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


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 9YMA entry

There are 3 chains in PDB entry 9YMA (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
B
 U 1 A 22
C
 A 6 U 25
A
 ALA 22ALA 859
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
Back to top of page

There are 21 helices in PDB entry 9YMA. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
AA1
A
69 82Right-handed alpha
Helix 2
AA2
A
82 87Right-handed alpha
Helix 3
AA3
A
140 148Right-handed alpha
Helix 4
AA4
A
155 173Right-handed alpha
Helix 5
AA5
A
373 386Right-handed alpha
Helix 6
AA6
A
387 391Right-handed 310
Helix 7
AA7
A
393 398Right-handed 310
Helix 8
AA8
A
463 482Right-handed alpha
Helix 9
AA9
A
497 499Right-handed 310
Helix 10
AB1
A
500 512Right-handed alpha
Helix 11
AB2
A
526 539Right-handed alpha
Helix 12
AB3
A
549 554Right-handed alpha
Helix 13
AB4
A
556 572Right-handed alpha
Helix 14
AB5
A
584 589Right-handed 310
Helix 15
AB6
A
642 658Right-handed alpha
Helix 16
AB7
A
672 674Right-handed 310
Helix 17
AB8
A
675 695Right-handed alpha
Helix 18
AB9
A
775 787Right-handed alpha
Helix 19
AC1
A
800 825Right-handed alpha
Helix 20
AC2
A
838 846Right-handed alpha
Helix 21
AC3
A
849 853Right-handed 310
Back to top of page

There are 7 sheets in PDB entry 9YMA. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7,

There are 9 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
591 594first strand
Strand 2
A
663 669parallel
Strand 3
A
702 707parallel
Strand 4
A
763 769anti-parallel
Strand 5
A
747 751anti-parallel
Strand 6
A
734 736anti-parallel
Strand 7
A
407 412anti-parallel
Strand 8
A
36 42anti-parallel
Strand 9
A
715 717anti-parallel
Back to list of sheets
Back to top of page

There are 3 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
44 46first strand
Strand 2
A
214 218anti-parallel
Strand 3
A
203 207anti-parallel
Back to list of sheets
Back to top of page

There are 5 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
93 94first strand
Strand 2
A
99 102anti-parallel
Strand 3
A
53 61anti-parallel
Strand 4
A
128 139anti-parallel
Strand 5
A
113 117anti-parallel
Back to list of sheets
Back to top of page

There are 3 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
427 428first strand
Strand 2
A
418 420anti-parallel
Strand 3
A
576 578anti-parallel
Back to list of sheets
Back to top of page

There are 3 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
451 455first strand
Strand 2
A
517 522parallel
Strand 3
A
543 548parallel
Back to list of sheets
Back to top of page

There are 2 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
611 612first strand
Strand 2
A
630 631anti-parallel
Back to list of sheets
Back to top of page

There are 2 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
615 617first strand
Strand 2
A
625 627anti-parallel
Back to list of sheets
Back to top of page
Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il