Contacts of the helix formed by residues 587 - 617 (chain A) in PDB entry 4L6V
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 GLY 587 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A ALA* 4.6 4.0 - - - +
552A GLY 4.0 21.3 - - - -
556A ALA* 5.1 10.7 + - - +
565A LYS* 5.2 0.4 - - - +
569A GLY 5.4 0.2 + - - -
570A PHE* 3.3 23.2 + - - +
586A SER* 1.3 71.8 - - - +
588A TRP* 1.3 63.5 + - - +
590A HIS* 3.0 15.5 + - - +
591A VAL* 3.1 17.0 + - - +
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Residues in contact with TRP 588 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A PHE* 3.2 45.2 + + + +
571A ARG* 3.7 33.1 - - + +
572A PHE 5.0 0.2 - - - +
586A SER* 3.2 4.2 - - - +
587A GLY* 1.3 75.6 - - - +
589A ASP* 1.3 78.1 + - - +
591A VAL* 3.1 10.2 + - + +
592A PHE* 2.9 46.4 + + + -
721A ILE* 3.7 37.9 - - + -
724A ARG* 4.1 8.3 - - + -
725A ALA* 3.8 30.1 - - + -
728A VAL* 5.7 1.8 - - + -
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Residues in contact with ASP 589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A PHE 3.1 14.2 - - - +
573A PRO 3.4 5.7 - - - +
584A GLN* 3.4 29.0 - - + +
586A SER* 2.5 25.7 + - - +
587A GLY 3.2 0.6 - - - -
588A TRP* 1.3 94.3 - - - +
590A HIS* 1.3 58.6 + - - +
591A VAL 3.4 0.2 - - - -
592A PHE* 3.5 9.4 - - + +
593A LEU* 3.4 30.5 + - - +
721A ILE* 4.0 1.3 - - - +
724A ARG* 2.5 34.0 + - - -
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Residues in contact with HIS 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A ILE* 3.3 37.6 - - + +
549A LEU* 3.6 7.6 - - - +
551A LYS* 3.3 37.9 + - + +
552A GLY* 3.3 31.0 - - - -
555A TYR* 5.5 2.0 - - + -
565A LYS* 4.8 4.3 - - - -
584A GLN 4.4 8.7 - - - -
585A VAL* 3.4 24.2 + - - -
586A SER 2.9 19.8 + - - -
587A GLY* 3.0 10.1 + - - +
589A ASP* 1.3 77.9 - - - +
591A VAL* 1.3 59.6 + - - +
592A PHE 3.3 0.2 - - - -
593A LEU* 5.1 3.6 - - + -
594A GLY* 3.1 20.3 + - - -
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Residues in contact with VAL 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A VAL* 4.0 21.3 - - + +
403A GLY* 5.7 0.2 - - - -
405A GLY 4.4 3.6 - - - +
406A ALA* 3.5 43.3 - - + +
549A LEU* 4.2 7.9 - - + -
570A PHE* 4.4 6.7 - - + -
587A GLY 3.1 13.4 + - - +
588A TRP* 3.1 12.4 + - + +
590A HIS* 1.3 76.2 - - + +
592A PHE* 1.3 65.2 + - - +
594A GLY 3.7 0.5 - - - -
595A LEU* 3.0 32.5 + - + +
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Residues in contact with PHE 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A GLN* 3.7 25.6 - - - -
588A TRP* 2.9 29.3 + + + +
589A ASP* 3.5 14.8 - - - +
591A VAL* 1.3 80.6 - - - +
593A LEU* 1.3 90.3 + - + +
595A LEU* 3.3 13.6 + - - +
596A PHE* 3.2 37.2 - + - -
686A LEU* 3.6 24.2 - - + -
724A ARG* 3.1 47.1 - - + -
728A VAL* 4.0 8.7 - - + +
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Residues in contact with LEU 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A ILE* 3.9 21.3 - - + +
584A GLN* 4.1 21.8 - - + +
589A ASP 3.4 15.6 + - - +
590A HIS* 5.7 3.8 - - + -
592A PHE* 1.3 104.9 - - + +
594A GLY* 1.3 65.8 + - - +
595A LEU 3.3 0.5 + - - -
596A PHE* 3.4 20.0 + - + +
597A TRP* 3.5 18.5 + - + -
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Residues in contact with GLY 594 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A VAL* 4.1 3.8 - - - +
545A THR* 3.7 7.9 - - - +
548A ILE* 3.5 15.8 - - - +
549A LEU* 4.0 14.8 - - - -
590A HIS 3.1 20.5 + - - -
591A VAL 3.3 2.9 + - - -
592A PHE 3.2 0.6 - - - -
593A LEU* 1.3 77.9 - - - +
595A LEU* 1.3 57.5 + - - +
596A PHE 3.5 0.2 - - - -
597A TRP* 3.6 1.1 + - - -
598A MET* 3.1 27.5 + - - +
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Residues in contact with LEU 595 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A PHE* 4.1 13.0 - - + -
402A VAL* 3.8 21.1 - - + -
591A VAL* 3.0 24.8 + - + +
592A PHE* 3.5 11.0 - - - +
593A LEU 3.1 0.8 - - - -
594A GLY* 1.3 77.3 - - - +
596A PHE* 1.3 66.2 + - - +
598A MET* 3.3 19.1 + - + +
599A TYR* 3.0 24.1 + - - +
728A VAL* 3.8 33.9 - - + -
732A LEU* 3.9 22.5 - - + +
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Residues in contact with PHE 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A PHE* 3.2 48.0 - + - -
593A LEU* 3.4 14.7 + - + +
595A LEU* 1.3 77.2 - - - +
597A TRP* 1.3 62.4 + - + +
599A TYR* 3.4 9.5 + - - +
600A ASN* 2.8 29.0 + - - +
686A LEU* 3.8 25.8 - - + -
728A VAL* 3.7 26.7 - - + -
731A TYR* 3.7 46.4 - + + -
732A LEU* 4.6 1.6 - - + -
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Residues in contact with TRP 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A PHE* 4.0 19.3 - + - -
541A THR* 3.8 35.4 - - + -
544A VAL* 3.4 43.0 - - + +
545A THR* 3.2 13.9 + - - +
548A ILE* 3.3 30.8 - - + +
593A LEU* 3.5 9.6 + - + +
594A GLY 4.1 3.4 - - - +
595A LEU 3.2 0.6 - - - -
596A PHE* 1.3 80.1 - - + +
598A MET* 1.3 61.3 + - - +
599A TYR 3.2 0.7 - - - -
600A ASN* 4.2 17.5 - - + -
601A SER* 2.9 30.7 + - - -
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Residues in contact with MET 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A TRP* 4.1 16.4 - - + -
398A GLY* 3.2 35.9 - - - +
399A PHE* 3.6 46.4 - - + -
401A ILE* 5.1 3.4 - - + -
402A VAL* 3.4 20.4 - - + -
545A THR* 3.8 11.6 - - + +
594A GLY 3.1 10.9 + - - +
595A LEU* 3.6 19.3 - - + +
597A TRP* 1.3 76.7 - - - +
599A TYR* 1.3 63.7 + - + +
601A SER* 4.4 2.0 - - - -
602A LEU* 3.1 29.8 + - + +
732A LEU* 4.9 1.8 - - + -
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Residues in contact with TYR 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A TRP* 3.5 23.8 - + + -
595A LEU 3.0 13.2 + - - +
596A PHE 3.4 9.2 - - - +
598A MET* 1.3 75.5 - - + +
600A ASN* 1.3 74.0 + - + +
601A SER 3.2 0.2 + - - -
602A LEU 3.2 1.4 + - - -
603A SER* 2.9 45.9 + - - -
679A PHE* 6.1 0.2 - - - -
731A TYR* 4.3 24.0 - + - -
732A LEU* 3.6 26.2 - - + -
735A GLY* 2.9 48.3 + - - -
736A ILE* 3.8 15.5 - - + -
739A THR* 4.7 0.5 + - - -
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Residues in contact with ASN 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A THR* 3.9 16.1 - - - +
596A PHE 2.8 20.6 + - - +
597A TRP* 4.1 22.8 - - + +
599A TYR* 1.3 82.8 - - + +
601A SER* 1.3 63.2 + - - +
603A SER* 3.8 5.2 + - - -
604A ILE* 3.3 27.5 + - - +
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Residues in contact with SER 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A HIS* 4.6 0.2 - - - -
541A THR* 3.0 45.0 + - - -
542A ILE* 4.0 12.1 + - - +
545A THR* 4.1 3.4 - - - -
597A TRP 2.9 21.9 + - - -
598A MET* 3.7 4.7 - - - -
600A ASN* 1.3 78.3 - - - +
602A LEU* 1.3 71.6 + - - +
604A ILE* 3.3 14.9 + - - +
605A VAL* 3.4 15.5 + - - +
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Residues in contact with LEU 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ILE* 5.7 5.4 - - + -
394A MET* 3.0 53.2 - - + +
395A TRP* 3.5 34.8 - - + +
398A GLY* 3.8 15.0 - - - -
401A ILE* 5.8 2.7 - - + -
542A ILE* 6.2 1.6 - - + -
598A MET* 3.1 18.8 + - + +
601A SER* 1.3 86.4 - - - +
603A SER* 1.3 65.6 + - - +
604A ILE 3.1 1.8 - - - -
605A VAL* 2.9 11.3 + - + +
606A ILE* 2.9 27.9 + - + +
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Residues in contact with SER 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A TRP* 3.6 8.8 - - - -
599A TYR* 2.9 44.4 + - - -
600A ASN* 4.0 7.9 - - - -
601A SER 3.3 0.2 - - - -
602A LEU* 1.3 76.9 - - - +
604A ILE* 1.3 61.5 + - - +
606A ILE* 3.2 11.9 - - - +
607A PHE* 3.0 46.6 + - - -
739A THR* 5.3 2.9 + - - -
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Residues in contact with ILE 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A VAL* 5.4 7.2 - - + +
537A ILE* 3.8 28.7 - - + -
538A HIS* 3.5 15.0 - - + +
541A THR* 4.9 3.8 - - + -
600A ASN* 3.3 26.0 - - - +
601A SER* 3.3 7.4 + - - +
602A LEU 3.1 0.6 - - - -
603A SER* 1.3 79.0 - - - +
605A VAL* 1.3 60.1 + - - +
607A PHE* 3.8 12.2 - - + +
608A HIS* 2.8 28.4 + - + +
645A TRP* 5.2 5.1 - - + -
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Residues in contact with VAL 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A GLN* 5.4 3.1 - - - +
390A PHE* 4.5 7.9 - - + -
394A MET* 3.5 35.9 - - + -
538A HIS* 3.2 36.3 - - + +
542A ILE* 6.2 3.1 - - + -
601A SER* 3.5 15.7 - - - +
602A LEU* 2.9 19.6 + - + +
604A ILE* 1.3 78.0 - - - +
606A ILE* 1.3 57.9 + - + +
608A HIS* 3.3 3.5 + - - +
609A PHE* 2.9 25.8 + - - +
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Residues in contact with ILE 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A PHE* 4.5 1.8 - - + -
391A THR* 3.4 38.7 - - + +
394A MET* 4.3 17.9 - - + -
395A TRP* 3.9 33.7 - - + +
602A LEU* 2.9 15.9 + - + +
603A SER* 3.2 19.3 - - - +
605A VAL* 1.3 76.0 - - + +
607A PHE* 1.3 64.3 + - + +
609A PHE* 3.7 7.8 - - - +
610A SER* 3.0 29.5 + - - -
739A THR* 3.9 16.4 - - + +
743A PHE* 3.4 21.1 - - + -
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Residues in contact with PHE 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A SER* 3.0 32.4 + - - +
604A ILE* 3.8 13.7 - - + +
606A ILE* 1.3 77.6 - - + +
608A HIS* 1.3 66.1 + - - +
611A TRP* 3.3 17.2 + - - +
645A TRP* 3.5 28.6 - + + -
649A PHE* 3.7 20.1 - + + -
650A LEU* 4.0 26.7 - - + -
739A THR* 3.2 35.7 - - + -
742A PHE* 4.4 6.1 - + - -
743A PHE* 3.7 15.5 - + - -
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Residues in contact with HIS 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A ASP* 4.1 15.2 + - - -
534A VAL* 3.1 39.5 - - + +
535A HIS* 4.2 21.8 - + - -
538A HIS* 3.4 22.3 - + + +
604A ILE* 2.8 19.1 + - + +
605A VAL 3.4 5.6 - - - +
607A PHE* 1.3 76.6 - - - +
609A PHE* 1.3 64.9 + - - +
611A TRP* 4.3 0.5 - - - +
612A LYS* 3.0 36.6 + - + +
635A PHE* 4.4 5.0 - + - -
645A TRP* 4.0 13.4 - - + -
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Residues in contact with PHE 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A GLN* 5.7 0.7 - - - -
371A TYR* 3.6 38.4 - + + -
386A GLN* 4.0 5.6 - - + -
387A LEU* 3.6 37.0 - - + -
390A PHE* 3.4 61.7 - + + -
605A VAL 2.9 11.6 + - - +
606A ILE 3.7 4.5 - - - +
607A PHE 3.3 0.2 - - - -
608A HIS* 1.3 81.8 - - - +
610A SER* 1.3 65.1 + - - +
612A LYS* 4.8 0.9 - - - -
613A MET* 3.1 45.9 + - + +
618A TRP* 4.1 16.8 - + - -
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Residues in contact with SER 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A LEU* 3.9 17.0 - - - +
606A ILE 3.0 18.5 + - - -
607A PHE 4.1 0.2 - - - -
608A HIS 3.4 0.2 - - - -
609A PHE* 1.3 78.3 - - - +
611A TRP* 1.3 61.4 + - - +
613A MET* 4.3 1.0 - - - +
614A GLN* 3.1 48.7 + - - +
618A TRP* 4.3 2.3 - - - -
649A PHE* 3.6 15.2 - - - -
653A GLN* 3.9 1.0 + - - -
742A PHE* 5.3 0.2 - - - -
743A PHE* 3.5 26.5 - - - -
746A ARG* 5.3 0.2 - - - +
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Residues in contact with TRP 611 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A PHE 3.3 11.7 + - - +
610A SER* 1.3 76.4 - - - +
612A LYS* 1.3 56.7 + - - +
614A GLN* 4.4 1.8 - - - -
615A SER* 2.7 45.8 + - - -
631A THR* 3.7 9.6 - - + +
634A ASN* 3.3 24.9 + - - +
635A PHE* 3.5 19.3 - + + -
638A SER* 3.7 11.4 - - - -
639A ALA* 3.4 31.9 - - + -
644A GLY 3.8 13.2 - - - -
645A TRP* 3.4 49.4 - + - -
648A ASP* 3.8 26.8 + - + -
649A PHE* 3.5 20.6 - + + -
653A GLN* 3.8 15.5 - - - +
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Residues in contact with LYS 612 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A ILE* 3.7 30.5 - - + -
526A THR* 3.2 17.2 + - - +
528A GLY 5.3 0.2 - - - +
531A ASP* 2.9 40.7 + - - +
608A HIS* 3.0 33.5 + - + +
609A PHE* 4.2 2.2 - - - +
611A TRP* 1.3 77.8 - - - +
613A MET* 1.3 60.9 + - + +
615A SER* 4.7 0.2 - - - -
616A ASP* 2.8 63.1 + - - +
617A VAL* 3.7 2.6 + - + +
635A PHE* 3.9 19.5 - - + -
636A ALA* 6.1 1.4 - - - +
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Residues in contact with MET 613 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A TYR* 4.1 16.4 - - + +
386A GLN* 5.7 2.2 - - - +
522A MET* 4.0 21.3 - - + -
525A ILE* 3.9 14.8 - - + -
609A PHE* 3.1 39.0 + - + +
612A LYS* 1.3 78.0 - - + +
614A GLN* 1.3 62.4 + - - +
617A VAL* 3.2 38.4 + - + -
618A TRP* 2.6 69.9 + - + +
----------------------------------------------------------
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Residues in contact with GLN 614 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A LEU* 5.4 3.4 - - - +
610A SER* 3.1 34.3 + - - +
611A TRP* 3.7 3.8 - - - +
613A MET* 1.3 80.4 - - - +
615A SER* 1.3 62.2 + - - +
618A TRP* 3.6 26.2 - - + +
629A HIS* 3.7 3.1 - - - +
630A VAL* 3.3 37.7 + - + +
631A THR* 3.3 6.7 - - - +
653A GLN* 3.2 24.9 + - - +
746A ARG* 2.5 53.3 + - - +
747A SER* 5.7 1.6 - - - +
750A ILE* 4.9 6.9 - - + +
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Residues in contact with SER 615 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A TRP* 2.7 23.4 + - - -
612A LYS 4.2 0.2 - - - -
614A GLN* 1.3 75.6 - - - +
616A ASP* 1.3 65.3 + - - +
617A VAL 3.7 0.4 - - - -
629A HIS* 3.1 20.8 - - - +
631A THR* 3.3 18.8 - - - +
633A GLY* 3.1 10.2 + - - -
634A ASN* 3.1 14.6 + - - -
635A PHE* 3.1 37.2 + - - -
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Residues in contact with ASP 616 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A MET* 4.9 3.5 - - - +
524A PRO 4.5 9.5 - - - +
525A ILE* 5.3 1.8 - - + -
526A THR* 5.5 5.6 - - - +
612A LYS* 2.8 47.7 + - - +
615A SER* 1.3 93.3 + - - +
617A VAL* 1.3 66.5 + - + +
629A HIS* 3.8 16.0 + - - -
633A GLY* 3.3 14.4 - - - +
635A PHE* 3.4 19.3 - - - +
636A ALA* 4.4 6.5 + - - +
----------------------------------------------------------
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Residues in contact with VAL 617 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A VAL* 3.5 10.9 - - + +
522A MET* 4.7 5.4 - - + -
523A MET* 3.3 49.8 - - + +
525A ILE* 3.8 24.5 - - + -
612A LYS 3.9 3.6 - - - +
613A MET* 3.2 51.2 + - + +
616A ASP* 1.3 86.6 - - + +
618A TRP* 1.3 76.0 + - + +
629A HIS* 3.4 6.1 + - - -
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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