Analysis of interatomic Contacts of Structural Units in PDB entry:
3KD4


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 3KD4 entry

There are 2 chains in PDB entry 3KD4 (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 ALA 23LEU 527
B
 ALA 23LEU 527
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 35 helices in PDB entry 3KD4. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
1
A
56 61Right-handed alpha
Helix 2
2
A
62 64Right-handed 310
Helix 3
3
A
96 98Right-handed 310
Helix 4
4
A
105 109Right-handed 310
Helix 5
5
A
111 115Right-handed 310
Helix 6
6
A
231 244Right-handed alpha
Helix 7
7
A
248 260Right-handed alpha
Helix 8
8
A
264 280Right-handed alpha
Helix 9
9
A
286 291Right-handed 310
Helix 10
10
A
296 304Right-handed alpha
Helix 11
11
A
307 322Right-handed alpha
Helix 12
12
A
337 341Right-handed 310
Helix 13
13
A
366 371Right-handed alpha
Helix 14
14
A
403 407Right-handed 310
Helix 15
15
A
420 425Right-handed 310
Helix 16
16
A
501 517Right-handed alpha
Helix 17
17
A
518 520Right-handed 310
Helix 18
18
B
56 61Right-handed alpha
Helix 19
19
B
62 64Right-handed 310
Helix 20
20
B
96 98Right-handed 310
Helix 21
21
B
105 109Right-handed 310
Helix 22
22
B
111 115Right-handed 310
Helix 23
23
B
231 246Right-handed alpha
Helix 24
24
B
248 260Right-handed alpha
Helix 25
25
B
264 280Right-handed alpha
Helix 26
26
B
286 291Right-handed 310
Helix 27
27
B
296 304Right-handed alpha
Helix 28
28
B
307 322Right-handed alpha
Helix 29
29
B
337 341Right-handed 310
Helix 30
30
B
342 346Right-handed 310
Helix 31
31
B
366 371Right-handed alpha
Helix 32
32
B
402 407Right-handed 310
Helix 33
33
B
420 425Right-handed 310
Helix 34
34
B
501 517Right-handed alpha
Helix 35
35
B
518 520Right-handed 310
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There are 16 sheets in PDB entry 3KD4. 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,

There are 8 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
92 94first strand
Strand 2
A
76 86anti-parallel
Strand 3
A
132 141anti-parallel
Strand 4
A
44 54anti-parallel
Strand 5
A
27 38anti-parallel
Strand 6
A
161 171parallel
Strand 7
A
195 205anti-parallel
Strand 8
A
188 192anti-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
66 71first strand
Strand 2
A
118 123anti-parallel
Strand 3
A
100 103anti-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
A
150 154first strand
Strand 2
A
223 227anti-parallel
Strand 3
A
177 181anti-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
281 282first strand
Strand 2
A
305 306parallel
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There are 5 strands in E sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
358 362first strand
Strand 2
A
348 355anti-parallel
Strand 3
A
326 333anti-parallel
Strand 4
A
374 378anti-parallel
Strand 5
A
383 384anti-parallel
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There are 5 strands in F sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
391 401first strand
Strand 2
A
444 454parallel
Strand 3
A
486 495anti-parallel
Strand 4
A
474 483anti-parallel
Strand 5
A
467 471anti-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
A
410 414first strand
Strand 2
A
522 526anti-parallel
Strand 3
A
459 460anti-parallel
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There are 2 strands in H sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
438 439first strand
Strand 2
A
499 500anti-parallel
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There are 8 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
92 94first strand
Strand 2
B
76 86anti-parallel
Strand 3
B
132 141anti-parallel
Strand 4
B
44 54anti-parallel
Strand 5
B
27 38anti-parallel
Strand 6
B
161 171parallel
Strand 7
B
195 205anti-parallel
Strand 8
B
188 189anti-parallel
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There are 3 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
66 71first strand
Strand 2
B
118 123anti-parallel
Strand 3
B
100 103anti-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
B
150 154first strand
Strand 2
B
223 227anti-parallel
Strand 3
B
177 181anti-parallel
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There are 2 strands in L sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
281 282first strand
Strand 2
B
305 306parallel
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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
B
358 362first strand
Strand 2
B
348 355anti-parallel
Strand 3
B
326 333anti-parallel
Strand 4
B
374 378anti-parallel
Strand 5
B
383 384anti-parallel
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There are 5 strands in N sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
391 401first strand
Strand 2
B
444 454parallel
Strand 3
B
486 495anti-parallel
Strand 4
B
474 483anti-parallel
Strand 5
B
467 471anti-parallel
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There are 3 strands in O sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
410 414first strand
Strand 2
B
522 526anti-parallel
Strand 3
B
459 460anti-parallel
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There are 2 strands in P sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
438 439first strand
Strand 2
B
499 500anti-parallel
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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il