Analysis of interatomic Contacts of Structural Units in PDB entry:
3UP4


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).
For CSU analysis of other PDB entry

This page provides analyses of contacts formed by:
For analysis of ligand-protein contacts, use: 3D structure can be seen in additional window with STING software for 3UP4 entry

There are 2 chains in PDB entry 3UP4 (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 LYS 6ALA 545
B
 LYS 6ALA 545
Residue contacts

1. List of contacts for up to 10 consecutive residues:
Chain ID from residue number to residue number


2. Detailed analyses of contacts for any single residue:
Residue number chain ID
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There are 45 helices in PDB entry 3UP4. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
1
A
18 31Right-handed alpha
Helix 2
2
A
46 51Right-handed alpha
Helix 3
3
A
61 66Right-handed alpha
Helix 4
4
A
66 71Right-handed alpha
Helix 5
5
A
85 101Right-handed alpha
Helix 6
6
A
102 104Right-handed 310
Helix 7
7
A
119 122Right-handed 310
Helix 8
8
A
156 160Right-handed 310
Helix 9
9
A
168 170Right-handed 310
Helix 10
10
A
194 205Right-handed alpha
Helix 11
11
A
230 240Right-handed alpha
Helix 12
12
A
240 251Right-handed alpha
Helix 13
13
A
268 281Right-handed alpha
Helix 14
14
A
285 290Right-handed alpha
Helix 15
15
A
298 317Right-handed alpha
Helix 16
16
A
319 326Right-handed alpha
Helix 17
17
A
343 348Right-handed alpha
Helix 18
18
A
403 407Right-handed 310
Helix 19
19
A
408 413Right-handed alpha
Helix 20
20
A
445 467Right-handed alpha
Helix 21
21
A
475 492Right-handed alpha
Helix 22
22
A
493 498Right-handed 310
Helix 23
23
A
523 537Right-handed alpha
Helix 24
24
B
18 31Right-handed alpha
Helix 25
25
B
46 51Right-handed alpha
Helix 26
26
B
61 66Right-handed alpha
Helix 27
27
B
66 71Right-handed alpha
Helix 28
28
B
85 101Right-handed alpha
Helix 29
29
B
102 104Right-handed 310
Helix 30
30
B
156 160Right-handed 310
Helix 31
31
B
194 206Right-handed alpha
Helix 32
32
B
230 240Right-handed alpha
Helix 33
33
B
240 249Right-handed alpha
Helix 34
34
B
268 281Right-handed alpha
Helix 35
35
B
285 290Right-handed alpha
Helix 36
36
B
298 317Right-handed alpha
Helix 37
37
B
319 326Right-handed alpha
Helix 38
38
B
344 350Right-handed 310
Helix 39
39
B
393 398Right-handed alpha
Helix 40
40
B
403 407Right-handed 310
Helix 41
41
B
408 413Right-handed alpha
Helix 42
42
B
445 467Right-handed alpha
Helix 43
43
B
475 491Right-handed alpha
Helix 44
44
B
492 498Right-handed 310
Helix 45
45
B
523 537Right-handed alpha
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There are 14 sheets in PDB entry 3UP4. 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,

There are 7 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
106 107first strand
Strand 2
A
35 38parallel
Strand 3
A
10 15parallel
Strand 4
A
132 141parallel
Strand 5
A
123 128anti-parallel
Strand 6
A
112 118anti-parallel
Strand 7
A
400 402parallel
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There are 5 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
106 107first strand
Strand 2
A
35 38parallel
Strand 3
A
10 15parallel
Strand 4
A
132 141parallel
Strand 5
A
431 433parallel
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There are 5 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
163 166first strand
Strand 2
A
382 385parallel
Strand 3
A
187 191parallel
Strand 4
A
210 215parallel
Strand 5
A
353 357parallel
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There are 2 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
222 223first strand
Strand 2
A
340 341parallel
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There are 3 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
363 366first strand
Strand 2
A
370 373anti-parallel
Strand 3
A
377 379anti-parallel
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There are 2 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
472 474first strand
Strand 2
A
542 544anti-parallel
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There are 2 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
503 504first strand
Strand 2
A
516 517anti-parallel
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There are 7 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
106 107first strand
Strand 2
B
35 38parallel
Strand 3
B
10 15parallel
Strand 4
B
132 141parallel
Strand 5
B
123 128anti-parallel
Strand 6
B
112 118anti-parallel
Strand 7
B
400 402parallel
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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
106 107first strand
Strand 2
B
35 38parallel
Strand 3
B
10 15parallel
Strand 4
B
132 141parallel
Strand 5
B
431 433parallel
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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
163 166first strand
Strand 2
B
382 385parallel
Strand 3
B
187 191parallel
Strand 4
B
210 215parallel
Strand 5
B
353 357parallel
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There are 2 strands in K sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
222 223first strand
Strand 2
B
340 341parallel
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There are 3 strands in L sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
363 366first strand
Strand 2
B
370 373anti-parallel
Strand 3
B
377 379anti-parallel
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There are 2 strands in M sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
472 474first strand
Strand 2
B
542 544anti-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
B
503 504first strand
Strand 2
B
516 517anti-parallel
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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il