Contacts of the helix formed by residues 469 - 494 (chain S) in PDB entry 5GJQ
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 469 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467S TYR* 2.9 13.6 + - - -
468S SER* 1.3 78.3 - - - +
470S ARG* 1.3 55.8 + - + +
472S PRO* 2.7 29.6 - - - +
473S GLN* 2.7 54.0 + - - +
335T LEU* 5.6 4.5 - - + -
250U TYR* 4.3 16.2 + - + -
253U THR* 3.5 18.2 - - + +
254U ASN* 2.3 32.7 + - - -
257U MET* 5.8 1.4 - - - +
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Residues in contact with ARG 470 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468S SER* 2.8 30.9 + - - +
469S THR* 1.3 76.5 - - + +
471S GLU* 1.3 67.0 + - + +
473S GLN* 3.5 13.7 + - - +
474S LEU* 3.2 29.8 + - + +
335T LEU* 5.6 7.9 - - + -
338T GLN* 5.5 0.5 + - - -
250U TYR* 5.1 15.4 + - - +
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Residues in contact with GLU 471 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366R TYR* 4.3 14.3 + - + +
465S ASP* 5.5 2.4 - - - +
468S SER* 3.4 24.0 + - - +
470S ARG* 1.3 72.9 - - + +
472S PRO* 1.3 74.9 - - + +
473S GLN 3.0 1.2 + - - -
474S LEU* 3.0 20.6 + - - +
475S ALA* 3.1 13.0 + - - +
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Residues in contact with PRO 472 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366R TYR* 3.5 26.7 - - + +
370R ILE* 5.4 0.2 - - + -
467S TYR* 3.6 18.8 - - + -
469S THR* 2.7 39.5 - - - +
471S GLU* 1.3 100.1 - - + +
473S GLN* 1.3 50.2 + - + +
475S ALA* 3.4 7.4 + - + +
476S PHE* 2.1 66.0 + - + -
254U ASN* 5.2 0.2 - - - +
257U MET* 6.6 0.2 - - + -
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Residues in contact with GLN 473 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469S THR* 2.7 39.1 - - + +
470S ARG* 3.6 14.0 - - - +
472S PRO* 1.3 81.8 - - + +
474S LEU* 1.3 52.4 + - - +
476S PHE* 3.0 7.7 + - - -
477S HIS* 2.7 19.8 + - - +
335T LEU* 3.7 24.7 - - - +
338T GLN* 3.7 23.7 + - - +
342T TYR* 2.6 33.0 + - + +
253U THR* 4.3 12.7 + - - -
257U MET* 4.5 28.6 - - + +
303V MET* 5.6 1.4 - - - +
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Residues in contact with LEU 474 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470S ARG* 3.2 17.7 + - + +
471S GLU* 3.0 10.5 + - - +
473S GLN* 1.3 77.7 - - - +
475S ALA* 1.3 64.1 + - - +
477S HIS* 3.1 14.5 + - + +
478S GLN* 2.8 35.2 + - + +
338T GLN* 3.3 27.4 - - - +
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Residues in contact with ALA 475 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366R TYR* 5.6 1.6 - - - +
370R ILE* 5.5 11.7 - - + -
471S GLU 3.1 9.7 + - - +
472S PRO* 3.6 11.2 - - + +
474S LEU* 1.3 76.7 - - - +
476S PHE* 1.3 63.3 + - + +
478S GLN* 3.5 12.4 + - - +
479S ARG* 2.9 43.8 + - - +
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Residues in contact with PHE 476 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366R TYR* 4.8 2.5 - + - -
369R THR* 5.6 3.6 - - + -
370R ILE* 3.5 27.6 - - + -
467S TYR* 4.8 7.0 - - - -
472S PRO* 2.1 65.2 + - + +
473S GLN* 3.3 7.0 - - + -
475S ALA* 1.3 71.3 - - - +
477S HIS* 1.3 58.2 - - - +
479S ARG* 3.1 6.6 + - - +
480S ILE* 1.8 42.9 + - + +
342T TYR* 3.2 11.2 - - - +
257U MET* 4.8 23.6 - - + -
258U VAL* 6.0 3.6 - - + -
261U TYR* 2.7 51.4 - + + -
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Residues in contact with HIS 477 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473S GLN 2.7 10.9 + - - +
474S LEU* 3.5 17.0 - - + +
476S PHE* 1.3 72.5 - - - +
478S GLN* 1.3 69.7 + - + +
480S ILE* 3.1 11.5 + - - +
481S SER* 3.2 13.1 + - - -
338T GLN* 5.5 7.2 - - + +
341T GLU* 5.3 11.4 + - + -
342T TYR* 2.6 39.5 + + + +
345T GLN* 3.1 45.6 + - + +
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Residues in contact with GLN 478 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474S LEU* 2.8 24.9 + - + +
475S ALA* 3.7 14.3 - - - +
477S HIS* 1.3 86.1 - - + +
479S ARG* 1.3 74.9 + - - +
481S SER* 2.7 26.2 + - - -
482S PHE* 3.4 6.8 + - - +
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Residues in contact with ARG 479 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370R ILE* 5.3 3.8 - - - +
374R ASP* 3.0 35.9 + - - +
377R LEU* 3.0 35.6 - - + +
475S ALA* 2.9 32.1 + - - +
476S PHE* 3.1 11.1 + - - +
478S GLN* 1.3 90.8 + - - +
480S ILE* 1.3 66.4 + - + +
482S PHE* 3.0 19.8 + - + +
483S CYS* 3.0 17.8 + - - -
261U TYR* 5.4 9.2 - - + +
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Residues in contact with ILE 480 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476S PHE* 1.8 50.5 - - + +
477S HIS* 3.4 9.6 - - - +
479S ARG* 1.3 79.7 - - + +
481S SER* 1.3 55.9 + - - +
483S CYS* 3.2 9.7 + - + +
484S LEU* 2.9 51.0 + - + +
342T TYR* 4.4 8.7 - - + -
345T GLN* 3.6 15.5 - - + +
346T LEU* 5.8 3.4 - - + -
349T ILE* 4.8 8.7 - - + -
260U VAL* 6.5 0.4 - - + -
261U TYR* 5.6 4.9 - - + -
264U SER* 4.8 19.5 - - - +
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Residues in contact with SER 481 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477S HIS* 3.2 9.0 + - - -
478S GLN* 2.7 22.9 + - - -
480S ILE* 1.3 77.3 - - - +
482S PHE* 1.3 56.3 + - - +
484S LEU* 3.5 12.7 - - - +
485S ASP* 2.9 41.2 + - - +
345T GLN* 3.6 19.6 + - - +
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Residues in contact with PHE 482 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377R LEU* 6.3 1.3 - - + -
381R GLN* 2.8 35.2 - - + -
307S ARG* 5.7 10.5 - - - -
314S ARG* 4.0 26.0 - - - -
478S GLN 3.4 6.7 + - - +
479S ARG* 3.0 14.2 + - + +
481S SER* 1.3 80.2 + - - +
483S CYS* 1.3 67.4 + - - +
485S ASP* 3.4 8.1 + - + +
486S ILE* 2.9 67.6 + - + +
489S MET* 6.3 0.7 - - - -
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Residues in contact with CYS 483 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377R LEU* 3.5 32.1 - - - -
380R VAL* 5.9 4.7 - - - -
479S ARG* 3.0 17.9 + - - -
480S ILE* 3.2 9.4 + - + +
482S PHE* 1.3 76.2 - - - +
484S LEU* 1.3 65.9 + - + +
486S ILE* 3.2 12.9 + - - +
487S HIS* 2.8 23.2 + - - +
265U LEU* 4.9 6.1 - - - -
268U SER* 4.6 25.5 - - - -
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Residues in contact with LEU 484 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480S ILE* 2.9 38.3 + - + +
481S SER* 3.5 9.2 - - - +
483S CYS* 1.3 76.0 - - + +
485S ASP* 1.3 52.4 + - - +
487S HIS* 2.5 31.1 + - + +
488S ASN* 2.7 31.2 + - - +
345T GLN* 3.8 34.5 - - - +
349T ILE* 3.5 41.3 - - + +
267U ARG* 5.6 3.8 - - - +
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Residues in contact with ASP 485 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481S SER* 2.9 29.8 + - - +
482S PHE* 3.7 8.3 - - + +
484S LEU* 1.3 73.0 - - - +
486S ILE* 1.3 57.9 + - + +
488S ASN* 2.8 15.7 + - - +
489S MET* 2.7 52.9 + - + +
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Residues in contact with ILE 486 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380R VAL* 5.6 6.7 - - + -
381R GLN* 3.2 28.0 - - + -
384R SER* 3.7 28.0 - - - +
314S ARG* 5.7 2.9 - - - +
482S PHE* 2.9 56.7 + - + +
483S CYS* 3.5 9.9 - - - +
485S ASP* 1.3 76.9 - - + +
487S HIS* 1.3 49.7 + - - +
489S MET* 4.3 11.1 - - - +
490S SER* 2.3 32.9 + - - -
272U LEU* 6.2 2.9 - - + -
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Residues in contact with HIS 487 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483S CYS 2.8 11.3 + - - +
484S LEU* 2.5 21.1 + - + +
486S ILE* 1.3 70.0 - - - +
488S ASN* 1.3 58.9 + - - +
490S SER* 3.1 10.5 + - - -
491S VAL* 2.5 46.4 - - + +
267U ARG* 4.4 15.4 + - - -
268U SER* 5.4 4.3 - - - -
271U ALA* 3.3 36.3 - - + +
272U LEU 5.2 0.7 - - - -
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Residues in contact with ASN 488 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484S LEU* 2.7 33.1 + - - +
485S ASP* 2.8 16.4 + - - +
487S HIS* 1.3 80.9 + - - +
489S MET* 1.3 60.0 + - + +
491S VAL* 3.0 5.9 + - - +
492S LYS* 2.9 56.1 + - - +
349T ILE* 4.9 9.1 - - - +
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Residues in contact with MET 489 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388R ASN* 4.8 10.8 - - - +
314S ARG* 5.1 13.7 - - - +
315S LYS* 5.9 3.6 - - - +
482S PHE* 6.3 0.7 - - - -
485S ASP* 2.7 41.4 + - + +
486S ILE* 4.2 11.2 - - - +
488S ASN* 1.3 73.5 - - + +
490S SER* 1.3 57.0 + - - +
492S LYS* 3.4 6.6 + - - +
493S ALA* 2.9 33.3 + - - +
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Residues in contact with SER 490 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388R ASN* 4.1 18.4 - - - -
486S ILE 2.3 28.5 + - - -
487S HIS* 3.1 16.1 + - - -
489S MET* 1.3 78.3 - - - +
491S VAL* 1.3 53.3 + - - +
494S MET* 2.6 39.1 + - - +
275U LEU* 3.5 23.4 - - - +
279U LYS* 4.1 7.0 - - - +
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Residues in contact with VAL 491 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45J LEU* 2.6 37.7 - - + +
49J ARG* 5.3 17.0 - - + +
487S HIS* 2.5 54.1 - - + +
488S ASN* 3.0 7.7 + - - +
490S SER* 1.3 77.7 - - - +
492S LYS* 1.3 53.1 + - + +
493S ALA 3.4 0.2 - - - -
494S MET* 4.7 2.0 - - - -
495S ARG* 3.0 11.6 - - + +
275U LEU* 4.9 7.4 - - + -
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Residues in contact with LYS 492 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41J ASN* 5.4 7.3 - - - +
42J LEU* 3.4 28.7 - - + +
45J LEU* 3.1 36.2 - - + +
488S ASN* 2.9 39.9 + - - +
489S MET* 4.0 6.3 - - - +
490S SER 3.4 0.2 - - - -
491S VAL* 1.3 80.9 - - + +
493S ALA* 1.3 58.7 + - - +
495S ARG* 4.5 0.3 + - - +
496S PHE* 4.9 4.3 + - - +
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Residues in contact with ALA 493 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388R ASN* 3.5 22.0 - - - +
489S MET 2.9 17.9 + - - +
492S LYS* 1.3 76.9 - - - +
494S MET* 1.3 52.7 + - - +
495S ARG 2.9 4.3 - - - -
496S PHE* 2.8 34.8 + - - +
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Residues in contact with MET 494 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388R ASN 5.3 0.2 - - - -
490S SER 2.6 24.2 + - - +
491S VAL* 4.7 1.1 - - - -
493S ALA* 1.3 77.1 - - - +
495S ARG* 1.3 57.6 + - - +
496S PHE 2.9 15.3 + - - +
275U LEU* 3.4 13.7 - - + -
278U ASN* 5.3 13.5 - - + +
279U LYS* 3.0 38.4 - - + +
282U ASN* 4.6 9.7 - - - +
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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