Contacts of the helix formed by residues 547 - 588 (chain A) in PDB entry 1HCI
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 547 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A VAL* 4.4 0.5 - - - +
546A HIS* 1.3 81.2 - - - +
548A ILE* 1.3 63.9 + - - +
549A GLU* 3.4 10.3 + - - +
550A GLU* 3.1 37.6 + - - +
551A ILE 3.3 9.7 + - - -
632A GLN* 3.2 13.9 + - - +
639A ARG* 5.1 2.7 - - - +
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Residues in contact with ILE 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A SER* 1.3 73.3 - - - +
549A GLU* 1.3 62.2 + - - +
551A ILE* 2.9 28.6 - - + +
552A GLN* 3.0 37.3 - - + +
629A LEU* 4.9 0.9 - - + -
632A GLN* 3.6 23.0 + - + +
633A HIS* 3.0 47.6 - - + +
636A GLU* 3.5 30.4 - - + +
639A ARG* 5.8 0.4 - - - +
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Residues in contact with GLU 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A SER* 3.1 8.6 + - - +
548A ILE* 1.3 79.9 - - - +
550A GLU* 1.3 64.1 + - - +
552A GLN* 3.2 13.5 + - - +
553A SER* 3.2 23.6 + - - +
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Residues in contact with GLU 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A ILE 4.6 1.2 - - - +
545A VAL* 3.3 21.9 - - + -
546A HIS* 2.8 36.2 + - - +
547A SER* 3.1 25.6 + - - +
549A GLU* 1.3 76.0 - - + +
551A ILE* 1.3 64.2 + - - +
552A GLN 2.9 1.7 + - - -
553A SER* 3.0 19.2 + - - -
554A LEU* 3.4 12.1 + - - +
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Residues in contact with ILE 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A PHE* 4.4 2.2 - - + -
545A VAL* 3.9 17.2 - - + +
547A SER 3.3 5.9 + - - +
548A ILE* 2.9 34.3 - - - +
550A GLU* 1.3 75.6 - - - +
552A GLN* 1.3 58.6 + - - +
554A LEU* 3.6 12.8 - - + +
555A ILE* 3.2 23.0 + - + +
625A LEU* 3.9 28.9 - - + +
628A GLU* 3.4 26.2 - - + -
629A LEU* 3.8 34.1 - - + +
632A GLN* 3.9 11.0 - - + -
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Residues in contact with GLN 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A ILE* 3.0 40.5 + - + +
549A GLU* 3.6 11.1 - - - +
550A GLU 2.9 1.0 + - - -
551A ILE* 1.3 75.3 - - - +
553A SER* 1.3 57.0 + - - +
554A LEU 3.1 1.6 - - - -
555A ILE* 3.0 10.1 + - + +
556A THR* 2.7 39.7 + - - +
629A LEU* 4.4 16.7 - - + +
633A HIS* 5.1 4.0 + - - -
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Residues in contact with SER 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A GLU* 3.2 17.4 + - - +
550A GLU* 3.0 11.1 + - - -
552A GLN* 1.3 75.8 - - - +
554A LEU* 1.3 62.8 + - - +
556A THR* 3.2 8.7 + - - -
557A ALA* 2.9 30.5 + - - +
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Residues in contact with LEU 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543A PHE* 3.5 47.8 - - + -
545A VAL* 4.3 14.6 - - + -
550A GLU 3.4 7.2 + - - +
551A ILE* 3.6 20.9 - - + +
552A GLN 3.1 0.2 - - - -
553A SER* 1.3 83.4 - - - +
555A ILE* 1.3 57.5 + - - +
557A ALA* 3.6 6.1 - - - +
558A HIS* 3.1 28.6 + - - +
621A ARG* 5.6 3.1 - - - +
625A LEU* 3.9 13.5 - - + +
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Residues in contact with ILE 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A ILE* 3.2 22.6 + - + +
552A GLN* 3.0 12.4 + - + +
554A LEU* 1.3 76.8 - - - +
556A THR* 1.3 66.9 + - - +
557A ALA 3.1 0.2 - - - -
558A HIS* 3.4 1.3 + - - +
559A GLU* 2.9 31.7 + - + +
625A LEU* 3.8 28.9 - - + +
626A GLN* 5.8 0.9 - - - +
629A LEU* 4.0 37.7 - - + -
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Residues in contact with THR 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A GLN* 2.7 25.9 + - - +
553A SER* 3.6 8.2 - - - -
555A ILE* 1.3 73.7 - - - +
557A ALA* 1.3 63.6 + - - +
559A GLU* 3.3 17.5 + - - +
560A GLN* 3.0 47.9 + - + +
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Residues in contact with ALA 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553A SER 2.9 16.7 + - - +
554A LEU* 3.6 8.3 - - + +
556A THR* 1.3 77.4 - - - +
558A HIS* 1.3 58.4 + - - +
560A GLN* 2.9 29.6 + - - +
561A PHE* 2.9 13.3 + - - +
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Residues in contact with HIS 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A LEU* 5.2 5.3 - - + +
554A LEU 3.1 15.8 + - - +
555A ILE* 3.9 2.9 + - - +
557A ALA* 1.3 79.6 - - - +
559A GLU* 1.3 62.5 + - - +
561A PHE* 3.3 15.6 + + - +
562A LYS* 3.0 63.6 + - + +
618A VAL* 4.0 10.9 + - + +
621A ARG* 3.6 39.5 - - + +
622A ASP* 3.6 21.3 - - + +
625A LEU* 3.6 15.0 - - + +
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Residues in contact with GLU 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A ILE* 2.9 23.7 + - + +
556A THR* 3.3 20.6 + - - +
558A HIS* 1.3 78.1 + - - +
560A GLN* 1.3 64.8 + - + +
562A LYS* 3.3 16.9 + - - +
563A ALA* 3.1 19.6 + - - +
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Residues in contact with GLN 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556A THR* 3.0 33.7 + - + +
557A ALA* 2.9 11.4 + - - +
559A GLU* 1.3 75.5 - - + +
561A PHE* 1.3 68.5 + - - +
563A ALA* 3.1 20.6 + - - +
564A THR* 3.4 11.0 - - - +
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Residues in contact with PHE 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531A TRP* 3.8 24.9 - + - -
535A ALA* 4.0 19.3 - - + -
538A ASP* 5.9 4.9 - - + -
539A LEU* 3.6 29.8 - - + -
557A ALA 2.9 12.8 + - - +
558A HIS* 3.4 17.9 - + - +
559A GLU 3.2 0.2 - - - -
560A GLN* 1.3 76.3 - - - +
562A LYS* 1.3 70.7 + - + +
564A THR* 2.6 48.9 + - - -
565A LEU* 3.5 27.1 + - + -
614A VAL* 4.4 3.4 - - + -
618A VAL* 4.3 15.0 - - + -
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Residues in contact with LYS 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558A HIS* 3.0 34.3 + - + +
559A GLU* 3.6 13.9 - - - +
561A PHE* 1.3 87.4 - - + +
563A ALA* 1.3 62.2 + - - +
565A LEU* 3.1 31.5 + - + +
566A PRO* 3.6 3.5 - - - +
618A VAL* 3.3 29.8 - - + -
622A ASP* 2.9 26.9 + - - +
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Residues in contact with ALA 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559A GLU 3.1 11.1 + - - +
560A GLN* 3.1 18.4 - - - +
561A PHE 2.8 0.8 + - - -
562A LYS* 1.3 77.2 - - - +
564A THR* 1.3 58.1 + - + +
566A PRO* 2.9 20.5 - - - +
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Residues in contact with THR 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531A TRP* 4.2 12.9 + - - -
560A GLN 3.4 11.7 - - - +
561A PHE* 2.6 43.9 + - + +
563A ALA* 1.3 72.3 - - + +
565A LEU* 1.3 63.8 + - - +
566A PRO* 3.0 5.9 - - - +
567A GLU* 3.4 14.4 + - - +
568A ALA* 3.1 19.4 + - - +
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Residues in contact with LEU 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531A TRP* 3.9 24.9 - - + -
561A PHE* 4.0 15.0 - - + -
562A LYS* 3.1 33.7 + - + +
564A THR* 1.3 79.3 + - - +
566A PRO* 1.3 68.5 - - + +
568A ALA* 3.1 4.4 + - - +
569A ASP* 3.0 19.9 + - - +
611A TRP* 3.8 13.6 - - + -
614A VAL* 4.2 11.4 - - + -
615A LYS* 4.2 24.4 + - + +
618A VAL* 4.0 25.8 - - + -
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Residues in contact with PRO 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562A LYS 3.6 5.8 - - - +
563A ALA* 2.9 24.5 - - - +
564A THR* 3.8 1.3 - - - +
565A LEU* 1.3 95.0 - - + +
567A GLU* 1.3 70.8 + - + +
569A ASP* 2.9 15.7 + - + +
570A GLY* 3.1 7.4 + - - -
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Residues in contact with GLU 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564A THR* 3.6 16.4 - - - +
566A PRO* 1.3 84.2 - - + +
568A ALA* 1.3 63.5 + - - +
570A GLY* 2.8 18.5 + - - +
571A GLU* 2.9 17.7 + - - +
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Residues in contact with ALA 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528A PHE* 3.6 13.7 - - + -
531A TRP* 3.7 26.5 - - + -
564A THR 3.1 12.1 + - - +
565A LEU 3.1 12.8 - - - +
567A GLU* 1.3 88.5 + - - +
569A ASP* 1.3 57.5 + - - +
571A GLU* 3.3 3.0 + - - +
572A ARG* 3.0 21.8 + - - +
611A TRP* 3.6 20.2 - - + -
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Residues in contact with ASP 569 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565A LEU 3.0 7.5 + - - +
566A PRO* 2.9 11.3 + - + +
568A ALA* 1.3 73.8 - - - +
570A GLY* 1.3 69.9 + - - +
572A ARG* 2.7 41.8 + - - -
573A GLN* 3.0 32.9 + - - +
611A TRP* 3.4 24.4 + - + -
615A LYS* 5.4 2.9 + - - -
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Residues in contact with GLY 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566A PRO 3.1 8.3 + - - -
567A GLU* 2.8 12.8 + - - -
569A ASP* 1.3 83.6 - - - +
571A GLU* 1.3 60.3 + - - -
573A GLN* 3.1 7.0 + - - +
574A SER* 2.9 22.5 + - - -
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Residues in contact with GLU 571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524A ARG* 3.0 47.8 + - - +
528A PHE* 3.8 24.0 - - + -
567A GLU* 2.9 16.2 + - - +
568A ALA* 3.6 8.3 - - - +
570A GLY* 1.3 70.8 - - - +
572A ARG* 1.3 65.7 - - - +
574A SER* 3.5 4.6 - - - -
575A ILE* 2.9 38.9 + - + +
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Residues in contact with ARG 572 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528A PHE* 3.8 24.9 - - + -
568A ALA 3.0 14.2 + - - +
569A ASP* 2.7 33.5 + - - +
571A GLU* 1.3 78.6 - - - +
573A GLN* 1.3 86.1 + - - +
575A ILE* 3.1 5.9 + - - +
576A MET* 3.0 54.7 + - + +
607A LEU* 5.8 4.7 - - + +
608A ARG* 3.7 24.6 - - - +
611A TRP* 3.4 37.4 - - + +
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Residues in contact with GLN 573 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569A ASP* 3.0 24.1 + - - +
570A GLY* 3.7 7.3 - - - +
572A ARG* 1.3 104.5 + - - +
574A SER* 1.3 65.0 + - - +
576A MET* 2.9 13.7 + - - +
577A ALA* 2.8 21.6 + - - +
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Residues in contact with SER 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A ARG* 2.9 32.3 + - - -
570A GLY 2.9 14.5 + - - -
571A GLU* 3.5 9.9 - - - -
573A GLN* 1.3 75.4 - - - +
575A ILE* 1.3 62.7 + - - +
577A ALA* 3.0 22.9 - - - +
578A ILE* 3.2 11.1 + - - +
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Residues in contact with ILE 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521A PHE* 3.8 15.2 - - + +
524A ARG* 3.3 39.0 - - + +
525A ALA* 4.0 5.2 - - + +
528A PHE* 3.8 20.4 - - + -
571A GLU* 2.9 44.4 + - + +
572A ARG* 3.5 4.5 - - - +
574A SER* 1.3 70.7 - - - +
576A MET* 1.3 62.1 + - - +
577A ALA 3.0 6.1 + - - -
578A ILE* 3.1 20.5 + - + +
579A GLN 3.2 8.7 + - - -
604A MET* 3.2 21.0 - - + +
607A LEU* 3.8 14.4 - - + -
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Residues in contact with MET 576 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572A ARG* 3.0 47.6 + - + +
573A GLN* 2.9 11.3 + - - +
575A ILE* 1.3 76.5 - - - +
577A ALA* 1.3 57.2 + - - +
579A GLN* 3.7 2.3 + - - +
580A ASN* 2.5 36.6 + - - +
604A MET* 3.1 43.5 - - + +
607A LEU* 5.7 0.4 - - + -
608A ARG* 3.8 37.0 - - + -
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Residues in contact with ALA 577 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573A GLN 2.8 10.2 + - - +
574A SER* 3.0 15.3 - - - +
576A MET* 1.3 76.4 - - - +
578A ILE* 1.3 70.6 + - + +
580A ASN* 2.7 19.9 + - - +
581A GLU* 3.1 11.2 + - - +
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Residues in contact with ILE 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517A LEU* 3.6 34.1 - - + +
520A GLU* 3.1 41.1 - - + +
521A PHE* 3.7 19.7 - - + +
524A ARG* 3.8 24.2 - - + +
574A SER 3.8 10.1 - - - +
575A ILE* 3.1 11.2 + - - +
577A ALA* 1.3 80.7 - - + +
579A GLN* 1.3 65.6 + - - +
581A GLU* 3.3 13.0 + - - +
582A VAL* 3.3 13.2 + - + +
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Residues in contact with GLN 579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518A HIS* 5.1 2.8 - - - -
521A PHE* 3.5 29.4 - - + +
575A ILE 3.2 2.8 + - - -
576A MET 3.8 8.3 - - - +
577A ALA 3.1 0.8 - - - -
578A ILE* 1.3 80.1 - - - +
580A ASN* 1.3 64.9 + - - +
582A VAL* 3.2 13.3 + - - +
583A GLU* 3.0 62.7 + - - +
595A SER* 4.6 11.6 - - - +
597A ASN* 4.7 7.9 - - - +
604A MET* 3.9 38.3 - - + +
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Residues in contact with ASN 580 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576A MET* 2.5 25.9 + - - +
577A ALA* 2.7 17.7 + - - +
579A GLN* 1.3 77.1 - - - +
581A GLU* 1.3 56.7 + - - +
583A GLU* 3.4 9.4 + - - +
584A LYS* 2.8 29.6 + - - +
604A MET* 6.0 0.7 - - - +
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Residues in contact with GLU 581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513A THR* 4.3 6.4 - - - +
517A LEU* 3.4 29.6 - - + +
577A ALA 3.1 9.9 + - - +
578A ILE* 3.3 9.8 + - - +
580A ASN* 1.3 71.2 - - - +
582A VAL* 1.3 69.0 + - - +
584A LYS* 2.7 25.5 + - - +
585A VAL* 2.7 32.5 + - + +
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Residues in contact with VAL 582 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ILE* 4.0 13.7 - - + -
517A LEU* 3.1 41.0 - - + +
518A HIS* 3.4 37.2 - - + +
578A ILE* 3.4 13.0 - - + +
579A GLN* 3.2 15.2 + - - +
581A GLU* 1.3 82.8 - - - +
583A GLU* 1.3 65.1 + - + +
584A LYS 2.8 2.8 + - - -
585A VAL* 3.2 6.0 + - - +
586A ILE* 3.1 29.0 + - + +
595A SER 4.5 3.1 - - - +
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Residues in contact with GLU 583 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A GLN* 3.0 50.7 + - - +
580A ASN* 3.8 7.7 + - - +
582A VAL* 1.3 80.2 - - + +
584A LYS* 1.3 57.6 + - - +
586A ILE* 4.1 3.1 - - - +
587A GLN* 3.2 32.0 + - + +
595A SER* 4.2 27.0 + - - +
604A MET* 5.5 0.5 - - - +
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Residues in contact with LYS 584 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A ASN 2.8 14.2 + - - +
581A GLU* 2.7 27.5 + - - +
583A GLU* 1.3 69.7 - - - +
585A VAL* 1.3 93.1 + - - +
586A ILE 3.1 1.1 - - - -
587A GLN* 3.0 8.1 + - - +
588A SER* 2.9 36.1 + - - +
589A TYR* 5.7 1.6 + - - -
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Residues in contact with VAL 585 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A LEU* 6.2 1.6 - - + -
513A THR* 4.7 10.5 - - + -
514A ILE* 3.5 32.5 - - + -
517A LEU* 4.7 2.2 - - + -
581A GLU* 2.7 40.8 + - - +
582A VAL* 3.3 12.3 - - - +
584A LYS* 1.3 89.3 - - - +
586A ILE* 1.3 68.6 + - - +
588A SER* 3.1 12.7 + - - -
589A TYR* 2.7 37.6 - - + -
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Residues in contact with ILE 586 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ILE* 3.4 31.0 - - + -
518A HIS* 5.0 0.9 - - + -
582A VAL* 3.1 25.9 + - + +
583A GLU* 4.1 4.7 - - - +
585A VAL* 1.3 87.6 - - - +
587A GLN* 1.3 67.4 + - + +
588A SER 2.9 0.5 + - - -
589A TYR 3.0 9.4 + - - -
590A ASN* 3.4 3.1 + - - -
591A ILE* 3.1 39.9 + - + +
592A ARG 4.5 3.6 - - - +
593A ILE* 3.9 12.1 - - + +
595A SER* 3.7 38.4 - - - +
----------------------------------------------------------
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Residues in contact with GLN 587 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A GLU* 3.2 19.6 + - + +
584A LYS* 3.0 6.8 + - - +
586A ILE* 1.3 82.5 - - + +
588A SER* 1.3 56.7 + - - +
589A TYR 3.2 4.1 + - - -
590A ASN* 3.8 9.6 + - - +
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Residues in contact with SER 588 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A LYS* 2.9 30.4 + - - +
585A VAL* 3.1 16.1 + - - -
586A ILE 2.9 0.8 + - - -
587A GLN* 1.3 73.0 - - - +
589A TYR* 1.3 81.4 + - - +
590A ASN* 4.9 0.4 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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