Analysis of interatomic Contacts of Structural Units in PDB entry:
3GD7

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 3GD7 entry

There are 4 chains in PDB entry 3GD7 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	ASP 1202	GLY 1579
B	ILE 1203	GLY 1579
C	TRP 1204	GLY 1579
D	ASP 1202	GLY 1579

There are 54 helices in PDB entry 3GD7. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	1249	1259	Right-handed alpha
Helix 2	2	A	1278	1285	Right-handed alpha
Helix 3	3	A	1300	1305	Right-handed alpha
Helix 4	4	A	1311	1322	Right-handed alpha
Helix 5	5	A	1324	1329	Right-handed alpha
Helix 6	6	A	1333	1336	Right-handed 310
Helix 7	7	A	1347	1362	Right-handed alpha
Helix 8	8	A	1371	1376	Right-handed alpha
Helix 9	9	A	1377	1390	Right-handed alpha
Helix 10	10	A	1404	1408	Right-handed 310
Helix 11	11	A	1426	1433	Right-handed alpha
Helix 12	12	A	1436	1443	Right-handed alpha
Helix 13	13	A	1495	1499	Right-handed 310
Helix 14	14	A	1557	1561	Right-handed 310
Helix 15	15	B	1249	1258	Right-handed alpha
Helix 16	16	B	1278	1284	Right-handed alpha
Helix 17	17	B	1300	1305	Right-handed alpha
Helix 18	18	B	1311	1322	Right-handed alpha
Helix 19	19	B	1324	1330	Right-handed alpha
Helix 20	20	B	1333	1336	Right-handed 310
Helix 21	21	B	1347	1362	Right-handed alpha
Helix 22	22	B	1371	1376	Right-handed alpha
Helix 23	23	B	1377	1391	Right-handed alpha
Helix 24	24	B	1403	1408	Right-handed 310
Helix 25	25	B	1426	1433	Right-handed alpha
Helix 26	26	B	1436	1443	Right-handed alpha
Helix 27	27	B	1557	1561	Right-handed 310
Helix 28	28	C	1249	1258	Right-handed alpha
Helix 29	29	C	1278	1283	Right-handed alpha
Helix 30	30	C	1299	1305	Right-handed alpha
Helix 31	31	C	1311	1320	Right-handed alpha
Helix 32	32	C	1327	1331	Right-handed 310
Helix 33	33	C	1333	1337	Right-handed 310
Helix 34	34	C	1347	1362	Right-handed alpha
Helix 35	35	C	1371	1376	Right-handed alpha
Helix 36	36	C	1377	1391	Right-handed alpha
Helix 37	37	C	1403	1407	Right-handed 310
Helix 38	38	C	1426	1433	Right-handed alpha
Helix 39	39	C	1436	1441	Right-handed alpha
Helix 40	40	C	1503	1505	Right-handed 310
Helix 41	41	C	1557	1561	Right-handed 310
Helix 42	42	D	1249	1258	Right-handed alpha
Helix 43	43	D	1278	1284	Right-handed alpha
Helix 44	44	D	1300	1305	Right-handed alpha
Helix 45	45	D	1311	1322	Right-handed alpha
Helix 46	46	D	1324	1330	Right-handed alpha
Helix 47	47	D	1333	1336	Right-handed 310
Helix 48	48	D	1347	1363	Right-handed alpha
Helix 49	49	D	1371	1376	Right-handed alpha
Helix 50	50	D	1377	1391	Right-handed alpha
Helix 51	51	D	1403	1408	Right-handed 310
Helix 52	52	D	1426	1433	Right-handed alpha
Helix 53	53	D	1436	1443	Right-handed alpha
Helix 54	54	D	1557	1561	Right-handed 310

There are 19 sheets in PDB entry 3GD7. 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,

There are 3 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	1227	1234	first strand
Strand 2	A	1210	1218	anti-parallel
Strand 3	A	1262	1269	anti-parallel

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There are 6 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	1286	1289	first strand
Strand 2	A	1366	1370	parallel
Strand 3	A	1397	1400	parallel
Strand 4	A	1239	1244	parallel
Strand 5	A	1412	1417	parallel
Strand 6	A	1420	1424	anti-parallel

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There are 2 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	1298	1299	first strand
Strand 2	A	1338	1339	anti-parallel

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There are 6 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	1474	1477	first strand
Strand 2	A	1463	1466	anti-parallel
Strand 3	A	1449	1458	anti-parallel
Strand 4	A	1489	1494	anti-parallel
Strand 5	A	1562	1564	anti-parallel
Strand 6	A	1570	1571	anti-parallel

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There are 5 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	1500	1501	first strand
Strand 2	A	1551	1555	anti-parallel
Strand 3	A	1508	1518	anti-parallel
Strand 4	A	1523	1528	anti-parallel
Strand 5	A	1536	1540	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	1227	1234	first strand
Strand 2	B	1210	1217	anti-parallel
Strand 3	B	1263	1269	anti-parallel
Strand 4	B	1272	1273	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	1286	1289	first strand
Strand 2	B	1366	1370	parallel
Strand 3	B	1396	1400	parallel
Strand 4	B	1239	1244	parallel
Strand 5	B	1412	1417	parallel
Strand 6	B	1420	1425	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	1298	1299	first strand
Strand 2	B	1338	1339	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	1473	1477	first strand
Strand 2	B	1462	1467	anti-parallel
Strand 3	B	1449	1459	anti-parallel
Strand 4	B	1489	1494	anti-parallel
Strand 5	B	1562	1564	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	B	1500	1501	first strand
Strand 2	B	1551	1556	anti-parallel
Strand 3	B	1507	1518	anti-parallel
Strand 4	B	1523	1528	anti-parallel
Strand 5	B	1536	1540	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	C	1225	1234	first strand
Strand 2	C	1210	1218	anti-parallel
Strand 3	C	1262	1269	anti-parallel
Strand 4	C	1272	1273	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	1286	1289	first strand
Strand 2	C	1366	1370	parallel
Strand 3	C	1396	1400	parallel
Strand 4	C	1239	1244	parallel
Strand 5	C	1412	1416	parallel
Strand 6	C	1421	1424	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	C	1474	1477	first strand
Strand 2	C	1462	1466	anti-parallel
Strand 3	C	1449	1459	anti-parallel
Strand 4	C	1489	1494	anti-parallel
Strand 5	C	1562	1564	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	1500	1501	first strand
Strand 2	C	1551	1555	anti-parallel
Strand 3	C	1508	1518	anti-parallel
Strand 4	C	1522	1528	anti-parallel
Strand 5	C	1536	1541	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	1225	1234	first strand
Strand 2	D	1210	1218	anti-parallel
Strand 3	D	1262	1269	anti-parallel
Strand 4	D	1272	1273	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	1286	1288	first strand
Strand 2	D	1366	1370	parallel
Strand 3	D	1396	1400	parallel
Strand 4	D	1239	1244	parallel
Strand 5	D	1412	1416	parallel
Strand 6	D	1421	1424	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	1298	1299	first strand
Strand 2	D	1338	1339	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	1474	1477	first strand
Strand 2	D	1463	1466	anti-parallel
Strand 3	D	1449	1458	anti-parallel
Strand 4	D	1489	1494	anti-parallel
Strand 5	D	1562	1564	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	1500	1501	first strand
Strand 2	D	1551	1555	anti-parallel
Strand 3	D	1508	1518	anti-parallel
Strand 4	D	1522	1528	anti-parallel
Strand 5	D	1535	1541	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: 3GD7

Analysis of interatomic Contacts of Structural Units in PDB entry:
3GD7