Analysis of interatomic Contacts of Structural Units in PDB entry:
5JMD


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 5JMD entry

There are 2 chains in PDB entry 5JMD (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 GLY 21ALA 56
A
 ALA 58LEU 666
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 22 helices in PDB entry 5JMD. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
AA1
A
28 33Right-handed alpha
Helix 2
AA2
A
40 49Right-handed alpha
Helix 3
AA3
A
51 66Right-handed alpha
Helix 4
AA4
A
82 94Right-handed alpha
Helix 5
AA5
A
122 128Right-handed alpha
Helix 6
AA6
A
129 132Right-handed 310
Helix 7
AA7
A
134 146Right-handed alpha
Helix 8
AA8
A
147 165Right-handed alpha
Helix 9
AA9
A
171 176Right-handed alpha
Helix 10
AB1
A
181 194Right-handed alpha
Helix 11
AB2
A
195 214Right-handed alpha
Helix 12
AB3
A
220 240Right-handed alpha
Helix 13
AB4
A
246 263Right-handed alpha
Helix 14
AB5
A
268 288Right-handed alpha
Helix 15
AB6
A
298 318Right-handed alpha
Helix 16
AB7
A
321 325Right-handed 310
Helix 17
AB8
A
326 344Right-handed alpha
Helix 18
AB9
A
360 375Right-handed alpha
Helix 19
AC1
A
378 387Right-handed alpha
Helix 20
AC2
A
463 471Right-handed alpha
Helix 21
AC3
A
472 476Right-handed 310
Helix 22
AC4
A
628 632Right-handed 310
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There are 5 sheets in PDB entry 5JMD. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5,

There are 2 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
96 97first strand
Strand 2
A
107 108anti-parallel
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There are 5 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
399 401first strand
Strand 2
A
406 410anti-parallel
Strand 3
A
418 423anti-parallel
Strand 4
A
439 443anti-parallel
Strand 5
A
446 447anti-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
479 481first strand
Strand 2
A
541 548anti-parallel
Strand 3
A
598 611anti-parallel
Strand 4
A
584 595anti-parallel
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There are 8 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
492 497first strand
Strand 2
A
502 512anti-parallel
Strand 3
A
515 524anti-parallel
Strand 4
A
528 536anti-parallel
Strand 5
A
617 626anti-parallel
Strand 6
A
572 578anti-parallel
Strand 7
A
562 565anti-parallel
Strand 8
A
554 555anti-parallel
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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
635 639first strand
Strand 2
A
648 655anti-parallel
Strand 3
A
658 665anti-parallel
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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il