	601	609	Right-handed alpha
Helix 40	AE4	B	620	626	Right-handed alpha
Helix 41	AE5	B	627	629	Right-handed 310
Helix 42	AE6	C	126	151	Right-handed alpha
Helix 43	AE7	C	178	185	Right-handed alpha
Helix 44	AE8	C	185	212	Right-handed alpha
Helix 45	AE9	C	221	246	Right-handed alpha
Helix 46	AF1	C	250	272	Right-handed alpha
Helix 47	AF2	C	297	301	Right-handed 310
Helix 48	AF3	C	318	323	Right-handed alpha
Helix 49	AF4	C	378	381	Right-handed 310
Helix 50	AF5	C	415	417	Right-handed 310
Helix 51	AF6	C	418	433	Right-handed alpha
Helix 52	AF7	C	448	464	Right-handed alpha
Helix 53	AF8	C	470	483	Right-handed alpha
Helix 54	AF9	C	499	504	Right-handed alpha
Helix 55	AG1	C	513	529	Right-handed alpha
Helix 56	AG2	C	529	535	Right-handed alpha
Helix 57	AG3	C	543	553	Right-handed alpha
Helix 58	AG4	C	593	600	Right-handed alpha
Helix 59	AG5	C	601	609	Right-handed alpha
Helix 60	AG6	C	621	625	Right-handed alpha
Helix 61	AG7	C	626	629	Right-handed 310
Helix 62	AG8	D	126	152	Right-handed alpha
Helix 63	AG9	D	182	185	Right-handed 310
Helix 64	AH1	D	186	212	Right-handed alpha
Helix 65	AH2	D	221	244	Right-handed alpha
Helix 66	AH3	D	251	272	Right-handed alpha
Helix 67	AH4	D	297	301	Right-handed 310
Helix 68	AH5	D	318	323	Right-handed alpha
Helix 69	AH6	D	415	417	Right-handed 310
Helix 70	AH7	D	418	433	Right-handed alpha
Helix 71	AH8	D	448	464	Right-handed alpha
Helix 72	AH9	D	470	483	Right-handed alpha
Helix 73	AI1	D	499	504	Right-handed alpha
Helix 74	AI2	D	513	529	Right-handed alpha
Helix 75	AI3	D	529	535	Right-handed alpha
Helix 76	AI4	D	543	553	Right-handed alpha
Helix 77	AI5	D	593	600	Right-handed alpha
Helix 78	AI6	D	601	609	Right-handed alpha
Helix 79	AI7	D	621	625	Right-handed alpha
Helix 80	AI8	D	626	629	Right-handed 310

There are 26 sheets in PDB entry 5D39. 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, AC1, AC2, AC3, AC4, AC5, AC6, AC7, AC8,

There are 4 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	273	277	first strand
Strand 2	A	291	295	anti-parallel
Strand 3	A	355	360	anti-parallel
Strand 4	A	348	350	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	A	282	284	first strand
Strand 2	A	411	413	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	A	313	317	first strand
Strand 2	A	384	392	anti-parallel
Strand 3	A	401	406	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	A	340	341	first strand
Strand 2	A	364	365	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	A	445	447	first strand
Strand 2	A	496	498	anti-parallel

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There are 6 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	619	620	first strand
Strand 2	A	614	615	anti-parallel
Strand 3	A	558	563	parallel
Strand 4	A	571	577	anti-parallel
Strand 5	A	585	589	anti-parallel
Strand 6	C	641	642	parallel

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There are 6 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	641	642	first strand
Strand 2	C	586	589	parallel
Strand 3	C	571	576	anti-parallel
Strand 4	C	558	563	anti-parallel
Strand 5	C	614	615	parallel
Strand 6	C	619	620	anti-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	A	645	649	first strand
Strand 2	C	645	649	anti-parallel

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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	B	273	277	first strand
Strand 2	B	288	295	anti-parallel
Strand 3	B	355	365	anti-parallel
Strand 4	B	340	341	anti-parallel

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There are 4 strands in AB1 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	288	295	anti-parallel
Strand 3	B	355	365	anti-parallel
Strand 4	B	348	350	anti-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	B	282	284	first strand
Strand 2	B	411	413	parallel

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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	B	312	317	first strand
Strand 2	B	384	392	anti-parallel
Strand 3	B	401	406	anti-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	B	445	447	first strand
Strand 2	B	496	498	anti-parallel

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There are 5 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	614	615	first strand
Strand 2	B	558	563	parallel
Strand 3	B	571	577	anti-parallel
Strand 4	B	585	589	anti-parallel
Strand 5	D	641	642	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	B	645	649	first strand
Strand 2	D	645	649	anti-parallel

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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	C	273	277	first strand
Strand 2	C	288	295	anti-parallel
Strand 3	C	355	365	anti-parallel
Strand 4	C	340	341	anti-parallel

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There are 4 strands in AB8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	273	277	first strand
Strand 2	C	288	295	anti-parallel
Strand 3	C	355	365	anti-parallel
Strand 4	C	348	350	anti-parallel

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There are 5 strands in AB9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	282	284	first strand
Strand 2	C	410	413	parallel
Strand 3	C	383	392	anti-parallel
Strand 4	C	310	317	anti-parallel
Strand 5	C	344	346	anti-parallel

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There are 4 strands in AC1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	282	284	first strand
Strand 2	C	410	413	parallel
Strand 3	C	383	392	anti-parallel
Strand 4	C	401	406	anti-parallel

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There are 2 strands in AC2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	445	447	first strand
Strand 2	C	496	498	anti-parallel

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There are 4 strands in AC3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	273	277	first strand
Strand 2	D	288	295	anti-parallel
Strand 3	D	355	365	anti-parallel
Strand 4	D	340	341	anti-parallel

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There are 4 strands in AC4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	273	277	first strand
Strand 2	D	288	295	anti-parallel
Strand 3	D	355	365	anti-parallel
Strand 4	D	348	350	anti-parallel

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There are 5 strands in AC5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	282	284	first strand
Strand 2	D	410	413	parallel
Strand 3	D	383	392	anti-parallel
Strand 4	D	310	317	anti-parallel
Strand 5	D	344	346	anti-parallel

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There are 4 strands in AC6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	282	284	first strand
Strand 2	D	410	413	parallel
Strand 3	D	383	392	anti-parallel
Strand 4	D	401	406	anti-parallel

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There are 2 strands in AC7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	445	447	first strand
Strand 2	D	496	498	anti-parallel

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There are 5 strands in AC8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	585	588	first strand
Strand 2	D	571	577	anti-parallel
Strand 3	D	558	563	anti-parallel
Strand 4	D	614	615	parallel
Strand 5	D	619	620	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: 5D39

Analysis of interatomic Contacts of Structural Units in PDB entry:
5D39