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


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 1NDM entry

There are 3 chains in PDB entry 1NDM (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 ASP 1CYS 214
B
 GLU 301ILE 521
C
 LYS 601LEU 729
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 16 helices in PDB entry 1NDM. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
1
A
79 83Right-handed 310
Helix 2
2
A
121 127Right-handed alpha
Helix 3
3
A
183 187Right-handed alpha
Helix 4
4
B
361 364Right-handed 310
Helix 5
5
B
386 390Right-handed 310
Helix 6
6
B
461 463Right-handed 310
Helix 7
7
B
494 497Right-handed 310
Helix 8
8
B
511 514Right-handed 310
Helix 9
9
C
604 615Right-handed alpha
Helix 10
10
C
619 623Right-handed 310
Helix 11
11
C
624 637Right-handed alpha
Helix 12
12
C
679 685Right-handed 310
Helix 13
13
C
688 700Right-handed alpha
Helix 14
14
C
703 707Right-handed 310
Helix 15
15
C
708 715Right-handed alpha
Helix 16
16
C
719 725Right-handed 310
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There are 11 sheets in PDB entry 1NDM. Click on sheet of interest to get list of strands forming it: A, B, C, D, E, F, G, H, I, J, K,

There are 4 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
4 5first strand
Strand 2
A
19 25anti-parallel
Strand 3
A
70 75anti-parallel
Strand 4
A
62 67anti-parallel
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There are 5 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
53 54first strand
Strand 2
A
45 49anti-parallel
Strand 3
A
33 38anti-parallel
Strand 4
A
84 90anti-parallel
Strand 5
A
97 98anti-parallel
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There are 6 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
53 54first strand
Strand 2
A
45 49anti-parallel
Strand 3
A
33 38anti-parallel
Strand 4
A
84 90anti-parallel
Strand 5
A
102 106anti-parallel
Strand 6
A
10 13parallel
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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
A
114 118first strand
Strand 2
A
129 139anti-parallel
Strand 3
A
173 182anti-parallel
Strand 4
A
159 163anti-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
A
153 154first strand
Strand 2
A
145 150anti-parallel
Strand 3
A
191 198anti-parallel
Strand 4
A
201 210anti-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
303 307first strand
Strand 2
B
318 325anti-parallel
Strand 3
B
377 382anti-parallel
Strand 4
B
367 371anti-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
B
311 312first strand
Strand 2
B
407 411parallel
Strand 3
B
391 397anti-parallel
Strand 4
B
334 339anti-parallel
Strand 5
B
345 351anti-parallel
Strand 6
B
357 359anti-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
B
420 424first strand
Strand 2
B
435 445anti-parallel
Strand 3
B
482 492anti-parallel
Strand 4
B
469 471anti-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
B
420 424first strand
Strand 2
B
435 445anti-parallel
Strand 3
B
482 492anti-parallel
Strand 4
B
475 477anti-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
451 455first strand
Strand 2
B
504 510anti-parallel
Strand 3
B
515 520anti-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
643 645first strand
Strand 2
C
651 653anti-parallel
Strand 3
C
658 659anti-parallel
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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il