Analysis of interatomic Contacts of Structural Units in PDB entry:
3KDM


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 3KDM entry

There are 4 chains in PDB entry 3KDM (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
L
ALA 3CYS 218
H
VAL 2LYS 223
A
ALA 3CYS 218
B
VAL 2LYS 223
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 3KDM. Click on helix of interest for CSU analysis.
Helix
number
Helix
ID
Chain
ID
Initial
residue
Terminal
residue
Helix class
Helix 1
1
L
81 85Right-handed 310
Helix 2
2
L
125 130Right-handed alpha
Helix 3
3
L
187 192Right-handed alpha
Helix 4
4
H
28 32Right-handed 310
Helix 5
5
H
61 66Right-handed alpha
Helix 6
6
H
87 91Right-handed 310
Helix 7
7
H
165 167Right-handed 310
Helix 8
8
H
196 200Right-handed 310
Helix 9
9
H
210 213Right-handed 310
Helix 10
10
A
81 85Right-handed 310
Helix 11
11
A
125 131Right-handed alpha
Helix 12
12
A
187 193Right-handed alpha
Helix 13
13
B
28 32Right-handed 310
Helix 14
14
B
87 91Right-handed 310
Helix 15
15
B
165 167Right-handed 310
Helix 16
16
B
196 200Right-handed 310
Helix 17
17
B
210 213Right-handed 310
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There are 22 sheets in PDB entry 3KDM. 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,

There are 5 strands in A sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
L
9 12first strand
Strand 2
L
106 110parallel
Strand 3
L
87 93anti-parallel
Strand 4
L
35 40anti-parallel
Strand 5
L
47 50anti-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
L
9 12first strand
Strand 2
L
106 110parallel
Strand 3
L
87 93anti-parallel
Strand 4
L
100 102anti-parallel
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There are 3 strands in C sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
L
18 23first strand
Strand 2
L
72 77anti-parallel
Strand 3
L
64 69anti-parallel
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There are 4 strands in D sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
L
118 122first strand
Strand 2
L
133 143anti-parallel
Strand 3
L
177 186anti-parallel
Strand 4
L
163 167anti-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
L
157 158first strand
Strand 2
L
149 154anti-parallel
Strand 3
L
195 201anti-parallel
Strand 4
L
209 214anti-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
H
3 7first strand
Strand 2
H
18 25anti-parallel
Strand 3
H
78 83anti-parallel
Strand 4
H
68 73anti-parallel
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There are 6 strands in G sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
H
10 12first strand
Strand 2
H
116 120parallel
Strand 3
H
92 98anti-parallel
Strand 4
H
34 39anti-parallel
Strand 5
H
45 51anti-parallel
Strand 6
H
58 60anti-parallel
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There are 4 strands in H sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
H
10 12first strand
Strand 2
H
116 120parallel
Strand 3
H
92 98anti-parallel
Strand 4
H
111 112anti-parallel
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There are 4 strands in I sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
H
129 133first strand
Strand 2
H
144 154anti-parallel
Strand 3
H
185 194anti-parallel
Strand 4
H
172 174anti-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
H
129 133first strand
Strand 2
H
144 154anti-parallel
Strand 3
H
185 194anti-parallel
Strand 4
H
178 179anti-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
H
160 163first strand
Strand 2
H
204 209anti-parallel
Strand 3
H
214 219anti-parallel
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There are 5 strands in L sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
A
9 12first strand
Strand 2
A
106 110parallel
Strand 3
A
86 93anti-parallel
Strand 4
A
35 40anti-parallel
Strand 5
A
47 50anti-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
A
9 12first strand
Strand 2
A
106 110parallel
Strand 3
A
86 93anti-parallel
Strand 4
A
100 102anti-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
A
18 23first strand
Strand 2
A
72 77anti-parallel
Strand 3
A
64 69anti-parallel
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There are 4 strands in O sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
A
118 122first strand
Strand 2
A
133 143anti-parallel
Strand 3
A
177 186anti-parallel
Strand 4
A
163 167anti-parallel
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There are 4 strands in P sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
A
157 158first strand
Strand 2
A
148 154anti-parallel
Strand 3
A
195 202anti-parallel
Strand 4
A
209 214anti-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
B
3 7first strand
Strand 2
B
19 25anti-parallel
Strand 3
B
78 83anti-parallel
Strand 4
B
68 71anti-parallel
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There are 6 strands in R sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
B
11 12first strand
Strand 2
B
116 120parallel
Strand 3
B
92 99anti-parallel
Strand 4
B
33 39anti-parallel
Strand 5
B
45 51anti-parallel
Strand 6
B
58 60anti-parallel
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There are 4 strands in S sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
B
11 12first strand
Strand 2
B
116 120parallel
Strand 3
B
92 99anti-parallel
Strand 4
B
111 112anti-parallel
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There are 4 strands in T sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
B
129 133first strand
Strand 2
B
144 154anti-parallel
Strand 3
B
185 194anti-parallel
Strand 4
B
172 174anti-parallel
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There are 4 strands in U sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
B
129 133first strand
Strand 2
B
144 154anti-parallel
Strand 3
B
185 194anti-parallel
Strand 4
B
178 179anti-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
B
160 163first strand
Strand 2
B
204 209anti-parallel
Strand 3
B
214 219anti-parallel
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