Analysis of interatomic Contacts of Structural Units in PDB entry:
1YDO


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 1YDO entry

There are 4 chains in PDB entry 1YDO (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 MSE 1SER 298
B
 MSE 1SER 298
C
 MSE 1SER 298
D
 MSE 1SER 298
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 68 helices in PDB entry 1YDO. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
1
A
12 17Right-handed alpha
Helix 2
2
A
18 21Right-handed 310
Helix 3
3
A
26 39Right-handed alpha
Helix 4
4
A
56 60Right-handed 310
Helix 5
5
A
61 69Right-handed alpha
Helix 6
6
A
83 94Right-handed alpha
Helix 7
7
A
105 111Right-handed alpha
Helix 8
8
A
116 134Right-handed alpha
Helix 9
9
A
155 170Right-handed alpha
Helix 10
10
A
184 197Right-handed alpha
Helix 11
11
A
200 202Right-handed 310
Helix 12
12
A
209 213Right-handed 310
Helix 13
13
A
214 226Right-handed alpha
Helix 14
14
A
233 237Right-handed 310
Helix 15
15
A
251 262Right-handed alpha
Helix 16
16
A
269 285Right-handed alpha
Helix 17
17
A
290 297Right-handed alpha
Helix 18
18
B
12 17Right-handed alpha
Helix 19
19
B
18 21Right-handed 310
Helix 20
20
B
26 39Right-handed alpha
Helix 21
21
B
56 60Right-handed 310
Helix 22
22
B
61 69Right-handed alpha
Helix 23
23
B
83 94Right-handed alpha
Helix 24
24
B
105 111Right-handed alpha
Helix 25
25
B
116 134Right-handed alpha
Helix 26
26
B
155 170Right-handed alpha
Helix 27
27
B
184 197Right-handed alpha
Helix 28
28
B
200 202Right-handed 310
Helix 29
29
B
209 213Right-handed 310
Helix 30
30
B
214 226Right-handed alpha
Helix 31
31
B
233 237Right-handed 310
Helix 32
32
B
251 262Right-handed alpha
Helix 33
33
B
269 285Right-handed alpha
Helix 34
34
B
290 297Right-handed alpha
Helix 35
35
C
12 17Right-handed alpha
Helix 36
36
C
18 21Right-handed 310
Helix 37
37
C
26 39Right-handed alpha
Helix 38
38
C
56 60Right-handed 310
Helix 39
39
C
61 69Right-handed alpha
Helix 40
40
C
83 94Right-handed alpha
Helix 41
41
C
105 111Right-handed alpha
Helix 42
42
C
116 134Right-handed alpha
Helix 43
43
C
155 170Right-handed alpha
Helix 44
44
C
184 197Right-handed alpha
Helix 45
45
C
200 202Right-handed 310
Helix 46
46
C
209 213Right-handed 310
Helix 47
47
C
214 226Right-handed alpha
Helix 48
48
C
233 237Right-handed 310
Helix 49
49
C
251 262Right-handed alpha
Helix 50
50
C
269 285Right-handed alpha
Helix 51
51
C
290 297Right-handed alpha
Helix 52
52
D
12 17Right-handed alpha
Helix 53
53
D
18 21Right-handed 310
Helix 54
54
D
26 39Right-handed alpha
Helix 55
55
D
56 60Right-handed 310
Helix 56
56
D
61 69Right-handed alpha
Helix 57
57
D
83 94Right-handed alpha
Helix 58
58
D
105 111Right-handed alpha
Helix 59
59
D
116 134Right-handed alpha
Helix 60
60
D
155 170Right-handed alpha
Helix 61
61
D
184 197Right-handed alpha
Helix 62
62
D
200 202Right-handed 310
Helix 63
63
D
209 213Right-handed 310
Helix 64
64
D
214 226Right-handed alpha
Helix 65
65
D
233 237Right-handed 310
Helix 66
66
D
251 262Right-handed alpha
Helix 67
67
D
269 285Right-handed alpha
Helix 68
68
D
290 297Right-handed alpha
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There are 8 sheets in PDB entry 1YDO. Click on sheet of interest to get list of strands forming it: A, B, C, D, E, F, G, H,

There are 9 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
8 11first strand
Strand 2
A
44 49parallel
Strand 3
A
76 80parallel
Strand 4
A
97 103parallel
Strand 5
A
137 143parallel
Strand 6
A
174 177parallel
Strand 7
A
204 207parallel
Strand 8
A
229 232parallel
Strand 9
A
8 11parallel
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There are 2 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
239 240first strand
Strand 2
A
243 247anti-parallel
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There are 9 strands in C sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
8 11first strand
Strand 2
B
44 49parallel
Strand 3
B
76 80parallel
Strand 4
B
97 103parallel
Strand 5
B
137 143parallel
Strand 6
B
174 177parallel
Strand 7
B
204 207parallel
Strand 8
B
229 232parallel
Strand 9
B
8 11parallel
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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
B
239 240first strand
Strand 2
B
243 247anti-parallel
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There are 9 strands in E sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
8 11first strand
Strand 2
C
44 49parallel
Strand 3
C
76 80parallel
Strand 4
C
97 103parallel
Strand 5
C
137 143parallel
Strand 6
C
174 177parallel
Strand 7
C
204 207parallel
Strand 8
C
229 232parallel
Strand 9
C
8 11parallel
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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
C
239 240first strand
Strand 2
C
243 247anti-parallel
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There are 9 strands in G sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
D
8 11first strand
Strand 2
D
44 49parallel
Strand 3
D
76 80parallel
Strand 4
D
97 103parallel
Strand 5
D
137 143parallel
Strand 6
D
174 177parallel
Strand 7
D
204 207parallel
Strand 8
D
229 232parallel
Strand 9
D
8 11parallel
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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
D
239 240first strand
Strand 2
D
243 247anti-parallel
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