Analysis of interatomic Contacts of Structural Units in PDB entry:
8YBM


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 8YBM entry

There are 4 chains in PDB entry 8YBM (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 GLU 3LYS 239
B
 VAL 3SER 129
C
 GLU 3LYS 239
D
 VAL 3SER 129
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 22 helices in PDB entry 8YBM. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
AA1
A
9 13Right-handed 310
Helix 2
AA2
A
15 19Right-handed 310
Helix 3
AA3
A
23 28Right-handed alpha
Helix 4
AA4
A
29 31Right-handed 310
Helix 5
AA5
A
72 80Right-handed alpha
Helix 6
AA6
A
159 175Right-handed alpha
Helix 7
AA7
A
211 217Right-handed alpha
Helix 8
AA8
A
218 220Right-handed 310
Helix 9
AA9
B
63 66Right-handed 310
Helix 10
AB1
B
88 92Right-handed 310
Helix 11
AB2
B
113 117Right-handed 310
Helix 12
AB3
C
9 13Right-handed 310
Helix 13
AB4
C
15 19Right-handed 310
Helix 14
AB5
C
23 28Right-handed alpha
Helix 15
AB6
C
29 31Right-handed 310
Helix 16
AB7
C
72 80Right-handed alpha
Helix 17
AB8
C
159 175Right-handed alpha
Helix 18
AB9
C
211 217Right-handed alpha
Helix 19
AC1
C
218 222Right-handed 310
Helix 20
AC2
D
63 66Right-handed 310
Helix 21
AC3
D
88 92Right-handed 310
Helix 22
AC4
D
113 117Right-handed 310
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There are 14 sheets in PDB entry 8YBM. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8, AA9, AB1, AB2, AB3, AB4, AB5,

There are 3 strands in AA1 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
35 40first strand
Strand 2
A
84 88anti-parallel
Strand 3
A
120 122anti-parallel
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There are 3 strands in AA2 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
50 54first strand
Strand 2
A
65 69anti-parallel
Strand 3
A
114 117parallel
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There are 6 strands in AA3 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
196 201first strand
Strand 2
A
184 193anti-parallel
Strand 3
A
231 238anti-parallel
Strand 4
A
127 140parallel
Strand 5
A
143 154anti-parallel
Strand 6
B
106 107parallel
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There are 2 strands in AA4 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
156 158first strand
Strand 2
A
224 226anti-parallel
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There are 4 strands in AA5 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
4 8first strand
Strand 2
B
19 26anti-parallel
Strand 3
B
79 84anti-parallel
Strand 4
B
69 74anti-parallel
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There are 6 strands in AA6 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
11 13first strand
Strand 2
B
124 128parallel
Strand 3
B
93 99anti-parallel
Strand 4
B
36 41anti-parallel
Strand 5
B
48 53anti-parallel
Strand 6
B
59 61anti-parallel
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There are 4 strands in AA7 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
11 13first strand
Strand 2
B
124 128parallel
Strand 3
B
93 99anti-parallel
Strand 4
B
119 120anti-parallel
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There are 3 strands in AA8 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
35 40first strand
Strand 2
C
84 88anti-parallel
Strand 3
C
120 122anti-parallel
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There are 3 strands in AA9 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
50 56first strand
Strand 2
C
63 69anti-parallel
Strand 3
C
114 117parallel
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There are 6 strands in AB1 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
196 201first strand
Strand 2
C
184 193anti-parallel
Strand 3
C
231 238anti-parallel
Strand 4
C
127 140parallel
Strand 5
C
143 154anti-parallel
Strand 6
D
106 107parallel
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There are 2 strands in AB2 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
156 158first strand
Strand 2
C
224 226anti-parallel
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There are 4 strands in AB3 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
D
4 8first strand
Strand 2
D
19 26anti-parallel
Strand 3
D
80 84anti-parallel
Strand 4
D
69 73anti-parallel
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There are 6 strands in AB4 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
D
11 14first strand
Strand 2
D
124 129parallel
Strand 3
D
93 99anti-parallel
Strand 4
D
36 41anti-parallel
Strand 5
D
48 53anti-parallel
Strand 6
D
59 61anti-parallel
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There are 4 strands in AB5 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
D
11 14first strand
Strand 2
D
124 129parallel
Strand 3
D
93 99anti-parallel
Strand 4
D
119 120anti-parallel
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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il