Analysis of interatomic Contacts of Structural Units in PDB entry:
5NEJ


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 5NEJ entry

There are 4 chains in PDB entry 5NEJ (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
1
 THR 1PRO 208
2
 ASP 12GLU 218
3
 GLY 1GLN 220
4
 SER 15ALA 85
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 11 helices in PDB entry 5NEJ. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
AA1
1
14 19Right-handed 310
Helix 2
AA2
1
52 56Right-handed 310
Helix 3
AA3
1
60 65Right-handed alpha
Helix 4
AA4
1
94 99Right-handed 310
Helix 5
AA5
2
56 59Right-handed 310
Helix 6
AA6
2
89 96Right-handed alpha
Helix 7
AA7
2
135 143Right-handed 310
Helix 8
AA8
3
43 51Right-handed alpha
Helix 9
AA9
3
90 95Right-handed alpha
Helix 10
AB1
3
137 142Right-handed 310
Helix 11
AB2
4
67 74Right-handed alpha
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There are 11 sheets in PDB entry 5NEJ. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8, AA9, AB1, AB2,

There are 4 strands in AA1 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
1
40 42first strand
Strand 2
1
172 188anti-parallel
Strand 3
1
69 83anti-parallel
Strand 4
1
113 116anti-parallel
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There are 4 strands in AA2 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
1
40 42first strand
Strand 2
1
172 188anti-parallel
Strand 3
1
69 83anti-parallel
Strand 4
1
126 127anti-parallel
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There are 4 strands in AA3 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
1
48 50first strand
Strand 2
1
167 169anti-parallel
Strand 3
1
86 89anti-parallel
Strand 4
1
105 106anti-parallel
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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
2
16 19first strand
Strand 2
2
22 25anti-parallel
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There are 5 strands in AA5 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
2
32 34first strand
Strand 2
2
155 160parallel
Strand 3
2
98 111anti-parallel
Strand 4
2
205 213anti-parallel
Strand 5
2
52 54anti-parallel
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There are 5 strands in AA6 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
2
32 34first strand
Strand 2
2
155 160parallel
Strand 3
2
98 111anti-parallel
Strand 4
2
197 203anti-parallel
Strand 5
2
62 69anti-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
2
79 83first strand
Strand 2
2
177 185anti-parallel
Strand 3
2
120 127anti-parallel
Strand 4
2
145 148anti-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
3
53 54first strand
Strand 2
3
198 205anti-parallel
Strand 3
3
63 65anti-parallel
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There are 4 strands in AA9 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
3
53 54first strand
Strand 2
3
198 205anti-parallel
Strand 3
3
105 111anti-parallel
Strand 4
3
154 159anti-parallel
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There are 4 strands in AB1 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
3
73 78first strand
Strand 2
3
183 192anti-parallel
Strand 3
3
118 126anti-parallel
Strand 4
3
145 148anti-parallel
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There are 3 strands in AB2 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
3
168 169first strand
Strand 2
3
98 102anti-parallel
Strand 3
3
210 214anti-parallel
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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il