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


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 4DEP entry

There are 6 chains in PDB entry 4DEP (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 ALA 1VAL 151
B
 LYS 7LEU 310
C
 ARG 3LYS 326
D
 SER 0VAL 151
E
 CYS 6VAL 314
F
 ASP 5LYS 328
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 17 helices in PDB entry 4DEP. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
1
A
32 39Right-handed 310
Helix 2
2
B
70 74Right-handed 310
Helix 3
3
B
170 174Right-handed 310
Helix 4
4
B
285 290Right-handed 310
Helix 5
5
C
37 44Right-handed alpha
Helix 6
6
C
67 70Right-handed 310
Helix 7
7
C
85 88Right-handed 310
Helix 8
8
C
183 187Right-handed 310
Helix 9
9
C
216 220Right-handed 310
Helix 10
10
D
32 39Right-handed 310
Helix 11
11
D
96 98Right-handed 310
Helix 12
12
E
70 74Right-handed 310
Helix 13
13
E
106 108Right-handed 310
Helix 14
14
E
285 291Right-handed 310
Helix 15
15
F
85 89Right-handed 310
Helix 16
16
F
183 187Right-handed 310
Helix 17
17
F
216 220Right-handed 310
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There are 36 sheets in PDB entry 4DEP. 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, AB, AC, AD, AE, AF, AG, AH, AI, AJ,

There are 7 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
5 12first strand
Strand 2
A
41 45anti-parallel
Strand 3
A
56 62anti-parallel
Strand 4
A
100 105anti-parallel
Strand 5
A
110 114anti-parallel
Strand 6
A
146 150anti-parallel
Strand 7
A
5 12anti-parallel
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There are 3 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
17 20first strand
Strand 2
A
26 29anti-parallel
Strand 3
A
130 131anti-parallel
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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
67 72first strand
Strand 2
A
79 84anti-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
121 123first strand
Strand 2
A
133 135anti-parallel
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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
B
8 11first strand
Strand 2
B
89 97parallel
Strand 3
B
16 18parallel
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There are 4 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
8 11first strand
Strand 2
B
89 97parallel
Strand 3
B
75 81anti-parallel
Strand 4
B
38 41anti-parallel
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There are 3 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
21 25first strand
Strand 2
B
63 69anti-parallel
Strand 3
B
57 60anti-parallel
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There are 5 strands in H sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
111 116first strand
Strand 2
B
188 201parallel
Strand 3
B
175 185anti-parallel
Strand 4
B
142 145anti-parallel
Strand 5
B
148 149anti-parallel
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There are 3 strands in I sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
121 124first strand
Strand 2
B
163 166anti-parallel
Strand 3
B
157 160anti-parallel
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There are 4 strands in J sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
210 213first strand
Strand 2
B
228 235anti-parallel
Strand 3
B
273 281anti-parallel
Strand 4
B
257 263anti-parallel
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There are 5 strands in K sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
217 218first strand
Strand 2
B
303 309parallel
Strand 3
B
293 298anti-parallel
Strand 4
B
240 245anti-parallel
Strand 5
B
248 249anti-parallel
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There are 3 strands in L sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
5 9first strand
Strand 2
C
102 112parallel
Strand 3
C
16 18parallel
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There are 5 strands in M sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
5 9first strand
Strand 2
C
102 112parallel
Strand 3
C
90 97anti-parallel
Strand 4
C
47 54anti-parallel
Strand 5
C
60 62anti-parallel
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There are 3 strands in N sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
23 26first strand
Strand 2
C
78 81anti-parallel
Strand 3
C
72 75anti-parallel
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There are 5 strands in O sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
126 130first strand
Strand 2
C
201 214parallel
Strand 3
C
188 198anti-parallel
Strand 4
C
154 159anti-parallel
Strand 5
C
162 163anti-parallel
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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
C
135 139first strand
Strand 2
C
176 180anti-parallel
Strand 3
C
170 173anti-parallel
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There are 4 strands in Q sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
224 226first strand
Strand 2
C
246 250anti-parallel
Strand 3
C
290 294anti-parallel
Strand 4
C
280 283anti-parallel
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There are 3 strands in R sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
259 263first strand
Strand 2
C
311 315anti-parallel
Strand 3
C
320 324anti-parallel
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There are 9 strands in S sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
D
77 84first strand
Strand 2
D
67 74anti-parallel
Strand 3
D
56 62anti-parallel
Strand 4
D
100 105anti-parallel
Strand 5
D
110 114anti-parallel
Strand 6
D
146 150anti-parallel
Strand 7
D
5 12anti-parallel
Strand 8
D
42 46anti-parallel
Strand 9
D
56 62anti-parallel
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There are 3 strands in T sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
D
17 22first strand
Strand 2
D
25 29anti-parallel
Strand 3
D
130 131anti-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
D
121 123first strand
Strand 2
D
133 135anti-parallel
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There are 3 strands in V sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
E
7 10first strand
Strand 2
E
86 97parallel
Strand 3
E
15 18parallel
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There are 4 strands in W sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
E
7 10first strand
Strand 2
E
86 97parallel
Strand 3
E
75 83anti-parallel
Strand 4
E
38 41anti-parallel
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There are 3 strands in X sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
E
23 25first strand
Strand 2
E
63 66anti-parallel
Strand 3
E
57 60anti-parallel
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There are 5 strands in Y sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
E
110 116first strand
Strand 2
E
188 201parallel
Strand 3
E
175 185anti-parallel
Strand 4
E
142 145anti-parallel
Strand 5
E
148 149anti-parallel
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There are 3 strands in Z sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
E
121 124first strand
Strand 2
E
163 166anti-parallel
Strand 3
E
157 160anti-parallel
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There are 4 strands in AA sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
E
210 213first strand
Strand 2
E
227 235anti-parallel
Strand 3
E
273 281anti-parallel
Strand 4
E
257 264anti-parallel
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There are 5 strands in AB sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
E
217 220first strand
Strand 2
E
302 311parallel
Strand 3
E
293 299anti-parallel
Strand 4
E
240 245anti-parallel
Strand 5
E
248 249anti-parallel
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There are 3 strands in AC sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
F
6 9first strand
Strand 2
F
102 112parallel
Strand 3
F
15 18parallel
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There are 4 strands in AD sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
F
6 9first strand
Strand 2
F
102 112parallel
Strand 3
F
90 97anti-parallel
Strand 4
F
47 51anti-parallel
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There are 2 strands in AE sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
F
25 26first strand
Strand 2
F
78 79anti-parallel
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There are 5 strands in AF sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
F
126 130first strand
Strand 2
F
203 214parallel
Strand 3
F
188 196anti-parallel
Strand 4
F
154 159anti-parallel
Strand 5
F
162 163anti-parallel
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There are 3 strands in AG sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
F
135 139first strand
Strand 2
F
176 180anti-parallel
Strand 3
F
170 173anti-parallel
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There are 4 strands in AH sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
F
224 227first strand
Strand 2
F
244 250anti-parallel
Strand 3
F
290 296anti-parallel
Strand 4
F
279 281anti-parallel
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There are 2 strands in AI sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
F
233 234first strand
Strand 2
F
326 327parallel
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There are 3 strands in AJ sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
F
259 264first strand
Strand 2
F
310 316anti-parallel
Strand 3
F
319 324anti-parallel
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