Analysis of interatomic Contacts of Structural Units in PDB entry:
4DDX


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 4DDX entry

There are 2 chains in PDB entry 4DDX (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 ALA 2GLU 1103
B
 ALA 2SER 388
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 82 helices in PDB entry 4DDX. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
1
A
40 48Right-handed alpha
Helix 2
2
A
53 75Right-handed alpha
Helix 3
3
A
80 93Right-handed alpha
Helix 4
4
A
105 119Right-handed alpha
Helix 5
5
A
130 143Right-handed alpha
Helix 6
6
A
161 172Right-handed alpha
Helix 7
7
A
182 188Right-handed alpha
Helix 8
8
A
188 195Right-handed alpha
Helix 9
9
A
204 209Right-handed alpha
Helix 10
10
A
214 221Right-handed alpha
Helix 11
11
A
225 239Right-handed alpha
Helix 12
12
A
267 274Right-handed alpha
Helix 13
13
A
297 309Right-handed alpha
Helix 14
14
A
318 332Right-handed alpha
Helix 15
15
A
344 353Right-handed alpha
Helix 16
16
A
399 411Right-handed alpha
Helix 17
17
A
422 432Right-handed alpha
Helix 18
18
A
433 445Right-handed alpha
Helix 19
19
A
461 470Right-handed alpha
Helix 20
20
A
471 473Right-handed 310
Helix 21
21
A
491 505Right-handed alpha
Helix 22
22
A
517 534Right-handed alpha
Helix 23
23
A
549 561Right-handed alpha
Helix 24
24
A
646 660Right-handed alpha
Helix 25
25
A
671 682Right-handed alpha
Helix 26
26
A
700 709Right-handed alpha
Helix 27
27
A
715 742Right-handed alpha
Helix 28
28
A
753 768Right-handed alpha
Helix 29
29
A
769 773Right-handed 310
Helix 30
30
A
817 829Right-handed alpha
Helix 31
31
A
832 845Right-handed alpha
Helix 32
32
A
860 875Right-handed alpha
Helix 33
33
A
876 880Right-handed 310
Helix 34
34
A
901 912Right-handed alpha
Helix 35
35
A
918 935Right-handed alpha
Helix 36
36
A
968 972Right-handed 310
Helix 37
37
A
1003 1014Right-handed alpha
Helix 38
38
A
1020 1033Right-handed alpha
Helix 39
39
A
1046 1060Right-handed alpha
Helix 40
40
A
1065 1081Right-handed alpha
Helix 41
41
A
1085 1101Right-handed alpha
Helix 42
42
B
40 48Right-handed alpha
Helix 43
43
B
53 75Right-handed alpha
Helix 44
44
B
80 93Right-handed alpha
Helix 45
45
B
105 119Right-handed alpha
Helix 46
46
B
130 143Right-handed alpha
Helix 47
47
B
161 172Right-handed alpha
Helix 48
48
B
182 188Right-handed alpha
Helix 49
49
B
188 195Right-handed alpha
Helix 50
50
B
204 209Right-handed alpha
Helix 51
51
B
214 221Right-handed alpha
Helix 52
52
B
225 239Right-handed alpha
Helix 53
53
B
267 274Right-handed alpha
Helix 54
54
B
297 309Right-handed alpha
Helix 55
55
B
318 332Right-handed alpha
Helix 56
56
B
344 353Right-handed alpha
Helix 57
57
B
399 411Right-handed alpha
Helix 58
58
B
422 432Right-handed alpha
Helix 59
59
B
433 445Right-handed alpha
Helix 60
60
B
461 470Right-handed alpha
Helix 61
61
B
471 473Right-handed 310
Helix 62
62
B
491 505Right-handed alpha
Helix 63
63
B
517 534Right-handed alpha
Helix 64
64
B
549 561Right-handed alpha
Helix 65
65
B
646 660Right-handed alpha
Helix 66
66
B
671 682Right-handed alpha
Helix 67
67
B
700 709Right-handed alpha
Helix 68
68
B
715 742Right-handed alpha
Helix 69
69
B
753 768Right-handed alpha
Helix 70
70
B
769 773Right-handed 310
Helix 71
71
B
817 829Right-handed alpha
Helix 72
72
B
832 845Right-handed alpha
Helix 73
73
B
860 875Right-handed alpha
Helix 74
74
B
876 880Right-handed 310
Helix 75
75
B
901 912Right-handed alpha
Helix 76
76
B
918 935Right-handed alpha
Helix 77
77
B
968 972Right-handed 310
Helix 78
78
B
1003 1014Right-handed alpha
Helix 79
79
B
1020 1033Right-handed alpha
Helix 80
80
B
1046 1060Right-handed alpha
Helix 81
81
B
1065 1081Right-handed alpha
Helix 82
82
B
1085 1101Right-handed alpha
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There are 22 sheets in PDB entry 4DDX. 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,

There are 4 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
18 19first strand
Strand 2
A
6 7anti-parallel
Strand 3
A
610 617parallel
Strand 4
A
593 595anti-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
18 19first strand
Strand 2
A
6 7anti-parallel
Strand 3
A
610 617parallel
Strand 4
A
604 607anti-parallel
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There are 6 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
96 98first strand
Strand 2
A
252 256parallel
Strand 3
A
199 202parallel
Strand 4
A
124 128parallel
Strand 5
A
177 181parallel
Strand 6
A
151 153parallel
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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
357 360first strand
Strand 2
A
312 315parallel
Strand 3
A
380 383parallel
Strand 4
A
483 488parallel
Strand 5
A
288 293parallel
Strand 6
A
510 512parallel
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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
388 392first strand
Strand 2
A
456 460anti-parallel
Strand 3
A
449 451anti-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
475 476first strand
Strand 2
A
479 480anti-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
A
562 566first strand
Strand 2
A
573 577anti-parallel
Strand 3
A
582 587anti-parallel
Strand 4
A
543 547parallel
Strand 5
A
662 665parallel
Strand 6
A
691 693parallel
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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
A
619 620first strand
Strand 2
A
627 628anti-parallel
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There are 6 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
787 790first strand
Strand 2
A
776 781anti-parallel
Strand 3
A
985 994anti-parallel
Strand 4
A
797 802anti-parallel
Strand 5
A
940 951anti-parallel
Strand 6
A
809 810anti-parallel
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There are 3 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
805 806first strand
Strand 2
A
940 951anti-parallel
Strand 3
A
954 966anti-parallel
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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
A
1035 1036first strand
Strand 2
A
1044 1045anti-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
B
18 19first strand
Strand 2
B
6 7anti-parallel
Strand 3
B
610 617parallel
Strand 4
B
593 595anti-parallel
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There are 4 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
18 19first strand
Strand 2
B
6 7anti-parallel
Strand 3
B
610 617parallel
Strand 4
B
604 607anti-parallel
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There are 6 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
96 98first strand
Strand 2
B
252 256parallel
Strand 3
B
199 202parallel
Strand 4
B
124 128parallel
Strand 5
B
177 181parallel
Strand 6
B
151 153parallel
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There are 6 strands in O sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
357 360first strand
Strand 2
B
312 315parallel
Strand 3
B
380 383parallel
Strand 4
B
483 488parallel
Strand 5
B
288 293parallel
Strand 6
B
510 512parallel
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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
B
388 392first strand
Strand 2
B
456 460anti-parallel
Strand 3
B
449 451anti-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
B
475 476first strand
Strand 2
B
479 480anti-parallel
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There are 6 strands in R sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
562 566first strand
Strand 2
B
573 577anti-parallel
Strand 3
B
582 587anti-parallel
Strand 4
B
543 547parallel
Strand 5
B
662 665parallel
Strand 6
B
691 693parallel
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There are 2 strands in S sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
619 620first strand
Strand 2
B
627 628anti-parallel
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There are 6 strands in T sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
787 790first strand
Strand 2
B
776 781anti-parallel
Strand 3
B
985 994anti-parallel
Strand 4
B
797 802anti-parallel
Strand 5
B
940 951anti-parallel
Strand 6
B
809 810anti-parallel
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There are 3 strands in U sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
805 806first strand
Strand 2
B
940 951anti-parallel
Strand 3
B
954 966anti-parallel
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There are 2 strands in V sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
1035 1036first strand
Strand 2
B
1044 1045anti-parallel
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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il