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


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 1YPZ entry

There are 8 chains in PDB entry 1YPZ (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 GLY 1GLY 276
B
 ALA -2MET 99
C
 GLY 1GLY 276
D
 ALA -2MET 99
E
 GLY 1ALA 207
F
 HIS 1LYS 230
G
 GLY 1ALA 207
H
 HIS 1LYS 230
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 1YPZ. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
1
A
60 84Right-handed alpha
Helix 2
2
A
105 108Right-handed 310
Helix 3
3
A
159 174Right-handed alpha
Helix 4
4
C
61 85Right-handed alpha
Helix 5
5
C
163 172Right-handed alpha
Helix 6
6
C
176 181Right-handed alpha
Helix 7
7
C
224 228Right-handed 310
Helix 8
8
C
252 255Right-handed 310
Helix 9
9
E
79 83Right-handed 310
Helix 10
10
F
27 33Right-handed 310
Helix 11
11
F
87 91Right-handed 310
Helix 12
12
F
138 146Right-handed alpha
Helix 13
13
F
198 202Right-handed 310
Helix 14
14
G
79 83Right-handed 310
Helix 15
15
G
202 204Right-handed 310
Helix 16
16
H
87 91Right-handed 310
Helix 17
17
H
138 146Right-handed alpha
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There are 34 sheets in PDB entry 1YPZ. 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,

There are 6 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
44 45first strand
Strand 2
A
31 35anti-parallel
Strand 3
A
21 28anti-parallel
Strand 4
A
3 12anti-parallel
Strand 5
A
94 104anti-parallel
Strand 6
A
109 117anti-parallel
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There are 4 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
189 191first strand
Strand 2
A
199 208anti-parallel
Strand 3
A
240 249anti-parallel
Strand 4
A
229 230anti-parallel
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There are 4 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
189 191first strand
Strand 2
A
199 208anti-parallel
Strand 3
A
240 249anti-parallel
Strand 4
A
234 236anti-parallel
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There are 3 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
214 218first strand
Strand 2
A
258 262anti-parallel
Strand 3
A
270 272anti-parallel
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There are 4 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
6 11first strand
Strand 2
B
21 30anti-parallel
Strand 3
B
62 70anti-parallel
Strand 4
B
50 51anti-parallel
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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
6 11first strand
Strand 2
B
21 30anti-parallel
Strand 3
B
62 70anti-parallel
Strand 4
B
55 56anti-parallel
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There are 4 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
44 45first strand
Strand 2
B
36 41anti-parallel
Strand 3
B
78 83anti-parallel
Strand 4
B
91 94anti-parallel
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There are 6 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
31 34first strand
Strand 2
C
21 28anti-parallel
Strand 3
C
3 12anti-parallel
Strand 4
C
94 103anti-parallel
Strand 5
C
111 118anti-parallel
Strand 6
C
131 132anti-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
C
186 188first strand
Strand 2
C
199 208anti-parallel
Strand 3
C
191 193anti-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
C
186 188first strand
Strand 2
C
199 208anti-parallel
Strand 3
C
241 249anti-parallel
Strand 4
C
229 230anti-parallel
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There are 3 strands in K sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
214 219first strand
Strand 2
C
257 262anti-parallel
Strand 3
C
270 272anti-parallel
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There are 4 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
9 11first strand
Strand 2
D
21 30anti-parallel
Strand 3
D
62 70anti-parallel
Strand 4
D
50 51anti-parallel
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There are 4 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
9 11first strand
Strand 2
D
21 30anti-parallel
Strand 3
D
62 70anti-parallel
Strand 4
D
55 56anti-parallel
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There are 4 strands in N sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
D
44 45first strand
Strand 2
D
36 41anti-parallel
Strand 3
D
78 83anti-parallel
Strand 4
D
91 94anti-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
E
4 6first strand
Strand 2
E
19 25anti-parallel
Strand 3
E
70 75anti-parallel
Strand 4
E
59 63anti-parallel
Strand 5
E
52 56anti-parallel
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There are 10 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
44 49first strand
Strand 2
E
31 37anti-parallel
Strand 3
E
84 91anti-parallel
Strand 4
E
112 117anti-parallel
Strand 5
E
10 14parallel
Strand 6
G
10 14anti-parallel
Strand 7
G
112 117parallel
Strand 8
G
84 95anti-parallel
Strand 9
G
31 37anti-parallel
Strand 10
G
43 49anti-parallel
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There are 8 strands in Q sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
E
107 108first strand
Strand 2
E
84 91anti-parallel
Strand 3
E
112 117anti-parallel
Strand 4
E
10 14parallel
Strand 5
G
10 14anti-parallel
Strand 6
G
112 117parallel
Strand 7
G
84 95anti-parallel
Strand 8
G
101 108anti-parallel
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There are 4 strands in R sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
E
127 133first strand
Strand 2
E
136 144anti-parallel
Strand 3
E
174 178anti-parallel
Strand 4
E
165 168anti-parallel
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There are 3 strands in S sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
E
150 154first strand
Strand 2
E
189 194anti-parallel
Strand 3
E
197 200anti-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
E
158 161first strand
Strand 2
E
180 182anti-parallel
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There are 5 strands in U sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
F
4 5first strand
Strand 2
F
19 25anti-parallel
Strand 3
F
78 83anti-parallel
Strand 4
F
67 72anti-parallel
Strand 5
F
59 62anti-parallel
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There are 5 strands in V sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
F
10 14first strand
Strand 2
F
113 118parallel
Strand 3
F
93 98anti-parallel
Strand 4
F
35 40anti-parallel
Strand 5
F
47 52anti-parallel
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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
F
10 14first strand
Strand 2
F
113 118parallel
Strand 3
F
93 98anti-parallel
Strand 4
F
108 109anti-parallel
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There are 4 strands in X sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
F
134 135first strand
Strand 2
F
148 157anti-parallel
Strand 3
F
188 197anti-parallel
Strand 4
F
178 179anti-parallel
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There are 4 strands in Y sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
F
134 135first strand
Strand 2
F
148 157anti-parallel
Strand 3
F
188 197anti-parallel
Strand 4
F
183 185anti-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
F
163 167first strand
Strand 2
F
206 211anti-parallel
Strand 3
F
221 225anti-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
G
5 6first strand
Strand 2
G
19 24anti-parallel
Strand 3
G
70 75anti-parallel
Strand 4
G
59 63anti-parallel
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There are 3 strands in AB sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
G
127 129first strand
Strand 2
G
140 144anti-parallel
Strand 3
G
174 175anti-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
G
150 154first strand
Strand 2
G
189 194anti-parallel
Strand 3
G
197 200anti-parallel
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There are 5 strands in AD sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
H
10 14first strand
Strand 2
H
113 118parallel
Strand 3
H
93 97anti-parallel
Strand 4
H
35 40anti-parallel
Strand 5
H
47 52anti-parallel
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There are 4 strands in AE sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
H
19 24first strand
Strand 2
H
78 83anti-parallel
Strand 3
H
67 70anti-parallel
Strand 4
H
60 62anti-parallel
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There are 2 strands in AF sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
H
134 135first strand
Strand 2
H
151 152anti-parallel
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There are 2 strands in AG sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
H
178 179first strand
Strand 2
H
193 194anti-parallel
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There are 2 strands in AH sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
H
183 184first strand
Strand 2
H
189 190anti-parallel
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