Analysis of interatomic Contacts of Structural Units in PDB entry:
3DMK

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 3DMK entry

There are 3 chains in PDB entry 3DMK (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	GLN 1	ALA 775
B	GLN 1	VAL 676
C	GLN 1	VAL 676

There are 31 helices in PDB entry 3DMK. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	67	71	Right-handed 310
Helix 2	2	A	72	76	Right-handed alpha
Helix 3	3	A	128	133	Right-handed alpha
Helix 4	4	A	172	176	Right-handed 310
Helix 5	5	A	215	218	Right-handed 310
Helix 6	6	A	279	283	Right-handed 310
Helix 7	7	A	362	366	Right-handed 310
Helix 8	8	A	552	557	Right-handed alpha
Helix 9	9	A	627	631	Right-handed 310
Helix 10	10	A	650	654	Right-handed 310
Helix 11	11	A	746	750	Right-handed 310
Helix 12	12	B	67	71	Right-handed 310
Helix 13	13	B	72	76	Right-handed alpha
Helix 14	14	B	128	133	Right-handed alpha
Helix 15	15	B	172	176	Right-handed 310
Helix 16	16	B	215	218	Right-handed 310
Helix 17	17	B	279	283	Right-handed 310
Helix 18	18	B	362	366	Right-handed 310
Helix 19	19	B	552	557	Right-handed alpha
Helix 20	20	B	627	631	Right-handed 310
Helix 21	21	B	650	654	Right-handed 310
Helix 22	22	C	67	71	Right-handed 310
Helix 23	23	C	72	76	Right-handed alpha
Helix 24	24	C	128	133	Right-handed alpha
Helix 25	25	C	172	176	Right-handed 310
Helix 26	26	C	215	218	Right-handed 310
Helix 27	27	C	279	283	Right-handed 310
Helix 28	28	C	362	366	Right-handed 310
Helix 29	29	C	552	557	Right-handed alpha
Helix 30	30	C	627	631	Right-handed 310
Helix 31	31	C	650	654	Right-handed 310

There are 59 sheets in PDB entry 3DMK. Click on sheet of interest to get list of strands forming it: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, AA, AB, AC, AD, AE, AF, AG, AH, AI, AJ, AK, AL, AM, AN, AO, AP, AQ, AR, AS, AT, AU, AV, AW, AX, AY, AZ, BA, BB, BC, BD, BE, BF, BG,

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	2	8	first strand
Strand 2	A	27	31	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	13	17	first strand
Strand 2	A	89	101	parallel
Strand 3	A	77	86	anti-parallel
Strand 4	A	35	40	anti-parallel

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There are 3 strands in C sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	22	25	first strand
Strand 2	A	60	63	anti-parallel
Strand 3	A	54	55	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	113	116	first strand
Strand 2	A	199	204	parallel
Strand 3	A	179	186	anti-parallel
Strand 4	A	135	142	anti-parallel
Strand 5	A	147	148	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	113	116	first strand
Strand 2	A	199	204	parallel
Strand 3	A	179	186	anti-parallel
Strand 4	A	192	194	anti-parallel

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There are 3 strands in F sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	121	123	first strand
Strand 2	A	166	168	anti-parallel
Strand 3	A	158	160	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	220	225	first strand
Strand 2	A	296	305	parallel
Strand 3	A	284	291	anti-parallel
Strand 4	A	244	250	anti-parallel
Strand 5	A	257	259	anti-parallel

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There are 3 strands in H sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	231	233	first strand
Strand 2	A	272	275	anti-parallel
Strand 3	A	266	269	anti-parallel

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There are 3 strands in I sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	307	314	first strand
Strand 2	A	326	335	anti-parallel
Strand 3	A	355	358	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	317	319	first strand
Strand 2	A	385	387	parallel
Strand 3	A	367	374	anti-parallel
Strand 4	A	339	344	anti-parallel
Strand 5	A	347	348	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	317	319	first strand
Strand 2	A	385	387	parallel
Strand 3	A	367	374	anti-parallel
Strand 4	A	379	382	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	396	400	first strand
Strand 2	A	412	419	anti-parallel
Strand 3	A	453	459	anti-parallel
Strand 4	A	441	447	anti-parallel

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There are 5 strands in M 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	479	489	parallel
Strand 3	A	468	476	anti-parallel
Strand 4	A	425	430	anti-parallel
Strand 5	A	433	434	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	494	495	first strand
Strand 2	A	515	516	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	501	504	first strand
Strand 2	A	571	581	parallel
Strand 3	A	558	566	anti-parallel
Strand 4	A	520	527	anti-parallel
Strand 5	A	530	531	anti-parallel

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There are 3 strands in P sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	509	512	first strand
Strand 2	A	545	548	anti-parallel
Strand 3	A	538	540	anti-parallel

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There are 3 strands in Q sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	596	597	first strand
Strand 2	A	676	684	parallel
Strand 3	A	702	706	anti-parallel

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There are 3 strands in R sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	601	606	first strand
Strand 2	A	641	647	anti-parallel
Strand 3	A	633	637	anti-parallel

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There are 3 strands in S sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	616	621	first strand
Strand 2	A	655	662	anti-parallel
Strand 3	A	667	674	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	689	692	first strand
Strand 2	A	765	774	parallel
Strand 3	A	751	758	anti-parallel
Strand 4	A	710	712	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	689	692	first strand
Strand 2	A	765	774	parallel
Strand 3	A	751	758	anti-parallel
Strand 4	A	715	716	anti-parallel

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There are 3 strands in V sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	697	700	first strand
Strand 2	A	739	742	anti-parallel
Strand 3	A	733	736	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	2	8	first strand
Strand 2	B	27	31	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	13	17	first strand
Strand 2	B	96	101	parallel
Strand 3	B	77	86	anti-parallel
Strand 4	B	35	40	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	13	17	first strand
Strand 2	B	96	101	parallel
Strand 3	B	77	86	anti-parallel
Strand 4	B	89	92	anti-parallel

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There are 3 strands in Z sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	22	25	first strand
Strand 2	B	60	63	anti-parallel
Strand 3	B	54	55	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	113	116	first strand
Strand 2	B	199	204	parallel
Strand 3	B	179	186	anti-parallel
Strand 4	B	135	142	anti-parallel
Strand 5	B	147	148	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	113	116	first strand
Strand 2	B	199	204	parallel
Strand 3	B	179	186	anti-parallel
Strand 4	B	192	194	anti-parallel

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There are 3 strands in AC sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	121	123	first strand
Strand 2	B	166	168	anti-parallel
Strand 3	B	158	160	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	220	225	first strand
Strand 2	B	296	305	parallel
Strand 3	B	284	291	anti-parallel
Strand 4	B	244	250	anti-parallel
Strand 5	B	257	259	anti-parallel

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There are 3 strands in AE sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	231	233	first strand
Strand 2	B	272	275	anti-parallel
Strand 3	B	266	269	anti-parallel

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There are 3 strands in AF sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	307	314	first strand
Strand 2	B	326	335	anti-parallel
Strand 3	B	355	358	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	317	320	first strand
Strand 2	B	385	388	parallel
Strand 3	B	367	374	anti-parallel
Strand 4	B	339	344	anti-parallel
Strand 5	B	347	348	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	317	320	first strand
Strand 2	B	385	388	parallel
Strand 3	B	367	374	anti-parallel
Strand 4	B	379	382	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	396	400	first strand
Strand 2	B	412	419	anti-parallel
Strand 3	B	453	459	anti-parallel
Strand 4	B	441	447	anti-parallel

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There are 5 strands in AJ 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	479	489	parallel
Strand 3	B	468	476	anti-parallel
Strand 4	B	425	430	anti-parallel
Strand 5	B	433	434	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	494	495	first strand
Strand 2	B	515	516	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	501	504	first strand
Strand 2	B	571	581	parallel
Strand 3	B	558	566	anti-parallel
Strand 4	B	520	527	anti-parallel
Strand 5	B	530	531	anti-parallel

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There are 3 strands in AM sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	509	512	first strand
Strand 2	B	545	548	anti-parallel
Strand 3	B	538	540	anti-parallel

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There are 3 strands in AN sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	601	606	first strand
Strand 2	B	641	647	anti-parallel
Strand 3	B	633	637	anti-parallel

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There are 3 strands in AO sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	616	621	first strand
Strand 2	B	655	662	anti-parallel
Strand 3	B	667	674	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	2	8	first strand
Strand 2	C	27	31	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	13	17	first strand
Strand 2	C	89	101	parallel
Strand 3	C	77	86	anti-parallel
Strand 4	C	35	40	anti-parallel

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There are 3 strands in AR sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	22	25	first strand
Strand 2	C	60	63	anti-parallel
Strand 3	C	54	55	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	113	116	first strand
Strand 2	C	199	204	parallel
Strand 3	C	179	186	anti-parallel
Strand 4	C	135	142	anti-parallel
Strand 5	C	147	148	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	113	116	first strand
Strand 2	C	199	204	parallel
Strand 3	C	179	186	anti-parallel
Strand 4	C	192	194	anti-parallel

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There are 3 strands in AU sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	121	123	first strand
Strand 2	C	166	168	anti-parallel
Strand 3	C	158	160	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	220	225	first strand
Strand 2	C	296	305	parallel
Strand 3	C	284	291	anti-parallel
Strand 4	C	244	250	anti-parallel
Strand 5	C	257	259	anti-parallel

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There are 3 strands in AW sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	231	233	first strand
Strand 2	C	272	275	anti-parallel
Strand 3	C	266	269	anti-parallel

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There are 3 strands in AX sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	307	314	first strand
Strand 2	C	326	335	anti-parallel
Strand 3	C	355	358	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	317	320	first strand
Strand 2	C	385	388	parallel
Strand 3	C	367	374	anti-parallel
Strand 4	C	339	344	anti-parallel
Strand 5	C	347	348	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	317	320	first strand
Strand 2	C	385	388	parallel
Strand 3	C	367	374	anti-parallel
Strand 4	C	379	382	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	396	400	first strand
Strand 2	C	412	419	anti-parallel
Strand 3	C	453	459	anti-parallel
Strand 4	C	441	447	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	404	406	first strand
Strand 2	C	479	489	parallel
Strand 3	C	468	476	anti-parallel
Strand 4	C	425	430	anti-parallel
Strand 5	C	433	434	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	494	495	first strand
Strand 2	C	515	516	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	501	503	first strand
Strand 2	C	571	580	parallel
Strand 3	C	558	566	anti-parallel
Strand 4	C	520	527	anti-parallel
Strand 5	C	530	531	anti-parallel

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There are 3 strands in BE sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	509	512	first strand
Strand 2	C	545	548	anti-parallel
Strand 3	C	538	540	anti-parallel

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There are 3 strands in BF sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	601	606	first strand
Strand 2	C	641	647	anti-parallel
Strand 3	C	633	637	anti-parallel

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There are 3 strands in BG sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	616	621	first strand
Strand 2	C	655	662	anti-parallel
Strand 3	C	667	674	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: 3DMK

Analysis of interatomic Contacts of Structural Units in PDB entry:
3DMK