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

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 5MDN entry

There are 2 chains in PDB entry 5MDN (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	MET 1	GLU 766
B	MET 1	GLU 766

There are 58 helices in PDB entry 5MDN. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	50	59	Right-handed alpha
Helix 2	AA2	A	88	90	Right-handed 310
Helix 3	AA3	A	91	101	Right-handed alpha
Helix 4	AA4	A	114	124	Right-handed alpha
Helix 5	AA5	A	208	223	Right-handed alpha
Helix 6	AA6	A	235	248	Right-handed alpha
Helix 7	AA7	A	264	266	Right-handed 310
Helix 8	AA8	A	278	283	Right-handed alpha
Helix 9	AA9	A	292	300	Right-handed alpha
Helix 10	AB1	A	304	308	Right-handed 310
Helix 11	AB2	A	312	314	Right-handed 310
Helix 12	AB3	A	315	321	Right-handed alpha
Helix 13	AB4	A	325	357	Right-handed alpha
Helix 14	AB5	A	361	366	Right-handed alpha
Helix 15	AB6	A	369	385	Right-handed alpha
Helix 16	AB7	A	423	432	Right-handed alpha
Helix 17	AB8	A	435	439	Right-handed 310
Helix 18	AB9	A	467	487	Right-handed alpha
Helix 19	AC1	A	488	490	Right-handed 310
Helix 20	AC2	A	494	513	Right-handed alpha
Helix 21	AC3	A	513	520	Right-handed alpha
Helix 22	AC4	A	527	552	Right-handed alpha
Helix 23	AC5	A	571	584	Right-handed alpha
Helix 24	AC6	A	627	644	Right-handed alpha
Helix 25	AC7	A	646	667	Right-handed alpha
Helix 26	AC8	A	671	676	Right-handed 310
Helix 27	AC9	A	692	698	Right-handed alpha
Helix 28	AD1	A	742	749	Right-handed alpha
Helix 29	AD2	A	750	757	Right-handed alpha
Helix 30	AD3	B	50	59	Right-handed alpha
Helix 31	AD4	B	88	90	Right-handed 310
Helix 32	AD5	B	91	100	Right-handed alpha
Helix 33	AD6	B	114	124	Right-handed alpha
Helix 34	AD7	B	208	223	Right-handed alpha
Helix 35	AD8	B	235	248	Right-handed alpha
Helix 36	AD9	B	264	266	Right-handed 310
Helix 37	AE1	B	278	283	Right-handed alpha
Helix 38	AE2	B	292	300	Right-handed alpha
Helix 39	AE3	B	312	314	Right-handed 310
Helix 40	AE4	B	315	321	Right-handed alpha
Helix 41	AE5	B	325	357	Right-handed alpha
Helix 42	AE6	B	361	366	Right-handed alpha
Helix 43	AE7	B	369	385	Right-handed alpha
Helix 44	AE8	B	423	432	Right-handed alpha
Helix 45	AE9	B	435	439	Right-handed 310
Helix 46	AF1	B	467	487	Right-handed alpha
Helix 47	AF2	B	488	490	Right-handed 310
Helix 48	AF3	B	494	513	Right-handed alpha
Helix 49	AF4	B	513	520	Right-handed alpha
Helix 50	AF5	B	527	552	Right-handed alpha
Helix 51	AF6	B	571	584	Right-handed alpha
Helix 52	AF7	B	627	644	Right-handed alpha
Helix 53	AF8	B	646	667	Right-handed alpha
Helix 54	AF9	B	671	676	Right-handed 310
Helix 55	AG1	B	692	698	Right-handed alpha
Helix 56	AG2	B	699	703	Right-handed 310
Helix 57	AG3	B	742	749	Right-handed alpha
Helix 58	AG4	B	750	757	Right-handed alpha

There are 15 sheets in PDB entry 5MDN. 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 5 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	5	12	first strand
Strand 2	A	17	24	anti-parallel
Strand 3	A	30	35	anti-parallel
Strand 4	A	144	155	parallel
Strand 5	A	131	141	anti-parallel

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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	A	64	74	first strand
Strand 2	A	77	86	anti-parallel
Strand 3	A	41	46	anti-parallel
Strand 4	A	105	109	anti-parallel

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There are 5 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	198	202	first strand
Strand 2	A	186	193	anti-parallel
Strand 3	A	165	172	anti-parallel
Strand 4	A	226	229	parallel
Strand 5	A	274	277	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	261	262	first strand
Strand 2	A	268	269	anti-parallel

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There are 7 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	404	406	first strand
Strand 2	A	556	560	anti-parallel
Strand 3	A	563	567	anti-parallel
Strand 4	A	411	420	anti-parallel
Strand 5	A	588	598	anti-parallel
Strand 6	A	605	609	anti-parallel
Strand 7	A	614	617	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	A	451	453	first strand
Strand 2	A	460	462	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	A	716	718	first strand
Strand 2	A	729	731	anti-parallel

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There are 5 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	5	12	first strand
Strand 2	B	17	24	anti-parallel
Strand 3	B	30	35	anti-parallel
Strand 4	B	144	155	parallel
Strand 5	B	131	136	anti-parallel

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There are 5 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	5	12	first strand
Strand 2	B	17	24	anti-parallel
Strand 3	B	30	35	anti-parallel
Strand 4	B	144	155	parallel
Strand 5	B	140	141	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	64	74	first strand
Strand 2	B	77	86	anti-parallel
Strand 3	B	41	46	anti-parallel
Strand 4	B	105	109	anti-parallel

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There are 5 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	198	202	first strand
Strand 2	B	186	193	anti-parallel
Strand 3	B	165	172	anti-parallel
Strand 4	B	226	229	parallel
Strand 5	B	274	277	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	B	261	262	first strand
Strand 2	B	268	269	anti-parallel

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There are 7 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	404	406	first strand
Strand 2	B	556	560	anti-parallel
Strand 3	B	563	567	anti-parallel
Strand 4	B	411	420	anti-parallel
Strand 5	B	588	598	anti-parallel
Strand 6	B	605	609	anti-parallel
Strand 7	B	614	617	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	B	451	453	first strand
Strand 2	B	460	462	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	B	716	718	first strand
Strand 2	B	729	731	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: 5MDN

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