Contacts of the helix formed by residues 503 - 534 (chain D) in PDB entry 5MG3
Residue contacts within the protein 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). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 503 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450D ILE* 3.9 12.8 - - - -
501D THR* 4.0 7.8 + - - -
502D LEU* 1.4 81.5 - - - +
504D MET* 1.4 58.6 - - - +
505D PRO* 3.8 14.1 - - - +
506D GLY* 2.9 33.4 + - - -
507D ILE* 3.1 15.0 + - - +
577D GLY* 4.5 8.5 - - - -
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Residues in contact with MET 504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446D GLY 5.6 0.2 - - - +
449D ASN* 3.7 35.7 - - + +
450D ILE* 3.8 17.4 - - + +
453D GLY* 4.1 3.4 - - - -
503D SER* 1.4 65.9 - - - +
505D PRO* 1.3 67.9 - - + +
507D ILE* 3.1 32.6 + - + +
508D ALA* 2.8 36.8 + - + +
511D VAL* 5.8 0.2 - - + -
198F THR* 6.1 3.6 - - + -
262F LEU* 4.2 21.5 - - + -
270F LEU* 4.1 20.6 - - + -
273F PHE* 3.8 28.9 - - + -
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Residues in contact with PRO 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503D SER* 3.9 11.9 - - - +
504D MET* 1.3 94.7 - - + +
506D GLY* 1.4 60.9 + - - +
508D ALA* 3.3 10.1 - - + +
509D GLY 3.1 16.1 + - - -
574D ALA* 3.3 48.5 - - + +
577D GLY* 4.6 0.7 - - - -
578D PHE* 3.1 17.6 - - + +
198F THR* 4.6 17.0 - - + -
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Residues in contact with GLY 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502D LEU* 5.6 2.7 - - - -
503D SER* 2.9 22.8 + - - -
505D PRO* 1.4 73.1 - - - +
507D ILE* 1.4 50.6 + - - +
509D GLY 3.1 1.0 + - - -
510D ILE* 2.9 28.1 + - - +
577D GLY 3.5 19.3 + - - -
581D THR* 2.7 28.6 + - - -
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Residues in contact with ILE 507 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450D ILE* 3.9 33.4 - - + +
453D GLY* 3.7 16.4 - - - +
454D LEU* 4.1 20.0 - - + -
457D CYS* 3.6 20.8 - - - -
502D LEU* 4.5 9.0 - - + -
503D SER 3.1 12.8 + - - +
504D MET* 3.1 23.4 + - + +
506D GLY* 1.4 70.2 - - - +
508D ALA* 1.4 62.3 + - - +
510D ILE* 3.0 26.8 + - + +
511D VAL* 2.8 26.9 + - + +
262F LEU* 6.0 0.2 - - + -
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Residues in contact with ALA 508 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504D MET* 2.8 18.1 + - - +
505D PRO* 3.3 16.4 - - + +
507D ILE* 1.4 72.5 - - - +
509D GLY* 1.3 56.5 + - - +
511D VAL* 3.1 11.8 + - - +
512D LEU* 2.8 28.8 + - - +
578D PHE* 3.9 14.8 - - + -
198F THR* 6.4 0.4 - - + -
201F ALA* 5.6 3.6 - - + -
205F SER* 4.8 1.6 + - - -
273F PHE* 3.8 30.3 - - + -
277F MET* 5.6 3.0 - - + +
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Residues in contact with GLY 509 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505D PRO 3.1 7.5 + - - -
506D GLY 3.1 10.4 + - - -
508D ALA* 1.3 73.2 - - - +
510D ILE* 1.3 56.8 + - - +
512D LEU* 3.4 2.2 - - - +
513D THR* 2.8 33.4 + - - +
578D PHE* 3.5 11.7 - - - -
581D THR* 3.5 9.4 - - - -
582D THR* 3.2 24.6 + - - -
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Residues in contact with ILE 510 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454D LEU* 5.9 4.5 - - + -
457D CYS* 4.2 21.5 - - + -
487D LEU* 6.2 4.0 - - + -
490D ILE* 6.2 3.4 - - + -
494D MET* 5.0 17.3 - - + -
502D LEU* 5.1 7.4 - - + -
506D GLY 2.9 14.5 + - - +
507D ILE* 3.0 37.9 + - + +
509D GLY* 1.3 77.8 - - - +
511D VAL* 1.4 51.4 + - - -
513D THR* 3.6 11.1 + - + +
514D LEU* 2.9 29.7 + - + +
581D THR* 4.5 10.1 - - + +
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Residues in contact with VAL 511 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456D ALA 6.1 0.2 - - - -
457D CYS* 3.5 24.0 - - - -
504D MET* 5.8 0.2 - - + -
507D ILE* 2.8 17.4 + - + +
508D ALA* 3.1 12.8 + - - +
510D ILE* 1.4 64.8 - - - +
512D LEU* 1.4 61.1 + - - +
514D LEU* 3.6 7.6 - - - +
515D ALA* 2.9 34.2 + - + +
258F VAL* 3.9 23.8 - - + +
259F ILE* 4.9 10.8 - - + -
262F LEU* 4.1 29.2 - - + -
277F MET* 5.0 13.9 - - + -
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Residues in contact with LEU 512 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508D ALA 2.8 19.2 + - - +
509D GLY* 3.4 5.4 - - - +
511D VAL* 1.4 74.7 - - - +
513D THR* 1.3 61.0 + - - +
515D ALA* 3.3 17.6 - - - +
516D VAL* 3.3 9.9 + - - +
560D THR* 4.2 6.2 - - + +
563D LYS* 4.1 12.3 - - - +
564D VAL* 4.1 13.7 - - + -
578D PHE* 3.3 35.0 - - + -
582D THR* 3.5 26.5 - - + +
204F MET 5.3 0.2 - - - +
205F SER* 4.1 11.9 - - - +
209F TYR* 3.3 38.3 + - + +
277F MET* 6.2 0.2 - - - +
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Residues in contact with THR 513 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486D ASN* 4.9 1.2 - - - +
487D LEU* 6.5 1.3 - - + -
490D ILE* 3.8 23.6 - - + +
509D GLY 2.8 24.9 + - - +
510D ILE* 3.6 15.9 - - + +
512D LEU* 1.3 70.2 - - - +
514D LEU* 1.3 63.9 + - - +
516D VAL* 3.7 10.3 + - - +
517D ALA* 3.5 21.0 + - - +
581D THR 4.7 7.4 - - - +
582D THR* 4.3 15.7 - - - -
585D GLY* 3.4 32.1 + - - -
589D SER* 5.0 0.7 + - - -
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Residues in contact with LEU 514 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457D CYS* 3.3 42.0 - - + +
461D LEU* 4.0 28.9 - - + +
483D LEU* 4.9 4.9 - - + -
487D LEU* 5.2 13.2 - - + +
510D ILE* 2.9 19.9 + - + +
511D VAL* 3.6 5.2 - - - +
513D THR* 1.3 73.6 - - - +
515D ALA* 1.3 59.2 + - - +
517D ALA* 3.5 4.8 - - - +
518D VAL* 3.0 44.7 + - + +
258F VAL* 3.9 27.6 - - + -
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Residues in contact with ALA 515 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511D VAL* 2.9 22.1 + - + +
512D LEU* 3.3 10.8 - - - +
513D THR 3.3 0.2 - - - -
514D LEU* 1.3 76.7 - - - +
516D VAL* 1.3 56.2 + - - +
518D VAL* 3.3 5.5 - - - +
519D ASP* 3.1 31.5 + - - +
209F TYR* 4.4 16.8 - - + -
255F THR* 3.3 28.8 - - + +
258F VAL* 5.3 2.5 - - + -
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Residues in contact with VAL 516 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512D LEU 3.3 9.7 + - - +
513D THR* 3.7 18.4 - - - +
514D LEU 3.3 0.6 - - - -
515D ALA* 1.3 77.0 - - - +
517D ALA* 1.3 60.2 + - - +
519D ASP* 5.2 1.1 - - - -
520D ALA* 3.0 34.0 + - - +
556D ALA* 4.7 5.8 - - + -
557D ASN* 3.2 42.4 - - - +
560D THR* 4.2 19.7 - - + +
586D VAL* 4.8 10.5 - - + -
589D SER* 4.0 13.2 - - - +
209F TYR* 4.2 17.7 - - + +
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Residues in contact with ALA 517 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483D LEU* 3.7 27.5 - - + +
486D ASN* 3.3 24.5 - - - +
487D LEU* 6.1 2.0 - - + -
513D THR 3.5 14.8 - - - +
514D LEU* 3.5 8.3 - - - +
516D VAL* 1.3 79.3 - - - +
518D VAL* 1.3 62.4 + - - +
520D ALA* 4.4 2.4 - - - +
521D ASN* 3.7 19.4 + - - +
589D SER* 3.9 6.5 - - - -
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Residues in contact with VAL 518 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461D LEU* 5.3 0.9 - - + -
464D SER* 3.5 26.5 - - - +
468D MET* 5.7 0.2 - - - +
483D LEU* 4.1 20.6 - - + -
514D LEU* 3.0 32.7 + - + +
515D ALA* 3.3 16.4 - - - +
517D ALA* 1.3 79.2 - - - +
519D ASP* 1.3 64.2 + - - +
521D ASN* 3.6 7.4 + - - +
522D VAL* 3.4 22.9 + - - +
254F THR* 4.1 33.3 - - + +
255F THR 4.3 1.1 - - - +
258F VAL* 4.3 4.3 - - + -
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Residues in contact with ASP 519 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515D ALA 3.1 17.5 + - - +
516D VAL* 4.6 1.3 - - - +
518D VAL* 1.3 73.9 - - - +
520D ALA* 1.3 54.9 + - - +
522D VAL* 3.1 4.9 + - + +
523D LEU* 2.8 37.9 + - + +
209F TYR* 3.9 9.2 - - + -
212F ASN* 3.3 16.3 + - - +
251F THR* 5.5 1.2 - - + +
252F SER* 2.7 33.8 + - - -
254F THR* 2.5 30.8 + - - -
255F THR* 2.7 28.2 + - - +
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Residues in contact with ALA 520 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516D VAL* 3.0 21.9 + - + +
517D ALA* 4.4 4.9 - - - +
519D ASP* 1.3 69.5 - - - +
521D ASN* 1.4 66.2 + - - +
523D LEU* 3.3 13.9 + - - +
524D ILE* 3.1 23.3 + - - +
553D ILE* 3.9 11.8 - - + +
557D ASN* 4.5 16.4 - - - +
589D SER* 5.4 1.3 - - - +
593D ALA* 4.6 19.5 - - + -
597D THR* 5.4 2.0 - - - +
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Residues in contact with ASN 521 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468D MET* 3.4 24.0 - - - +
479D ALA 2.9 27.5 + - - +
480D THR* 4.9 3.0 - - - +
482D ALA* 6.4 1.3 - - + -
483D LEU* 5.2 15.0 - - + +
517D ALA 3.7 12.6 + - - +
518D VAL* 3.6 10.8 + - - +
519D ASP 3.3 0.2 - - - -
520D ALA* 1.4 79.8 - - - +
522D VAL* 1.4 55.7 + - - +
524D ILE* 3.1 17.1 - - - +
525D ASN* 2.7 46.9 + - - -
597D THR* 4.7 14.3 - - + +
600D ILE* 4.7 3.5 - - - +
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Residues in contact with VAL 522 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467D PHE* 4.5 6.3 - - + -
468D MET* 4.1 18.2 - - - -
472D TYR* 4.1 12.7 + - - +
518D VAL 3.4 4.8 + - - +
519D ASP* 3.1 10.1 + - + +
521D ASN* 1.4 73.6 - - - +
523D LEU* 1.4 65.4 + - - +
525D ASN* 4.7 4.5 - - - +
526D GLU* 3.1 25.9 + - + +
250F ILE* 4.3 13.0 - - + +
251F THR* 4.1 30.5 - - + +
254F THR* 3.3 39.0 - - + +
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Residues in contact with LEU 523 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519D ASP* 2.8 20.9 + - + +
520D ALA* 3.6 12.1 - - - +
522D VAL* 1.4 72.2 - - - +
524D ILE* 1.4 61.8 + - - +
526D GLU* 5.4 0.2 - - - -
527D ARG* 3.2 13.0 + - - +
552D SER* 3.4 33.4 - - - +
553D ILE* 3.9 17.3 - - + +
556D ALA* 4.2 12.8 - - + -
212F ASN* 4.6 15.5 - - + +
216F VAL* 4.0 13.9 - - + -
247F ARG* 3.1 38.9 + - - +
251F THR* 4.0 25.4 - - + -
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Residues in contact with ILE 524 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520D ALA 3.1 9.5 + - - +
521D ASN* 3.1 21.8 - - - +
523D LEU* 1.4 77.6 - - - +
525D ASN* 1.4 65.9 + - - +
526D GLU 3.4 0.2 - - - -
527D ARG* 3.6 3.9 + - + -
528D ILE* 3.4 20.9 + - + +
549D ALA* 3.4 42.0 - - + +
550D PHE* 4.0 10.3 - - + -
553D ILE* 3.7 11.6 - - + +
597D THR* 3.9 39.5 - - - +
600D ILE* 4.1 11.5 - - + +
601D VAL* 3.9 15.3 - - + -
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Residues in contact with ASN 525 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468D MET* 3.8 17.8 - - - +
472D TYR* 3.7 27.9 - - + +
479D ALA* 4.5 5.0 - - - +
521D ASN* 2.7 49.2 + - - +
522D VAL 3.4 1.1 + - - +
524D ILE* 1.4 74.8 - - - +
526D GLU* 1.3 67.6 + - - +
527D ARG 3.4 0.2 + - - -
528D ILE 3.7 2.4 + - - -
529D LYS* 3.4 11.6 - - - +
600D ILE* 3.5 28.1 - - - +
603D LEU* 4.9 2.4 - - - +
604D LEU* 3.2 32.7 - - + +
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Residues in contact with GLU 526 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472D TYR* 2.7 34.2 + - - +
522D VAL* 3.1 19.8 + - + +
525D ASN* 1.3 78.8 - - - +
527D ARG* 1.4 61.8 + - - +
529D LYS* 2.6 36.0 + - - +
530D GLU* 3.2 42.5 - - + +
246F HIS* 5.3 4.0 + - - -
247F ARG* 3.9 41.5 - - + +
250F ILE* 3.8 21.0 - - + +
251F THR* 5.2 0.9 - - - +
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Residues in contact with ARG 527 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523D LEU 3.2 21.2 + - - +
524D ILE* 3.9 7.6 - - - +
525D ASN 3.2 0.6 - - - -
526D GLU* 1.4 75.7 - - - +
528D ILE* 1.3 62.0 + - + +
530D GLU* 4.1 1.6 - - - +
531D GLU* 3.0 65.9 + - - +
536D ARG* 4.3 25.3 - - - +
544D GLU 5.0 3.0 + - - -
545D GLY* 6.1 0.4 - - - -
548D GLY* 3.2 35.8 + - - -
549D ALA* 3.8 30.2 - - + +
551D SER* 5.5 1.8 + - - -
219F ASP* 5.8 2.6 + - - -
220F ARG* 5.3 5.1 - - - +
223F GLU* 5.0 6.7 + - - -
247F ARG* 3.9 27.4 - - - +
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Residues in contact with ILE 528 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524D ILE* 3.4 24.0 + - + +
525D ASN 3.7 0.2 + - - -
526D GLU 3.5 0.4 - - - -
527D ARG* 1.3 78.9 - - + +
529D LYS* 1.3 63.4 + - - +
531D GLU* 3.7 3.2 + - - +
532D LEU* 3.1 24.8 + - - +
545D GLY* 4.5 4.0 - - - -
549D ALA* 3.5 29.6 - - + -
600D ILE 4.8 1.3 - - - +
601D VAL* 3.8 39.3 - - + +
604D LEU* 3.8 23.1 - - + -
605D TYR* 3.5 34.0 - - + -
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Residues in contact with LYS 529 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413C LYS* 5.3 6.1 - - - +
472D TYR* 4.1 19.9 - - + -
525D ASN 3.4 16.7 + - - +
526D GLU* 2.6 43.9 + - - +
528D ILE* 1.3 80.1 - - - +
530D GLU* 1.4 68.5 + - - +
532D LEU* 3.3 9.6 - - - +
533D SER* 2.7 36.7 + - - -
604D LEU* 4.6 17.7 - - + +
612D LYS* 4.0 31.8 + - + +
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Residues in contact with GLU 530 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413C LYS* 4.3 8.5 + - - -
526D GLU* 3.2 45.0 + - + +
527D ARG* 4.1 2.0 - - - +
529D LYS* 1.4 79.6 + - + +
531D GLU* 1.4 62.5 + - + +
533D SER* 3.4 6.8 + - - -
534D ASN* 2.8 44.0 + - - +
612D LYS 4.1 13.5 - - - +
243F GLN 4.7 12.3 - - - +
244F THR* 6.0 0.2 - - - -
246F HIS* 4.4 13.7 + - - +
247F ARG* 4.3 25.0 + - + +
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Residues in contact with GLU 531 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527D ARG* 3.0 50.4 + - - +
528D ILE* 4.2 3.4 - - - +
530D GLU* 1.4 77.5 - - + +
532D LEU* 1.3 53.1 + - - +
534D ASN* 3.2 8.4 + - - +
535D GLY 3.1 10.2 + - - -
536D ARG* 2.7 66.9 + - + +
605D TYR* 5.4 1.1 - - - +
220F ARG* 2.6 53.5 + - - +
247F ARG* 5.9 0.6 + - - +
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Residues in contact with LEU 532 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528D ILE 3.1 19.0 + - - +
529D LYS* 3.3 5.4 - - - +
531D GLU* 1.3 73.5 - - - +
533D SER* 1.3 61.1 + - - +
535D GLY* 3.5 10.9 + - - -
536D ARG* 4.0 11.2 + - - +
538D VAL* 4.1 17.7 - - + -
604D LEU 3.3 26.5 - - - +
605D TYR* 3.9 37.2 + - + +
606D GLY 5.5 0.4 - - - +
608D LYS 5.4 0.9 - - - +
609D ARG* 4.9 21.0 - - + +
610D VAL 5.3 0.9 - - - +
611D LYS* 5.1 1.6 + - - +
612D LYS* 4.2 25.4 - - + -
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Residues in contact with SER 533 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C LYS* 4.6 0.5 + - - -
529D LYS 2.7 21.0 + - - -
530D GLU* 3.5 14.4 + - - -
532D LEU* 1.3 73.1 - - - +
534D ASN* 1.3 59.9 + - - +
535D GLY 3.3 1.2 + - - -
611D LYS* 2.9 41.2 + - - +
612D LYS 2.6 43.9 + - - +
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Residues in contact with ASN 534 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530D GLU* 2.8 34.1 + - - +
531D GLU* 3.2 8.6 + - - +
533D SER* 1.3 73.5 + - - +
535D GLY* 1.4 56.8 + - - +
536D ARG 3.7 0.4 - - - -
611D LYS* 4.9 2.9 - - - +
15F LYS* 5.9 0.5 + - - -
220F ARG* 4.2 21.4 + - - +
243F GLN* 3.8 46.5 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il