Contacts of the helix formed by residues 553 - 583 (chain A) in PDB entry 5QSY
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 THR 553 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A VAL 5.3 1.3 - - - +
552A LEU* 1.3 76.3 - - - +
554A ALA* 1.3 59.3 + - - +
555A LYS* 3.5 8.3 + - - +
556A GLU* 3.0 42.7 + - - +
557A ARG* 3.0 27.9 + - - +
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Residues in contact with ALA 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A THR* 1.3 74.6 - - - +
555A LYS* 1.3 58.8 + - - +
557A ARG* 3.4 6.2 + - - +
558A LYS* 2.9 29.7 + - - +
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Residues in contact with LYS 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A THR* 3.3 7.0 + - - +
554A ALA* 1.3 77.0 - - - +
556A GLU* 1.3 56.6 + - + +
558A LYS* 3.4 9.7 + - + +
559A THR* 2.7 46.0 + - - +
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Residues in contact with GLU 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A ALA* 5.3 2.6 - - + +
551A VAL 4.2 2.9 - - - +
552A LEU* 3.5 30.1 - - + +
553A THR* 3.0 42.8 + - - +
555A LYS* 1.3 74.9 - - + +
557A ARG* 1.3 57.9 + - - +
559A THR* 3.2 7.9 + - - -
560A GLN* 2.9 30.2 + - - +
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Residues in contact with ARG 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A LEU* 4.3 16.8 - - + +
553A THR 3.0 18.1 + - - +
554A ALA* 3.6 6.7 - - - +
556A GLU* 1.3 76.6 - - - +
558A LYS* 1.3 61.8 + - - +
560A GLN* 2.8 42.1 + - - +
561A ILE* 3.1 50.8 + - + +
564A ARG* 5.0 10.7 - - - +
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Residues in contact with LYS 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A ALA 2.9 17.6 + - - +
555A LYS* 3.8 11.7 - - + +
556A GLU 3.4 0.2 - - - -
557A ARG* 1.3 72.8 - - - +
559A THR* 1.3 65.5 + - - +
561A ILE* 3.5 9.5 + - + +
562A ASP* 2.9 61.3 + - - +
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Residues in contact with THR 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A GLN* 4.2 9.2 - - - +
497A LYS* 3.4 15.3 - - - +
555A LYS* 2.7 37.4 + - - +
556A GLU* 3.2 8.9 + - - -
558A LYS* 1.3 76.4 - - - +
560A GLN* 1.3 54.5 + - - +
562A ASP* 3.4 6.0 + - - +
563A ASP* 2.8 56.9 + - - +
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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
----------------------------------------------------------
536A ALA 4.1 8.7 - - - +
537A ALA 2.6 31.0 + - - +
538A GLU* 3.7 13.3 + - - +
539A ALA* 3.8 14.4 - - + -
552A LEU* 3.6 17.3 - - - +
556A GLU 2.9 13.5 + - - +
557A ARG* 2.8 36.9 + - - +
559A THR* 1.3 72.5 - - - +
561A ILE* 1.3 60.8 + - + +
563A ASP* 3.6 7.0 - - - +
564A ARG* 2.8 50.7 + - - +
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Residues in contact with ILE 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A ARG* 3.1 54.1 + - + +
558A LYS* 3.9 7.9 - - + +
560A GLN* 1.3 78.9 - - + +
562A ASP* 1.3 64.7 + - - +
564A ARG* 3.4 10.7 + - - +
565A ASN* 3.0 28.0 + - + +
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Residues in contact with ASP 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A LYS* 2.9 57.8 + - - +
559A THR* 3.8 5.6 - - - +
561A ILE* 1.3 79.5 - - - +
563A ASP* 1.3 56.4 + - - +
565A ASN* 3.2 8.1 + - - +
566A LYS* 2.8 34.4 + - - +
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Residues in contact with ASP 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A GLN* 4.3 2.4 + - - -
497A LYS* 2.7 46.7 + - - +
499A TRP* 4.0 5.9 - - + -
536A ALA* 4.1 26.0 - - + +
559A THR* 2.8 33.9 + - - +
560A GLN* 3.6 5.2 + - - +
562A ASP* 1.3 74.2 - - - +
564A ARG* 1.3 58.2 + - - +
566A LYS* 3.1 8.6 + - - +
567A LEU* 2.9 34.1 + - - +
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Residues in contact with ARG 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A ALA* 3.0 47.7 + - + +
538A GLU* 4.8 2.6 - - - +
557A ARG* 5.0 10.9 - - - +
560A GLN* 2.8 38.0 + - - +
561A ILE* 3.6 9.0 - - - +
563A ASP* 1.3 76.9 - - - +
565A ASN* 1.3 59.4 + - - +
567A LEU* 3.6 8.4 - - - +
568A THR* 2.7 35.3 + - - +
598A TYR 4.7 10.4 + - - +
600A ASP* 5.1 12.1 - - + +
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Residues in contact with ASN 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A ILE* 3.0 15.3 + - + +
562A ASP* 3.2 11.9 + - - +
564A ARG* 1.3 77.9 - - - +
566A LYS* 1.3 63.1 + - - +
568A THR* 3.9 0.7 - - - -
569A GLU* 3.1 42.1 + - - +
600A ASP* 5.3 2.5 + - - +
603A ILE* 3.4 30.0 - - - +
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Residues in contact with LYS 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A LYS* 3.3 26.9 + - + +
498A ASP* 4.6 6.1 + - - +
499A TRP* 4.0 20.2 - - + +
500A GLU* 4.2 28.3 + - - +
562A ASP 2.8 16.0 + - - +
563A ASP* 3.1 10.3 + - - +
565A ASN* 1.3 75.1 + - - +
567A LEU* 1.3 58.6 + - - +
569A GLU* 4.0 4.1 - - - +
570A HIS* 2.9 29.7 + - + +
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Residues in contact with LEU 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A TRP* 3.6 32.8 - - + -
533A ILE* 3.8 37.7 - - + +
536A ALA* 4.5 0.7 - - + -
537A ALA* 4.4 13.0 - - + +
563A ASP 2.9 23.7 + - - +
564A ARG* 3.6 12.6 - - - +
566A LYS* 1.3 75.9 - - - +
568A THR* 1.3 72.5 + - - +
570A HIS* 4.4 0.7 - - - +
571A PHE* 3.0 45.3 + - + +
595A ILE* 5.6 0.4 - - + -
598A TYR* 4.2 18.6 - - + +
599A PHE* 4.5 8.1 - - + -
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Residues in contact with THR 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A ARG 2.7 23.2 + - - -
565A ASN 3.9 2.2 - - - -
567A LEU* 1.3 77.0 - - - +
569A GLU* 1.3 65.8 + - - +
572A ILE* 2.9 51.9 + - + +
598A TYR 4.2 0.9 + - - -
599A PHE* 3.5 17.9 - - + -
600A ASP* 3.0 45.8 + - - +
603A ILE* 3.9 13.7 - - + -
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Residues in contact with GLU 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A ASN* 3.1 33.3 + - - +
566A LYS* 4.0 4.1 - - - +
568A THR* 1.3 78.6 - - - +
570A HIS* 1.3 64.0 + - - +
571A PHE 3.4 0.2 + - - -
572A ILE* 4.7 0.7 - - - -
573A ILE* 3.4 30.7 + - + +
603A ILE* 4.4 13.4 - - + +
607A GLY* 5.8 3.1 - - - -
609A MET* 3.7 27.9 - - + +
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Residues in contact with HIS 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A TRP* 3.7 10.9 + - + -
500A GLU* 3.5 34.8 + - + +
503A THR* 2.8 40.1 + - + +
566A LYS* 2.9 24.3 + - + +
567A LEU* 3.4 4.2 + - - +
568A THR 3.2 0.2 - - - -
569A GLU* 1.3 78.8 - - - +
571A PHE* 1.3 75.6 + + + +
573A ILE* 3.7 4.8 - - - +
574A THR* 2.8 52.8 + - + +
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Residues in contact with PHE 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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499A TRP* 3.6 34.5 - + + -
503A THR* 3.5 22.2 - - + -
529A MET* 3.7 28.9 - - + -
533A ILE* 3.4 30.1 - - + -
567A LEU* 3.0 30.7 + - + +
570A HIS* 1.3 79.0 - + - +
572A ILE* 1.3 61.9 + - - +
573A ILE 3.2 0.4 - - - -
574A THR* 3.4 10.3 - - - -
575A LEU* 2.7 37.0 + - + +
578A LEU* 4.1 7.4 - - + -
595A ILE* 4.0 17.7 - - + -
599A PHE* 3.7 19.0 - - + -
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Residues in contact with ILE 572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A THR* 2.9 45.4 + - + +
569A GLU* 4.0 4.0 - - - +
571A PHE* 1.3 77.3 - - - +
573A ILE* 1.3 62.3 + - - +
576A PRO* 3.1 21.7 - - - +
599A PHE* 3.8 10.9 - - + -
603A ILE* 3.8 20.4 - - + -
604A TYR* 3.5 51.3 + - + +
609A MET* 3.7 18.6 - - + -
612A HIS* 3.4 28.7 - - + +
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Residues in contact with ILE 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A GLU* 3.4 19.6 + - + +
570A HIS* 3.7 7.2 - - - +
571A PHE 3.2 0.2 - - - -
572A ILE* 1.3 79.9 - - - +
574A THR* 1.3 71.9 + - + +
576A PRO* 3.4 9.0 - - - +
577A MET* 3.7 21.8 - - + +
609A MET* 3.6 16.6 - - + -
612A HIS* 3.6 38.5 - - + +
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Residues in contact with THR 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A THR* 3.5 17.1 - - - +
507A LEU* 4.7 1.1 - - + -
570A HIS* 2.8 61.8 + - + +
571A PHE* 3.4 11.4 - - - -
573A ILE* 1.3 79.6 - - + +
575A LEU* 1.3 66.1 + - - +
576A PRO 3.3 0.4 - - - -
577A MET* 3.1 31.0 + - + +
578A LEU* 2.9 23.2 + - - +
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Residues in contact with LEU 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A PHE* 2.7 29.1 + - + +
574A THR* 1.3 73.4 + - - +
576A PRO* 1.3 60.7 - - + +
578A LEU* 3.4 6.7 + - + -
579A LEU* 2.9 40.1 + - + +
592A LEU* 3.9 45.1 - - + +
593A LEU* 5.2 1.3 - - + -
595A ILE* 4.3 10.8 - - + -
596A PRO* 3.6 36.1 - - + -
599A PHE* 4.4 8.3 - - + -
616A LEU* 3.7 19.5 - - + -
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Residues in contact with PRO 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A PHE 3.8 0.2 - - - +
572A ILE 3.1 24.2 - - - +
573A ILE 3.4 9.9 - - - +
575A LEU* 1.3 94.0 - - + +
577A MET* 1.3 56.5 - - + +
579A LEU* 4.6 4.9 - - + -
580A SER* 3.0 30.0 + - - -
604A TYR* 6.1 0.2 - - - +
612A HIS* 4.0 4.5 - - + +
615A ALA* 3.7 31.0 - - + +
616A LEU* 3.7 23.6 - - + +
619A GLN* 3.4 15.2 - - + +
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Residues in contact with MET 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A LEU* 3.8 25.0 - - + +
573A ILE* 3.7 23.6 - - + +
574A THR* 3.1 41.4 + - + +
576A PRO* 1.3 76.1 - - + +
578A LEU* 1.3 64.5 + - - +
580A SER* 3.3 7.9 + - - -
581A LYS* 3.1 25.1 + - - +
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Residues in contact with LEU 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A THR* 4.0 23.6 - - + -
506A LEU* 3.9 24.9 - - + -
507A LEU* 3.7 31.6 - - + -
526A ILE* 5.8 0.2 - - + -
529A MET* 4.0 9.9 - - + -
571A PHE* 4.1 9.9 - - + -
574A THR* 2.9 19.3 + - - +
575A LEU* 3.6 11.0 - - + +
577A MET* 1.3 76.8 - - - +
579A LEU* 1.3 61.2 + - - +
582A TYR* 3.1 36.7 + - + +
592A LEU* 3.9 32.3 - - + +
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Residues in contact with LEU 579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A LEU* 2.9 31.7 + - + +
576A PRO 3.9 2.7 - - - +
578A LEU* 1.3 69.8 - - - +
580A SER* 1.3 61.0 + - - +
582A TYR 5.2 0.4 - - - -
583A SER* 2.8 35.6 + - - +
589A VAL* 4.0 26.7 - - + -
592A LEU* 3.9 26.5 - - + -
593A LEU* 4.0 20.2 - - + -
616A LEU* 3.4 33.2 - - + -
619A GLN* 4.0 21.8 - - + +
620A ILE* 4.9 2.9 - - + +
623A VAL* 4.8 6.4 - - + +
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Residues in contact with SER 580 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A PRO 3.0 18.3 + - - -
577A MET* 3.5 8.5 - - - -
579A LEU* 1.3 79.0 - - - +
581A LYS* 1.3 63.6 - - - +
583A SER* 3.5 12.5 - - - -
619A GLN* 3.5 27.8 + - - -
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Residues in contact with LYS 581 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A LEU 5.3 0.2 + - - -
506A LEU 2.7 31.1 + - - +
507A LEU* 3.9 21.8 - - + +
508A GLU 4.3 10.3 + - - -
509A GLU* 5.6 6.9 + - - -
522A GLU* 3.8 10.3 + - - -
577A MET 3.1 17.0 + - - +
578A LEU 3.9 3.1 - - - +
579A LEU 3.3 0.2 - - - -
580A SER* 1.3 77.2 - - - +
582A TYR* 1.3 85.7 + - + +
583A SER 3.4 1.8 + - - -
----------------------------------------------------------
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Residues in contact with TYR 582 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A LEU* 2.7 49.5 + - + +
522A GLU* 3.2 32.3 + - - -
526A ILE* 4.3 13.2 - - + -
578A LEU* 3.1 32.4 + - + +
579A LEU 3.6 1.6 - - - -
581A LYS* 1.3 103.0 + - + +
583A SER* 1.3 63.8 + - - +
584A ALA 3.2 2.5 - - - -
585A ASP* 3.0 21.1 + - + +
588A LYS* 3.6 33.0 - - + -
589A VAL* 3.3 9.4 - - - +
592A LEU* 4.4 11.7 - - + -
----------------------------------------------------------
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Residues in contact with SER 583 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A LEU 2.8 18.9 + - - -
580A SER* 3.5 12.5 + - - -
581A LYS 3.4 2.8 + - - -
582A TYR* 1.3 76.7 - - - +
584A ALA* 1.3 49.7 + - - +
585A ASP 3.6 0.3 + - - -
589A VAL* 3.6 12.1 - - - +
619A GLN* 4.8 2.8 + - - -
622A PHE* 4.6 14.0 + - - +
623A VAL* 4.2 15.8 - - - +
626A LYS* 5.2 6.8 - - - +
627A HIS* 2.7 30.3 + - - -
----------------------------------------------------------
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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