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


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 4RKD entry

There are 4 chains in PDB entry 4RKD (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 MET 1ASP 398
B
 MET 1ASP 398
C
 MET 1ASP 398
D
 MET 1LEU 82
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 are144 helices in PDB entry 4RKD. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
1
A
13 23Right-handed alpha
Helix 2
2
A
46 57Right-handed alpha
Helix 3
3
A
71 84Right-handed alpha
Helix 4
4
A
87 92Right-handed alpha
Helix 5
5
A
101 118Right-handed alpha
Helix 6
6
A
131 140Right-handed alpha
Helix 7
7
A
158 168Right-handed alpha
Helix 8
8
A
190 204Right-handed alpha
Helix 9
9
A
220 225Right-handed alpha
Helix 10
10
A
225 234Right-handed alpha
Helix 11
11
A
250 254Right-handed 310
Helix 12
12
A
264 284Right-handed alpha
Helix 13
13
A
287 299Right-handed alpha
Helix 14
14
A
300 333Right-handed alpha
Helix 15
15
A
339 344Right-handed alpha
Helix 16
16
A
354 366Right-handed alpha
Helix 17
17
A
378 380Right-handed 310
Helix 18
18
A
384 397Right-handed alpha
Helix 19
19
B
13 23Right-handed alpha
Helix 20
20
B
46 57Right-handed alpha
Helix 21
21
B
71 84Right-handed alpha
Helix 22
22
B
87 92Right-handed alpha
Helix 23
23
B
102 118Right-handed alpha
Helix 24
24
B
130 139Right-handed alpha
Helix 25
25
B
158 168Right-handed alpha
Helix 26
26
B
190 204Right-handed alpha
Helix 27
27
B
220 225Right-handed alpha
Helix 28
28
B
225 234Right-handed alpha
Helix 29
29
B
250 253Right-handed 310
Helix 30
30
B
264 281Right-handed alpha
Helix 31
31
B
287 300Right-handed alpha
Helix 32
32
B
300 333Right-handed alpha
Helix 33
33
B
339 344Right-handed alpha
Helix 34
34
B
354 366Right-handed alpha
Helix 35
35
B
378 380Right-handed 310
Helix 36
36
B
384 398Right-handed alpha
Helix 37
37
C
13 23Right-handed alpha
Helix 38
38
C
46 57Right-handed alpha
Helix 39
39
C
71 84Right-handed alpha
Helix 40
40
C
87 92Right-handed alpha
Helix 41
41
C
102 118Right-handed alpha
Helix 42
42
C
130 139Right-handed alpha
Helix 43
43
C
158 168Right-handed alpha
Helix 44
44
C
190 204Right-handed alpha
Helix 45
45
C
220 225Right-handed alpha
Helix 46
46
C
225 234Right-handed alpha
Helix 47
47
C
250 253Right-handed 310
Helix 48
48
C
264 283Right-handed alpha
Helix 49
49
C
287 300Right-handed alpha
Helix 50
50
C
300 333Right-handed alpha
Helix 51
51
C
339 344Right-handed alpha
Helix 52
52
C
354 364Right-handed alpha
Helix 53
53
C
378 380Right-handed 310
Helix 54
54
C
384 397Right-handed alpha
Helix 55
55
D
13 23Right-handed alpha
Helix 56
56
D
46 57Right-handed alpha
Helix 57
57
D
71 84Right-handed alpha
Helix 58
58
D
87 92Right-handed alpha
Helix 59
59
D
102 118Right-handed alpha
Helix 60
60
D
130 139Right-handed alpha
Helix 61
61
D
158 168Right-handed alpha
Helix 62
62
D
190 205Right-handed alpha
Helix 63
63
D
220 225Right-handed alpha
Helix 64
64
D
225 234Right-handed alpha
Helix 65
65
D
250 253Right-handed 310
Helix 66
66
D
264 283Right-handed alpha
Helix 67
67
D
287 300Right-handed alpha
Helix 68
68
D
300 333Right-handed alpha
Helix 69
69
D
339 344Right-handed alpha
Helix 70
70
D
354 366Right-handed alpha
Helix 71
71
D
378 380Right-handed 310
Helix 72
72
D
384 398Right-handed alpha
Helix 73
73
E
13 23Right-handed alpha
Helix 74
74
E
46 57Right-handed alpha
Helix 75
75
E
71 84Right-handed alpha
Helix 76
76
E
87 92Right-handed alpha
Helix 77
77
E
102 118Right-handed alpha
Helix 78
78
E
130 139Right-handed alpha
Helix 79
79
E
158 167Right-handed alpha
Helix 80
80
E
190 205Right-handed alpha
Helix 81
81
E
220 225Right-handed alpha
Helix 82
82
E
225 234Right-handed alpha
Helix 83
83
E
250 253Right-handed 310
Helix 84
84
E
264 281Right-handed alpha
Helix 85
85
E
287 300Right-handed alpha
Helix 86
86
E
300 333Right-handed alpha
Helix 87
87
E
339 344Right-handed alpha
Helix 88
88
E
354 365Right-handed alpha
Helix 89
89
E
378 380Right-handed 310
Helix 90
90
E
384 398Right-handed alpha
Helix 91
91
F
11 23Right-handed alpha
Helix 92
92
F
46 58Right-handed alpha
Helix 93
93
F
71 84Right-handed alpha
Helix 94
94
F
87 92Right-handed alpha
Helix 95
95
F
102 118Right-handed alpha
Helix 96
96
F
131 139Right-handed alpha
Helix 97
97
F
158 168Right-handed alpha
Helix 98
98
F
190 204Right-handed alpha
Helix 99
99
F
220 225Right-handed alpha
Helix 100
100
F
225 235Right-handed alpha
Helix 101
101
F
250 253Right-handed 310
Helix 102
102
F
264 283Right-handed alpha
Helix 103
103
F
287 300Right-handed alpha
Helix 104
104
F
300 333Right-handed alpha
Helix 105
105
F
339 344Right-handed alpha
Helix 106
106
F
354 366Right-handed alpha
Helix 107
107
F
378 380Right-handed 310
Helix 108
108
F
384 398Right-handed alpha
Helix 109
109
G
11 23Right-handed alpha
Helix 110
110
G
46 58Right-handed alpha
Helix 111
111
G
71 84Right-handed alpha
Helix 112
112
G
87 92Right-handed alpha
Helix 113
113
G
101 118Right-handed alpha
Helix 114
114
G
130 139Right-handed alpha
Helix 115
115
G
158 168Right-handed alpha
Helix 116
116
G
190 205Right-handed alpha
Helix 117
117
G
222 224Right-handed 310
Helix 118
118
G
225 234Right-handed alpha
Helix 119
119
G
250 254Right-handed 310
Helix 120
120
G
264 284Right-handed alpha
Helix 121
121
G
287 300Right-handed alpha
Helix 122
122
G
300 333Right-handed alpha
Helix 123
123
G
339 344Right-handed alpha
Helix 124
124
G
354 366Right-handed alpha
Helix 125
125
G
378 380Right-handed 310
Helix 126
126
G
384 398Right-handed alpha
Helix 127
127
H
11 23Right-handed alpha
Helix 128
128
H
46 58Right-handed alpha
Helix 129
129
H
71 84Right-handed alpha
Helix 130
130
H
87 92Right-handed alpha
Helix 131
131
H
102 118Right-handed alpha
Helix 132
132
H
131 140Right-handed alpha
Helix 133
133
H
158 167Right-handed alpha
Helix 134
134
H
190 204Right-handed alpha
Helix 135
135
H
220 225Right-handed alpha
Helix 136
136
H
225 234Right-handed alpha
Helix 137
137
H
250 253Right-handed 310
Helix 138
138
H
264 281Right-handed alpha
Helix 139
139
H
287 300Right-handed alpha
Helix 140
140
H
300 333Right-handed alpha
Helix 141
141
H
339 344Right-handed alpha
Helix 142
142
H
354 366Right-handed alpha
Helix 143
143
H
378 380Right-handed 310
Helix 144
144
H
384 398Right-handed alpha
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There are 27 sheets in PDB entry 4RKD. 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,

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
29 30first strand
Strand 2
A
367 368parallel
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There are 7 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
95 100first strand
Strand 2
A
256 261anti-parallel
Strand 3
A
239 243anti-parallel
Strand 4
A
207 212parallel
Strand 5
A
174 177parallel
Strand 6
A
122 127parallel
Strand 7
A
143 148parallel
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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
150 151first strand
Strand 2
A
156 157anti-parallel
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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
348 350first strand
Strand 2
A
374 376anti-parallel
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There are 2 strands in E sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
29 30first strand
Strand 2
B
367 368parallel
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There are 7 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
95 101first strand
Strand 2
B
255 261anti-parallel
Strand 3
B
239 243anti-parallel
Strand 4
B
207 212parallel
Strand 5
B
174 177parallel
Strand 6
B
122 127parallel
Strand 7
B
143 148parallel
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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
B
348 350first strand
Strand 2
B
374 376anti-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
C
29 30first strand
Strand 2
C
367 368parallel
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There are 7 strands in I sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
95 101first strand
Strand 2
C
255 261anti-parallel
Strand 3
C
239 243anti-parallel
Strand 4
C
207 212parallel
Strand 5
C
174 177parallel
Strand 6
C
123 127parallel
Strand 7
C
144 148parallel
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There are 2 strands in J sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
348 350first strand
Strand 2
C
374 376anti-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
D
29 30first strand
Strand 2
D
367 368parallel
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There are 7 strands in L sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
D
95 101first strand
Strand 2
D
255 261anti-parallel
Strand 3
D
239 243anti-parallel
Strand 4
D
207 212parallel
Strand 5
D
174 177parallel
Strand 6
D
122 127parallel
Strand 7
D
143 148parallel
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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
D
348 350first strand
Strand 2
D
374 376anti-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
E
29 30first strand
Strand 2
E
367 368parallel
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There are 7 strands in O sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
E
95 101first strand
Strand 2
E
255 261anti-parallel
Strand 3
E
239 243anti-parallel
Strand 4
E
207 212parallel
Strand 5
E
174 177parallel
Strand 6
E
122 127parallel
Strand 7
E
143 148parallel
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There are 2 strands in P sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
E
348 350first strand
Strand 2
E
374 376anti-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
F
29 30first strand
Strand 2
F
367 368parallel
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There are 7 strands in R sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
F
95 101first strand
Strand 2
F
255 261anti-parallel
Strand 3
F
239 243anti-parallel
Strand 4
F
207 212parallel
Strand 5
F
174 177parallel
Strand 6
F
123 127parallel
Strand 7
F
144 148parallel
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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
F
150 151first strand
Strand 2
F
156 157anti-parallel
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There are 2 strands in T sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
F
348 350first strand
Strand 2
F
374 376anti-parallel
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There are 2 strands in U sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
G
29 30first strand
Strand 2
G
367 368parallel
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There are 7 strands in V sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
G
95 100first strand
Strand 2
G
256 261anti-parallel
Strand 3
G
239 243anti-parallel
Strand 4
G
207 212parallel
Strand 5
G
174 177parallel
Strand 6
G
122 127parallel
Strand 7
G
143 148parallel
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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
G
348 350first strand
Strand 2
G
374 376anti-parallel
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There are 2 strands in X sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
H
29 30first strand
Strand 2
H
367 368parallel
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There are 7 strands in Y sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
H
95 101first strand
Strand 2
H
255 261anti-parallel
Strand 3
H
239 243anti-parallel
Strand 4
H
207 212parallel
Strand 5
H
174 177parallel
Strand 6
H
122 126parallel
Strand 7
H
143 147parallel
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There are 2 strands in Z sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
H
150 151first strand
Strand 2
H
156 157anti-parallel
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There are 2 strands in AA sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
H
348 350first strand
Strand 2
H
374 376anti-parallel
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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il