Contacts of the helix formed by residues 476 - 498 (chain S) in PDB entry 1I84
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 476 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474S ILE* 3.1 12.3 + - - -
475S ASN* 1.3 83.4 - - - +
477S PHE* 1.3 74.2 + - - +
478S GLU* 2.9 17.8 + - - -
479S GLN* 3.4 17.5 + - - +
480S LEU 3.3 11.3 + - - -
592S TYR* 3.6 3.6 - - - -
593S ASN* 4.5 5.3 + - - +
595S SER 5.3 0.9 + - - -
597S TRP* 3.8 12.7 + - - +
600S LYS* 3.2 23.1 + - - +
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Residues in contact with PHE 477 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476S SER* 1.3 77.0 + - - +
478S GLU* 1.3 63.6 + - + +
480S LEU* 2.5 60.9 + - + +
481S CYS* 3.1 20.4 + - - -
538S LEU* 3.4 30.3 - - + -
541S LEU* 4.1 10.3 - - + -
597S TRP* 3.2 34.9 - + + +
600S LYS* 4.8 20.4 - - + -
601S ASN* 3.9 19.5 - - + -
659S VAL* 3.7 28.7 - - + -
660S GLY* 4.6 0.4 - - - -
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Residues in contact with GLU 478 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273S GLU* 4.2 26.7 - - + +
275S SER* 2.8 31.5 + - - +
476S SER* 2.9 24.9 + - - -
477S PHE* 1.3 75.0 + - + +
479S GLN* 1.3 70.5 + - - +
480S LEU 2.9 0.9 + - - -
481S CYS* 3.1 9.7 + - - +
482S ILE* 2.9 37.1 + - + +
600S LYS* 3.7 19.8 + - - +
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Residues in contact with GLN 479 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273S GLU* 3.8 6.8 + - - +
470S GLU* 3.6 35.9 - - + +
472S PHE* 4.3 13.6 - - + -
474S ILE 3.1 22.4 + - - -
475S ASN* 4.1 15.7 - - - +
476S SER* 3.5 24.2 - - - +
477S PHE 3.2 0.6 - - - -
478S GLU* 1.3 90.8 - - - +
480S LEU* 1.3 57.6 + - - +
482S ILE* 3.9 8.1 - - - -
483S ASN* 2.9 35.4 + - - +
590S VAL* 6.1 0.2 - - + -
592S TYR* 3.4 11.3 + - + -
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Residues in contact with LEU 480 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476S SER 3.3 2.5 + - - +
477S PHE* 2.5 45.7 + - + +
479S GLN* 1.3 72.9 - - - +
481S CYS* 1.3 58.3 + - - +
483S ASN 3.9 0.9 - - - -
484S TYR* 3.0 26.3 + - - +
528S ILE* 3.2 35.0 - - + -
537S VAL* 4.2 9.2 - - + -
538S LEU* 5.1 3.4 - - + -
583S ILE* 3.7 17.3 - - + -
585S HIS* 5.0 2.0 + - + +
592S TYR* 3.2 32.8 + - + +
597S TRP* 3.3 31.4 - - + -
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Residues in contact with CYS 481 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271S LEU* 4.0 25.8 - - + -
477S PHE* 3.6 45.1 - - - -
478S GLU* 3.1 7.1 + - - +
480S LEU* 1.3 74.0 - - - +
482S ILE* 1.3 55.1 + - - +
484S TYR* 2.9 11.3 - - + +
485S THR* 2.6 38.9 + - - -
528S ILE* 5.7 0.4 - - - -
538S LEU* 5.3 5.6 - - + -
659S VAL* 6.0 0.9 - - - -
660S GLY* 6.2 1.3 - - - -
663S TYR* 4.1 14.4 - - + -
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Residues in contact with ILE 482 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247S ARG* 4.5 9.6 - - - +
248S PHE* 6.5 0.2 - - - -
271S LEU* 4.8 23.1 - - + +
273S GLU* 4.9 5.2 - - + +
467S ALA* 4.2 25.8 - - + +
468S GLY 4.1 13.2 - - - +
470S GLU* 3.8 38.1 - - + +
478S GLU* 2.9 26.8 + - + +
479S GLN* 3.9 2.2 - - - +
481S CYS* 1.3 74.4 - - - +
483S ASN* 1.3 76.5 + - - +
484S TYR 2.9 8.3 + - - -
485S THR* 3.2 7.3 + - - -
486S ASN* 3.1 25.3 + - - -
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Residues in contact with ASN 483 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469S PHE* 3.0 47.2 - - + -
470S GLU 2.7 29.2 + - - +
471S ILE* 3.9 2.6 - - - +
479S GLN* 2.9 23.7 + - - +
480S LEU 3.9 0.7 - - - -
482S ILE* 1.3 87.9 - - - +
484S TYR* 1.3 59.0 + - - +
486S ASN* 3.9 11.1 - - - +
487S GLU* 3.3 21.3 + - - +
585S HIS* 3.6 17.2 + - + +
590S VAL* 4.5 2.5 - - - +
592S TYR* 3.4 16.3 + - - +
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Residues in contact with TYR 484 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480S LEU 3.0 17.7 + - - +
481S CYS* 2.9 17.3 - - - +
482S ILE 2.9 0.4 - - - -
483S ASN* 1.3 76.3 - - - +
485S THR* 1.3 56.9 + - - +
487S GLU* 2.9 12.4 + - + +
488S LYS* 2.7 44.0 + - + -
525S ILE* 3.5 26.7 - - + -
528S ILE* 4.0 30.1 - - + -
529S GLU* 2.8 35.9 + - + +
538S LEU* 4.7 12.6 - - + -
585S HIS* 5.2 4.5 - - - -
663S TYR* 4.1 16.8 - + - -
664S LYS* 4.3 17.3 - - + +
667S LEU* 4.0 18.7 - - + +
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Residues in contact with THR 485 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271S LEU* 4.1 6.4 - - + +
466S ILE* 4.9 20.2 - - + -
467S ALA 5.8 0.2 - - - -
481S CYS 2.6 20.6 + - - -
482S ILE* 3.3 7.7 + - - -
484S TYR* 1.3 74.0 - - - +
486S ASN* 1.3 55.4 - - - +
488S LYS* 2.8 12.1 + - + +
489S LEU* 2.7 39.0 + - + +
663S TYR* 3.0 26.5 + - - +
667S LEU* 3.4 22.0 - - + -
670S LEU* 5.7 0.7 - - + -
671S MET* 5.6 4.0 - - + -
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Residues in contact with ASN 486 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177S GLY 4.4 4.9 - - - +
466S ILE* 3.2 15.1 - - - +
467S ALA 2.5 29.3 + - - -
468S GLY* 3.3 4.7 - - - -
469S PHE* 2.5 35.2 + - + +
482S ILE 3.1 16.8 + - - +
483S ASN* 3.9 9.4 - - - +
485S THR* 1.3 79.5 - - - +
487S GLU* 1.3 62.3 + - - +
489S LEU* 3.7 5.5 + - - +
490S GLN* 3.2 23.7 + - - +
586S TYR* 3.5 24.1 + - + +
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Residues in contact with GLU 487 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483S ASN 3.3 8.3 + - - +
484S TYR* 2.9 14.2 + - + +
486S ASN* 1.3 78.8 - - - +
488S LYS* 1.3 64.0 + - - +
491S GLN* 3.3 16.8 + - - +
521S LEU* 3.5 32.5 - - + +
524S CYS* 3.3 31.1 - - + +
525S ILE* 4.9 8.2 - - + +
584S LEU 4.0 0.2 - - - +
585S HIS* 2.8 41.0 + - + +
586S TYR* 3.0 30.3 + - - +
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Residues in contact with LYS 488 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484S TYR* 2.7 34.6 + - + +
485S THR* 2.8 21.9 + - + +
487S GLU* 1.3 74.0 - - - +
489S LEU* 1.3 64.7 + - - +
491S GLN* 3.1 23.1 + - - +
492S LEU* 3.3 4.9 + - - +
522S GLN* 4.7 4.4 + - - +
525S ILE* 4.2 21.3 - - + +
529S GLU* 3.0 33.0 + - - -
667S LEU* 4.5 13.0 - - + -
668S THR* 6.2 4.5 - - - -
671S MET* 4.3 26.0 - - + +
675S ARG* 4.4 18.4 + - - +
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Residues in contact with LEU 489 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174S LEU* 4.6 9.9 - - + -
175S CYS 5.6 3.6 - - - +
176S THR* 4.8 17.3 - - + -
464S LEU* 3.4 33.2 - - + -
466S ILE* 4.3 20.9 - - + -
485S THR* 2.7 19.2 + - + +
486S ASN* 4.0 5.8 - - - +
488S LYS* 1.3 72.9 - - - +
490S GLN* 1.3 56.4 + - - +
492S LEU* 2.6 47.7 + - + +
493S PHE 3.3 1.0 + - - -
671S MET* 5.2 11.8 - - + +
674S LEU* 5.4 2.2 - - + -
681S PHE* 4.2 24.2 - - + -
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Residues in contact with GLN 490 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176S THR* 6.1 0.7 - - - -
486S ASN 3.2 16.1 + - - +
487S GLU 3.8 4.7 - - - +
488S LYS 3.3 0.2 - - - -
489S LEU* 1.3 78.0 - - - +
491S GLN* 1.3 55.0 + - - +
493S PHE* 2.8 23.3 + - - +
494S ASN* 2.4 48.3 + - - +
519S LEU* 4.9 3.4 - - - +
521S LEU* 3.6 17.5 - - + +
586S TYR* 3.7 20.2 - - + -
683S ARG* 3.3 25.3 + - - +
707S CYS 3.5 17.1 + - - +
708S ASN* 3.3 31.1 + - - +
709S GLY* 4.3 2.0 - - - +
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Residues in contact with GLN 491 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487S GLU 3.3 9.6 + - - +
488S LYS* 3.1 13.8 + - - +
490S GLN* 1.3 80.6 - - - +
492S LEU* 1.3 61.2 + - - +
494S ASN* 3.1 17.3 + - - +
495S HIS* 2.9 27.0 + - + +
499S ILE* 4.4 13.9 - - - +
519S LEU 4.3 1.2 + - - -
520S ASP* 3.5 20.1 + - - +
521S LEU* 2.6 41.8 + - + +
522S GLN* 3.8 24.7 - - - +
525S ILE* 4.3 11.7 - - + -
675S ARG* 6.0 4.0 - - - +
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Residues in contact with LEU 492 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174S LEU* 4.6 5.2 - - + -
488S LYS 3.3 3.7 + - - +
489S LEU* 2.6 33.4 + - + +
491S GLN* 1.3 73.1 - - - +
493S PHE* 1.3 54.5 + - - +
495S HIS* 3.0 8.5 + - + +
496S THR* 2.4 53.5 + - + +
671S MET* 4.0 18.2 - - - -
674S LEU* 3.8 37.0 - - + +
675S ARG* 4.6 31.4 - - + +
679S PRO* 6.0 2.7 - - + -
681S PHE* 4.5 10.5 - - + -
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Residues in contact with PHE 493 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120S PHE* 4.1 32.3 - + - -
176S THR* 5.9 0.2 - - + -
489S LEU* 3.3 2.5 + - + +
490S GLN* 2.8 12.7 + - - +
492S LEU* 1.3 78.5 - - - +
494S ASN* 1.3 62.1 + - - +
496S THR* 3.6 1.5 + - - -
497S MET* 2.7 77.7 + - + +
498S PHE* 4.3 6.3 - + - -
681S PHE* 3.4 48.0 - + + -
683S ARG* 2.9 34.1 - - - +
708S ASN 3.5 14.4 - - - -
709S GLY* 4.0 11.0 - - - -
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Residues in contact with ASN 494 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490S GLN* 2.4 57.2 + - - +
491S GLN* 3.1 19.3 + - - +
493S PHE* 1.3 76.4 - - - +
495S HIS* 1.3 62.0 + - - +
498S PHE* 3.0 40.4 + - + -
499S ILE* 3.6 7.3 + - - +
519S LEU* 3.3 50.6 - - - +
521S LEU* 4.0 7.8 - - - +
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Residues in contact with HIS 495 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491S GLN* 2.9 19.4 + - + +
492S LEU* 3.0 13.4 + - + +
494S ASN* 1.3 76.5 - - - +
496S THR* 1.3 59.5 + - - +
499S ILE* 3.1 49.7 + - + +
500S LEU* 2.8 69.9 + - + +
503S GLU* 5.6 0.8 + - - -
522S GLN* 5.7 3.3 + - - -
675S ARG* 6.0 7.4 - - - +
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Residues in contact with THR 496 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492S LEU* 2.4 47.7 + - + +
493S PHE* 3.6 5.4 - - - -
495S HIS* 1.3 77.4 - - - +
497S MET* 1.3 67.1 + - - +
500S LEU* 3.4 27.6 - - + +
501S GLU* 4.2 13.5 + - - +
675S ARG* 6.2 2.7 - - + -
679S PRO* 4.4 23.1 - - + -
681S PHE* 4.3 7.3 - - - -
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Residues in contact with MET 497 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119S LEU* 3.5 32.5 - - + -
120S PHE* 4.5 10.3 - - - -
493S PHE* 2.7 61.4 + - + +
495S HIS 3.1 0.2 - - - -
496S THR* 1.3 86.6 - - - +
498S PHE* 1.3 81.2 + - + +
501S GLU* 3.8 19.9 - - - +
681S PHE* 5.0 7.6 - - - -
713S GLY* 4.3 10.1 - - - +
716S ILE* 4.1 17.4 - - + +
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Residues in contact with PHE 498 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493S PHE* 4.3 5.8 - + - -
494S ASN* 3.0 39.6 + - + +
497S MET* 1.3 93.0 - - + +
499S ILE* 1.3 70.9 + - + +
500S LEU 3.7 0.2 - - - -
501S GLU* 3.8 1.5 + - - +
502S GLN* 3.0 31.5 + - - +
514S PHE* 6.0 0.7 - - + -
517S PHE* 3.4 41.1 - + + -
519S LEU* 3.4 39.5 - - + -
709S GLY 4.2 4.3 - - - -
712S GLU* 3.3 36.6 - - + -
713S GLY* 3.7 10.5 - - - -
716S ILE* 5.1 3.6 - - + -
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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