Analysis of interatomic Contacts of Structural Units in PDB entry:
6PKD


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 6PKD entry

There are 2 chains in PDB entry 6PKD (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 TYR 235MET 504
B
 GLY 244LYS 503
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 5 helices in PDB entry 6PKD. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
AA1
A
303 310Right-handed alpha
Helix 2
AA2
A
323 327Right-handed 310
Helix 3
AA3
A
424 426Right-handed 310
Helix 4
AA4
B
303 310Right-handed alpha
Helix 5
AA5
B
424 426Right-handed 310
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There are 12 sheets in PDB entry 6PKD. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8, AA9, AB1, AB2, AB3,

There are 3 strands in AA1 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
248 251first strand
Strand 2
A
494 501anti-parallel
Strand 3
A
255 256anti-parallel
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There are 4 strands in AA2 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
248 251first strand
Strand 2
A
494 501anti-parallel
Strand 3
A
485 489anti-parallel
Strand 4
A
476 480anti-parallel
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There are 4 strands in AA3 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
270 271first strand
Strand 2
A
285 288anti-parallel
Strand 3
A
297 301anti-parallel
Strand 4
A
314 317anti-parallel
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There are 4 strands in AA4 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
328 330first strand
Strand 2
A
333 337anti-parallel
Strand 3
A
343 348anti-parallel
Strand 4
A
353 359anti-parallel
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There are 4 strands in AA5 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
380 384first strand
Strand 2
A
387 392anti-parallel
Strand 3
A
400 406anti-parallel
Strand 4
A
413 422anti-parallel
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There are 4 strands in AA6 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
428 432first strand
Strand 2
A
435 439anti-parallel
Strand 3
A
446 454anti-parallel
Strand 4
A
460 468anti-parallel
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There are 3 strands in AA7 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
248 251first strand
Strand 2
B
494 501anti-parallel
Strand 3
B
255 256anti-parallel
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There are 4 strands in AA8 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
248 251first strand
Strand 2
B
494 501anti-parallel
Strand 3
B
485 489anti-parallel
Strand 4
B
476 480anti-parallel
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There are 4 strands in AA9 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
270 271first strand
Strand 2
B
285 288anti-parallel
Strand 3
B
297 301anti-parallel
Strand 4
B
314 317anti-parallel
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There are 4 strands in AB1 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
328 330first strand
Strand 2
B
333 337anti-parallel
Strand 3
B
343 348anti-parallel
Strand 4
B
354 359anti-parallel
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There are 4 strands in AB2 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
380 384first strand
Strand 2
B
387 392anti-parallel
Strand 3
B
400 406anti-parallel
Strand 4
B
413 422anti-parallel
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There are 4 strands in AB3 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
428 432first strand
Strand 2
B
435 439anti-parallel
Strand 3
B
446 454anti-parallel
Strand 4
B
460 468anti-parallel
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