Analysis of interatomic Contacts of Structural Units in PDB entry:
9YMD


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 9YMD entry

There are 2 chains in PDB entry 9YMD (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 ALA 22ALA 859
B
 U 1 G 23
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 23 helices in PDB entry 9YMD. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
AA1
A
67 82Right-handed alpha
Helix 2
AA2
A
139 148Right-handed alpha
Helix 3
AA3
A
155 174Right-handed alpha
Helix 4
AA4
A
229 238Right-handed alpha
Helix 5
AA5
A
253 263Right-handed alpha
Helix 6
AA6
A
340 342Right-handed 310
Helix 7
AA7
A
357 369Right-handed alpha
Helix 8
AA8
A
371 387Right-handed alpha
Helix 9
AA9
A
388 390Right-handed 310
Helix 10
AB1
A
391 397Right-handed alpha
Helix 11
AB2
A
463 482Right-handed alpha
Helix 12
AB3
A
497 499Right-handed 310
Helix 13
AB4
A
500 512Right-handed alpha
Helix 14
AB5
A
526 539Right-handed alpha
Helix 15
AB6
A
549 554Right-handed alpha
Helix 16
AB7
A
556 571Right-handed alpha
Helix 17
AB8
A
584 589Right-handed 310
Helix 18
AB9
A
641 658Right-handed alpha
Helix 19
AC1
A
672 674Right-handed 310
Helix 20
AC2
A
675 695Right-handed alpha
Helix 21
AC3
A
775 787Right-handed alpha
Helix 22
AC4
A
800 816Right-handed alpha
Helix 23
AC5
A
840 846Right-handed alpha
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There are 8 sheets in PDB entry 9YMD. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8,

There are 11 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
625 632first strand
Strand 2
A
610 617anti-parallel
Strand 3
A
591 599anti-parallel
Strand 4
A
663 669parallel
Strand 5
A
701 708parallel
Strand 6
A
763 770anti-parallel
Strand 7
A
747 751anti-parallel
Strand 8
A
734 736anti-parallel
Strand 9
A
406 412anti-parallel
Strand 10
A
36 42anti-parallel
Strand 11
A
715 717anti-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
175 177first strand
Strand 2
A
180 182anti-parallel
Strand 3
A
196 207anti-parallel
Strand 4
A
191 193anti-parallel
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There are 6 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
175 177first strand
Strand 2
A
180 182anti-parallel
Strand 3
A
196 207anti-parallel
Strand 4
A
213 225anti-parallel
Strand 5
A
44 48anti-parallel
Strand 6
A
400 401anti-parallel
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There are 5 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
93 94first strand
Strand 2
A
99 102anti-parallel
Strand 3
A
54 62anti-parallel
Strand 4
A
127 138anti-parallel
Strand 5
A
113 118anti-parallel
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There are 2 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
267 269first strand
Strand 2
A
344 346anti-parallel
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There are 3 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
281 284first strand
Strand 2
A
328 330anti-parallel
Strand 3
A
338 339anti-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
A
427 428first strand
Strand 2
A
418 419anti-parallel
Strand 3
A
577 578anti-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
A
492 494first strand
Strand 2
A
451 455parallel
Strand 3
A
517 522parallel
Strand 4
A
544 548parallel
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