Contacts of the helix formed by residues 554 - 586 (chain A) in PDB entry 2O8C
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 554 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A ASN* 3.4 24.1 + - - +
553A ASN* 1.3 75.9 - - - +
555A LYS* 1.3 59.5 + - - +
557A THR* 3.0 19.6 + - - -
558A SER* 3.8 9.9 + - - -
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Residues in contact with LYS 555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A THR* 4.4 22.9 - - + -
553A ASN* 3.2 19.8 - - - +
554A SER* 1.3 82.0 - - - +
556A LEU* 1.3 57.8 + - - +
558A SER* 4.0 4.3 + - - -
559A LEU* 3.3 28.9 + - + +
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Residues in contact with LEU 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A MET* 3.8 27.8 - - + -
495A THR* 5.6 3.1 - - + +
521A TYR* 3.3 28.0 - - + +
522A TYR* 4.3 5.6 - - - -
523A PHE* 3.6 34.5 - - + -
552A THR* 3.7 21.1 - - + -
553A ASN* 3.0 19.0 + - - +
555A LYS* 1.3 78.1 - - - +
557A THR* 1.3 57.7 + - - +
559A LEU* 2.9 8.9 + - + +
560A ASN* 2.7 49.8 + - + +
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Residues in contact with THR 557 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A SER* 5.2 8.1 - - - +
552A THR* 3.5 20.2 - - - +
553A ASN 3.2 15.5 + - - +
554A SER* 3.0 23.2 + - - -
556A LEU* 1.3 79.6 - - - +
558A SER* 1.3 60.8 + - - +
560A ASN* 3.5 3.7 + - - +
561A GLU* 3.3 32.0 + - - +
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Residues in contact with SER 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A SER 3.8 12.0 + - - -
555A LYS* 4.0 4.9 + - - -
557A THR* 1.3 79.5 + - - +
559A LEU* 1.3 64.3 + - - +
561A GLU* 4.0 9.5 - - - +
562A GLU* 3.3 26.3 + - - +
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Residues in contact with LEU 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A LEU* 3.8 32.7 - - + +
491A LYS* 5.1 15.0 - - + +
492A MET* 3.8 29.7 - - - +
495A THR* 5.0 13.2 - - + -
555A LYS* 3.3 27.8 - - + +
556A LEU* 2.9 8.6 + - - +
558A SER* 1.3 80.5 + - - +
560A ASN* 1.3 61.3 + - - +
562A GLU* 4.0 12.9 - - - +
563A TYR* 3.3 21.0 + - - +
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Residues in contact with ASN 560 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A PHE* 3.2 24.5 + - - +
520A GLY* 4.0 1.4 - - - -
521A TYR* 3.6 41.7 + - + +
552A THR* 6.0 0.4 - - - +
556A LEU* 2.7 31.7 + - + +
557A THR* 3.8 5.6 - - - +
559A LEU* 1.3 73.2 - - - +
561A GLU* 1.3 61.4 + - + +
562A GLU 3.2 0.4 - - - -
563A TYR* 3.1 5.9 + - - +
564A THR* 2.9 37.6 + - - +
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Residues in contact with GLU 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A THR* 3.3 21.2 + - - +
558A SER* 4.2 7.9 - - - +
559A LEU 3.5 0.2 - - - -
560A ASN* 1.3 78.9 - - + +
562A GLU* 1.3 60.6 + - - +
564A THR* 2.8 21.1 + - - +
565A LYS* 3.3 25.5 + - - +
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Residues in contact with GLU 562 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A LEU* 5.1 8.5 - - + -
558A SER 3.3 17.6 + - - +
559A LEU* 4.0 16.0 - - + +
560A ASN 3.2 0.4 - - - -
561A GLU* 1.3 76.2 - - - +
563A TYR* 1.3 63.8 + - - +
565A LYS* 3.7 11.5 + - + +
566A ASN* 3.3 29.8 + - - +
----------------------------------------------------------
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Residues in contact with TYR 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A MET* 3.6 53.3 + - + +
488A LEU* 3.6 29.6 - - + +
489A GLU* 5.2 4.5 - - + +
492A MET* 6.2 3.8 - - + -
521A TYR* 3.0 47.1 + + + -
559A LEU 3.3 15.5 + - - +
560A ASN* 3.1 14.8 + - - +
562A GLU* 1.3 78.6 - - - +
564A THR* 1.3 64.8 + - + +
566A ASN* 3.3 16.1 + - - +
567A LYS* 3.4 35.6 + - + +
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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
----------------------------------------------------------
519A PHE 5.2 5.6 - - - +
520A GLY* 5.5 3.1 - - - -
560A ASN* 2.9 29.0 + - - +
561A GLU* 2.8 28.3 + - - +
563A TYR* 1.3 79.3 - - + +
565A LYS* 1.3 62.6 + - - +
566A ASN 3.2 0.2 - - - -
567A LYS* 3.3 23.7 + - + +
568A THR* 3.3 20.3 + - - +
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Residues in contact with LYS 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A GLU* 3.3 22.8 + - - +
562A GLU* 4.0 11.0 - - + +
563A TYR 3.3 0.8 - - - -
564A THR* 1.3 78.4 + - - +
566A ASN* 1.3 64.3 + - - +
568A THR* 2.8 22.5 + - - +
569A GLU* 3.4 21.2 + - - +
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Residues in contact with ASN 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A LEU* 4.1 19.5 - - + +
484A ILE* 3.4 34.7 - - - +
485A MET* 3.7 19.2 - - - +
488A LEU* 4.6 8.9 - - - +
562A GLU* 3.3 21.0 + - - +
563A TYR 3.3 8.9 + - - +
564A THR 3.2 0.4 - - - -
565A LYS* 1.3 81.0 - - - +
567A LYS* 1.3 58.3 + - - +
569A GLU* 3.9 10.5 - - - +
570A TYR* 3.1 27.9 + - - +
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Residues in contact with LYS 567 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A MET* 3.9 18.8 - - + -
515A SER* 5.6 6.3 - - - -
516A SER 5.4 6.5 + - - -
517A ALA* 6.3 0.6 - - - +
520A GLY* 6.3 1.0 - - - -
521A TYR* 5.2 6.2 + - - -
563A TYR* 3.4 33.7 + - + +
564A THR* 3.3 18.6 + - + +
565A LYS 3.3 0.2 - - - -
566A ASN* 1.3 78.1 - - - +
568A THR* 1.3 61.5 + - + +
570A TYR* 3.7 5.2 - - - +
571A GLU* 2.9 45.0 + - + +
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Residues in contact with THR 568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A THR* 3.3 12.5 + - - +
565A LYS* 2.8 27.2 + - - +
567A LYS* 1.3 77.7 - - + +
569A GLU* 1.3 61.2 + - - +
571A GLU* 4.3 9.1 - - - +
572A GLU* 3.3 30.7 + - - +
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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
----------------------------------------------------------
481A LEU* 4.5 15.5 - - + +
565A LYS* 3.4 20.4 + - - +
566A ASN* 3.6 9.8 + - - +
567A LYS 3.2 0.4 - - - -
568A THR* 1.3 79.8 + - - +
570A TYR* 1.3 64.5 + - - +
572A GLU* 3.4 21.3 - - - +
573A ALA* 3.3 22.2 + - - +
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Residues in contact with TYR 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A LEU* 6.3 0.4 - - + -
470A VAL 4.8 1.2 + - - -
472A PRO* 4.4 18.7 - - - +
478A LEU* 3.7 41.8 + - + +
481A LEU* 3.6 28.7 - - + +
482A ARG* 4.6 11.5 - - + +
485A MET* 5.2 10.5 - - + -
566A ASN 3.1 19.1 + - - +
567A LYS* 3.3 7.4 + - - +
569A GLU* 1.3 77.0 - - - +
571A GLU* 1.3 60.5 + - + +
573A ALA* 3.2 5.0 + - - +
574A GLN* 3.1 61.3 + - + +
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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
----------------------------------------------------------
567A LYS* 2.9 28.9 + - + +
568A THR* 4.3 9.3 - - - +
570A TYR* 1.3 80.7 - - + +
572A GLU* 1.3 55.2 + - - +
573A ALA 3.2 2.8 + - - -
574A GLN* 4.3 9.1 - - - +
575A ASP* 3.0 29.5 + - - +
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Residues in contact with GLU 572 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A THR* 3.3 20.9 + - - +
569A GLU* 3.4 26.5 - - - +
571A GLU* 1.3 74.8 - - - +
573A ALA* 1.3 56.8 + - - +
575A ASP* 3.2 20.3 - - - +
576A ALA* 3.4 14.0 - - - +
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Residues in contact with ALA 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A ASP* 5.6 1.3 - - - +
477A ASN* 4.8 11.9 - - - +
478A LEU* 3.9 20.6 - - + -
481A LEU* 5.8 0.7 - - + -
569A GLU 3.3 16.9 + - - +
570A TYR* 3.2 6.3 + - - +
571A GLU 3.2 0.4 - - - -
572A GLU* 1.3 79.9 - - + +
574A GLN* 1.3 63.5 + - - +
575A ASP 3.6 0.4 - - - -
576A ALA* 3.5 5.7 + - - +
577A ILE* 3.3 28.9 + - + +
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Residues in contact with GLN 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A LEU* 3.4 31.0 - - - +
470A VAL* 3.6 46.5 + - + +
478A LEU* 4.6 8.5 - - + +
570A TYR* 3.1 50.0 + - + +
571A GLU* 3.8 8.9 + - - +
573A ALA* 1.3 73.6 - - - +
575A ASP* 1.3 60.3 + - - +
577A ILE* 3.0 12.3 + - - +
578A VAL* 3.0 30.2 + - + +
----------------------------------------------------------
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Residues in contact with ASP 575 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A GLU 3.0 21.6 + - - +
572A GLU* 3.2 17.1 - - - +
574A GLN* 1.3 75.4 - - - +
576A ALA* 1.3 65.7 + - - +
578A VAL* 3.6 13.6 - - + +
579A LYS* 2.9 45.0 + - + +
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Residues in contact with ALA 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A GLU 3.4 19.7 - - - +
573A ALA* 3.5 8.5 - - - +
574A GLN 3.1 0.6 - - - -
575A ASP* 1.3 81.8 + - - +
577A ILE* 1.3 62.8 + - + +
579A LYS* 3.9 9.7 + - - +
580A GLU* 3.8 15.9 + - - +
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Residues in contact with ILE 577 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A THR* 5.7 0.4 - - + -
470A VAL* 4.6 18.8 - - + -
474A PHE* 5.1 14.4 - - + -
475A ASP* 4.3 24.2 - - + +
478A LEU* 4.3 15.9 - - + -
573A ALA* 3.3 17.0 - - + +
574A GLN* 3.0 7.9 + - - +
576A ALA* 1.3 75.1 - - + +
578A VAL* 1.3 61.2 + - - +
580A GLU* 3.1 14.3 + - - +
581A ILE* 2.9 44.2 + - + +
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Residues in contact with VAL 578 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ALA 5.7 0.4 - - - +
400A ASN* 5.2 3.4 - - - +
401A LEU* 4.2 45.3 - - + +
470A VAL* 4.2 10.8 - - + -
574A GLN* 3.0 21.6 + - + +
575A ASP* 3.4 13.9 + - + +
577A ILE* 1.3 76.7 - - - +
579A LYS* 1.3 53.4 + - + +
581A ILE* 3.0 9.7 + - + +
582A VAL* 2.8 47.8 + - + +
----------------------------------------------------------
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Residues in contact with LYS 579 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A ASP* 2.9 32.0 + - + +
576A ALA* 4.1 10.3 - - - +
577A ILE 3.3 0.4 - - - -
578A VAL* 1.3 77.6 - - + +
580A GLU* 1.3 56.8 + - - +
582A VAL* 3.8 6.7 + - - +
583A ASN* 3.2 34.9 + - - +
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Residues in contact with GLU 580 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A ALA 3.8 9.1 + - - +
577A ILE* 3.1 15.8 + - - +
579A LYS* 1.3 75.5 - - - +
581A ILE* 1.3 56.9 + - + +
583A ASN* 3.0 7.5 + - + +
584A ILE* 2.7 62.4 + - + +
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Residues in contact with ILE 581 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A LEU* 4.7 15.0 - - + -
404A CYS* 4.5 19.7 - - + -
450A PHE* 6.0 0.7 - - + -
453A MET* 4.1 26.3 - - + +
454A ILE* 5.9 2.9 - - + -
457A THR* 4.4 27.6 - - + +
458A LEU* 4.9 4.3 - - + -
470A VAL* 5.3 4.9 - - + -
577A ILE* 2.9 39.2 + - + +
578A VAL* 3.0 13.9 + - + +
580A GLU* 1.3 76.6 - - + +
582A VAL* 1.3 55.7 + - + +
584A ILE* 3.4 10.3 + - + +
585A SER* 2.9 29.4 + - - -
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Residues in contact with VAL 582 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A PHE* 4.1 9.7 - - + +
397A GLN* 4.9 13.2 - - - +
399A ALA* 3.9 40.8 - - + +
400A ASN 4.5 11.2 - - - +
404A CYS* 4.9 7.4 - - - -
578A VAL* 2.8 33.1 + - + +
579A LYS* 3.9 7.9 - - - +
581A ILE* 1.3 76.3 - - + +
583A ASN* 1.3 65.7 + - - +
585A SER* 2.8 18.9 + - - -
586A SER* 2.9 17.3 + - - -
----------------------------------------------------------
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Residues in contact with ASN 583 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A PHE 5.7 0.2 - - - +
397A GLN* 4.9 11.8 - - - +
579A LYS* 3.2 19.3 + - - +
580A GLU* 3.0 9.6 + - + +
582A VAL* 1.3 83.7 - - - +
584A ILE* 1.3 62.5 + - + +
586A SER* 2.8 22.5 + - - +
587A GLY* 3.7 5.5 + - - -
----------------------------------------------------------
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Residues in contact with ILE 584 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A MET* 3.8 29.4 - - + -
580A GLU* 2.7 49.7 + - + +
581A ILE* 3.9 8.3 - - + +
583A ASN* 1.3 73.6 - - - +
585A SER* 1.3 58.6 + - - +
586A SER 3.2 0.2 - - - -
587A GLY* 3.2 16.0 + - - -
588A TYR* 3.3 22.0 - - + -
----------------------------------------------------------
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Residues in contact with SER 585 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A PHE* 3.3 32.0 - - - -
404A CYS* 4.9 3.0 - - - -
407A LEU* 5.7 2.8 - - - +
450A PHE* 3.7 27.6 - - - -
453A MET* 5.1 0.6 - - - +
581A ILE* 2.9 15.7 + - - -
582A VAL* 2.8 20.6 + - - -
584A ILE* 1.3 73.2 - - - +
586A SER* 1.3 55.2 + - - +
587A GLY 3.0 5.4 - - - -
588A TYR* 3.1 33.4 + - - +
589A VAL* 4.6 1.2 - - - +
592A MET* 5.6 2.1 - - - +
----------------------------------------------------------
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Residues in contact with SER 586 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A PHE* 3.4 28.9 - - - -
395A GLN* 5.3 1.1 - - - -
582A VAL 2.9 14.5 + - - -
583A ASN* 2.8 30.8 + - - +
585A SER* 1.3 75.0 - - - +
587A GLY* 1.3 56.9 - - - +
588A TYR 3.2 1.1 - - - -
589A VAL* 3.2 24.8 - - - +
----------------------------------------------------------
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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