Contacts of the helix formed by residues 488 - 514 (chain C) in PDB entry 2HYE
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 488 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476C LEU* 4.4 10.1 - - + +
479C LEU* 3.5 35.7 - - + -
480C LYS* 3.7 16.5 - - - +
484C GLY 3.5 11.6 + - - +
485C ALA 3.8 2.3 + - - -
487C PHE* 1.3 90.0 - - + +
489C SER* 1.3 68.1 + - - +
490C LYS 3.0 4.5 + - - -
491C LEU* 3.1 22.7 + - + +
492C GLU* 2.8 35.8 + - - +
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Residues in contact with SER 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485C ALA 3.1 17.6 + - - -
486C ALA* 2.8 23.1 + - - -
488C THR* 1.3 76.8 - - - +
490C LYS* 1.3 65.3 + - - +
492C GLU* 3.3 10.5 + - - +
493C GLY* 3.2 12.8 + - - -
74D VAL* 5.1 5.7 - - - +
102D GLU* 6.0 1.7 - - - -
104D GLN* 3.0 27.8 + - - +
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Residues in contact with LYS 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450C GLU* 4.3 20.5 + - - +
454C LYS* 3.7 28.0 - - + +
486C ALA 4.3 5.9 + - - +
487C PHE 5.5 1.6 + - - +
488C THR 3.0 1.6 + - - -
489C SER* 1.3 78.1 - - - +
491C LEU* 1.3 55.4 + - + +
493C GLY* 2.6 24.9 + - - -
494C MET* 2.9 13.7 + - - +
532C TYR* 3.6 33.2 - - - +
695C GLN* 5.9 2.8 - - - +
104D GLN* 2.9 55.6 + - + +
105D LYS* 4.7 6.5 - - - +
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Residues in contact with LEU 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450C GLU* 4.4 16.6 - - - +
453C TYR* 3.8 25.4 - - + -
454C LYS* 3.5 44.2 - - + +
457C LEU* 4.7 6.2 - - + +
476C LEU* 3.4 32.8 - - + -
479C LEU* 4.5 12.3 - - + -
487C PHE* 5.8 1.8 - - + -
488C THR* 3.1 13.8 + - + +
490C LYS* 1.3 77.8 - - + +
492C GLU* 1.3 62.8 + - - +
494C MET* 3.0 25.6 + - + +
495C PHE* 3.2 15.9 + - - -
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Residues in contact with GLU 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476C LEU* 4.4 22.1 - - + +
480C LYS* 3.5 32.4 + - - -
485C ALA* 4.1 6.0 - - - +
488C THR* 2.8 38.2 + - - +
489C SER* 3.5 10.8 - - - +
491C LEU* 1.3 76.8 - - - +
493C GLY* 1.3 59.3 + - - +
495C PHE* 3.6 6.0 + - - +
496C LYS* 3.3 22.6 + - - +
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Residues in contact with GLY 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489C SER 3.2 5.2 + - - -
490C LYS 2.6 17.5 + - - -
492C GLU* 1.3 70.9 - - - +
494C MET* 1.3 65.2 + - - -
495C PHE 3.0 2.6 + - - -
496C LYS* 3.1 8.5 + - - +
497C ASP* 3.0 25.8 + - - +
532C TYR* 3.8 25.3 - - - -
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Residues in contact with MET 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454C LYS* 3.7 34.8 - - + +
457C LEU* 3.9 15.5 - - + -
458C ALA* 3.8 35.9 - - + +
461C LEU* 4.6 8.9 - - + +
490C LYS 2.9 5.5 + - - +
491C LEU* 3.0 27.1 + - + +
493C GLY* 1.3 76.1 - - - +
495C PHE* 1.3 63.6 + - - +
497C ASP* 3.5 5.5 + - - +
498C MET* 3.4 13.7 + - - +
532C TYR* 4.4 2.2 - - + +
533C TRP* 3.5 59.8 - - + +
534C PRO* 4.4 0.2 - - - -
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Residues in contact with PHE 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C LEU* 4.0 19.3 - - + -
461C LEU* 4.1 28.7 - - + -
469C VAL* 5.7 6.1 - - + -
472C GLU* 3.4 36.6 - - + -
473C LYS* 5.3 16.8 - - + -
476C LEU* 3.5 33.4 - - + -
491C LEU 3.2 12.3 + - - -
492C GLU* 3.7 8.7 - - - +
494C MET* 1.3 78.2 - - - +
496C LYS* 1.3 58.6 + - - +
498C MET* 2.6 36.8 + - + +
499C GLU* 3.2 11.1 + - + +
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Residues in contact with LYS 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492C GLU 3.3 13.3 + - - +
493C GLY* 3.1 11.7 + - - +
495C PHE* 1.3 76.4 - - - +
497C ASP* 1.3 56.0 + - - +
499C GLU* 2.7 61.8 + - + +
500C LEU* 3.0 27.9 + - + +
532C TYR* 6.1 1.6 - - + -
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Residues in contact with ASP 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493C GLY 3.0 7.3 + - - +
494C MET 3.5 11.2 - - - +
495C PHE 3.1 0.2 - - - -
496C LYS* 1.3 76.1 - - - +
498C MET* 1.3 53.9 + - - +
500C LEU* 3.9 19.6 - - - +
501C SER* 2.6 39.0 + - - -
527C ILE* 3.8 16.5 - - - +
528C LEU* 4.5 0.7 - - + -
529C THR* 2.8 51.6 + - - -
532C TYR* 3.7 8.5 - - - -
533C TRP* 3.6 16.5 + - + +
33D TRP* 4.3 3.8 + - - -
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Residues in contact with MET 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C LEU* 2.9 65.1 - - + +
462C LEU* 3.8 7.9 - - + -
494C MET 3.4 4.0 + - - +
495C PHE* 2.6 28.5 + - + +
497C ASP* 1.3 75.0 - - - +
499C GLU* 1.3 59.0 + - + +
501C SER* 3.4 5.1 + - - -
502C LYS* 3.3 33.2 + - - +
526C ASN* 3.1 30.3 + - - +
528C LEU* 4.7 2.0 - - - -
533C TRP* 4.1 16.6 - - + -
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Residues in contact with GLU 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495C PHE* 4.1 7.8 - - - +
496C LYS* 2.7 54.4 + - + +
498C MET* 1.3 75.1 - - + +
500C LEU* 1.3 61.3 + - + +
502C LYS* 3.2 22.5 - - + +
503C ASP* 3.0 27.3 + - - +
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Residues in contact with LEU 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496C LYS* 3.0 29.9 + - + +
497C ASP* 3.9 23.3 - - - +
499C GLU* 1.3 74.2 - - + +
501C SER* 1.3 66.7 + - - +
502C LYS 3.0 1.6 - - - -
503C ASP* 3.0 17.5 + - - +
504C ILE* 2.9 37.7 + - + +
527C ILE* 5.4 3.6 - - + -
562C HIS* 6.4 2.2 - - + -
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Residues in contact with SER 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497C ASP 2.6 23.4 + - - -
498C MET 3.6 4.0 - - - -
499C GLU 3.4 0.2 - - - -
500C LEU* 1.3 74.9 - - - +
502C LYS* 1.3 56.9 + - - +
504C ILE* 4.0 3.7 - - - +
505C MET* 3.0 36.2 + - - +
525C VAL 4.1 1.6 - - - +
526C ASN* 3.1 31.8 + - - -
527C ILE* 3.0 38.7 + - - +
528C LEU* 5.1 0.5 - - - +
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Residues in contact with LYS 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498C MET* 3.3 21.5 + - - +
499C GLU* 3.2 21.2 + - + +
500C LEU 3.0 0.4 - - - -
501C SER* 1.3 76.4 - - - +
503C ASP* 1.3 70.3 + - - +
505C MET* 3.1 8.4 + - - +
506C VAL* 2.9 25.0 + - + +
526C ASN* 6.0 1.6 - - - +
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Residues in contact with ASP 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499C GLU* 3.0 19.0 - - - +
500C LEU* 3.3 22.7 - - + +
502C LYS* 1.3 77.2 - - - +
504C ILE* 1.3 68.2 + - + +
506C VAL* 2.8 26.3 + - - +
507C HIS* 3.3 15.8 + - + +
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Residues in contact with ILE 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500C LEU* 2.9 25.3 + - + +
501C SER* 4.0 4.3 - - - +
503C ASP* 1.3 80.5 - - + +
505C MET* 1.3 57.4 + - + +
507C HIS* 2.7 35.5 + - + +
508C PHE* 2.9 10.9 + - - +
527C ILE* 4.4 12.6 - - + -
554C PHE* 4.4 25.8 - - + -
557C PHE* 4.5 13.5 - - + -
558C TYR* 3.7 34.1 - - + -
562C HIS* 4.0 15.3 - - + +
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Residues in contact with MET 505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501C SER* 3.0 20.5 + - - +
502C LYS* 3.1 9.4 + - - +
504C ILE* 1.3 81.3 - - + +
506C VAL* 1.3 61.1 + - + +
508C PHE* 3.6 13.6 + - - +
509C LYS* 3.2 33.6 + - + +
523C LEU 4.6 4.3 - - - +
524C THR* 4.0 25.8 - - + -
525C VAL* 3.0 41.5 - - + +
554C PHE* 3.7 31.6 - - + -
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Residues in contact with VAL 506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502C LYS* 2.9 17.6 + - + +
503C ASP* 2.8 18.3 + - - +
505C MET* 1.3 71.7 - - + +
507C HIS* 1.3 65.2 + - + +
509C LYS* 3.3 7.1 + - - +
510C GLN* 3.0 46.7 + - + +
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Residues in contact with HIS 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503C ASP* 3.3 26.6 + - + +
504C ILE* 2.7 16.7 + - + +
506C VAL* 1.3 78.5 - - + +
508C PHE* 1.3 64.9 + - - +
509C LYS 3.0 2.0 - - - -
510C GLN* 3.1 10.0 + - - +
511C HIS* 2.9 26.9 + - - +
557C PHE* 4.0 16.8 - - + -
561C LYS* 4.0 14.8 + - + +
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Residues in contact with PHE 508 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504C ILE 2.9 9.2 + - - +
505C MET* 3.9 17.7 - - - +
507C HIS* 1.3 75.9 - - - +
509C LYS* 1.3 66.6 + - + +
511C HIS* 3.8 1.9 - + - +
512C MET* 2.8 66.1 + - + +
523C LEU* 4.8 17.0 - - + -
550C LEU* 4.8 3.1 - - - -
553C VAL* 4.1 7.2 - - + -
554C PHE* 3.7 54.3 - + + -
557C PHE* 3.5 43.6 - + + -
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Residues in contact with LYS 509 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505C MET* 3.2 20.8 + - + +
506C VAL* 3.5 9.9 - - - +
507C HIS 3.0 0.6 - - - -
508C PHE* 1.3 85.9 - - + +
510C GLN* 1.3 61.8 + - + +
511C HIS 3.1 1.3 - - - -
512C MET* 3.7 7.9 - - + +
513C GLN* 2.9 33.1 + - - +
522C ASP* 4.2 20.8 + - - +
523C LEU 5.2 9.6 - - - +
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Residues in contact with GLN 510 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506C VAL* 3.0 33.5 + - + +
507C HIS* 3.1 10.4 + - - +
509C LYS* 1.3 76.1 - - + +
511C HIS* 1.3 58.8 + - - +
513C GLN* 3.2 19.7 - - - +
514C ASN* 3.3 12.1 + - - -
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Residues in contact with HIS 511 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507C HIS 2.9 16.2 + - - +
508C PHE* 3.8 7.0 - + - +
510C GLN* 1.3 76.1 - - - +
512C MET* 1.3 94.1 + - + +
513C GLN 2.8 9.8 + - - -
514C ASN* 3.2 31.6 + - - +
515C GLN* 5.0 2.6 + - - +
553C VAL* 5.6 1.4 - - - +
557C PHE* 4.1 31.5 - + + +
561C LYS* 5.7 1.6 - - - +
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Residues in contact with MET 512 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508C PHE* 2.8 50.7 + - + +
509C LYS* 3.5 10.5 + - + +
511C HIS* 1.3 101.9 - - + +
513C GLN* 1.3 64.3 + - - +
515C GLN* 3.1 51.0 - - - +
517C ASP* 4.5 19.3 - - - +
553C VAL* 3.9 18.6 - - + -
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Residues in contact with GLN 513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509C LYS* 2.9 17.0 + - - +
510C GLN* 3.2 19.4 - - - +
511C HIS 2.8 1.2 - - - -
512C MET* 1.3 79.3 - - - +
514C ASN* 1.3 54.9 + - + +
515C GLN 2.6 15.6 + - - -
516C SER* 3.6 7.4 + - - -
517C ASP* 4.5 4.4 + - - +
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Residues in contact with ASN 514 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510C GLN 3.3 19.2 + - - -
511C HIS* 3.2 20.4 + - - +
513C GLN* 1.3 72.9 - - + +
515C GLN* 1.3 57.8 + - - +
516C SER* 3.7 1.6 - - - +
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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