Contacts of the helix formed by residues 434 - 461 (chain r) in PDB entry 6QX2
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 434 (chain r).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431r ARG* 3.4 22.2 + - - +
432r ARG 3.4 0.6 - - - -
433r LEU* 1.3 81.4 - - - +
435r GLY* 1.3 63.3 - - - +
436r LEU* 4.2 1.2 + - - +
437r GLU* 3.5 13.2 + - - +
438r ARG* 3.2 21.7 + - - +
398t ILE* 3.7 18.2 - - + +
401t SER 3.3 11.2 - - - +
402t ASP 3.7 8.2 + - - -
403t THR* 3.7 18.6 - - - +
404t ASP* 3.4 18.1 + - - +
407t ALA* 4.2 12.1 - - + -
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Residues in contact with GLY 435 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434r THR* 1.3 67.5 - - - +
436r LEU* 1.3 63.3 + - - -
437r GLU 3.4 0.5 + - - -
438r ARG* 3.4 34.2 + - - +
439r ASP* 3.4 19.9 + - - +
401t SER 3.0 8.4 + - - -
402t ASP* 2.9 22.0 + - - -
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Residues in contact with LEU 436 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434r THR* 4.2 2.0 + - - +
435r GLY* 1.3 73.2 - - - +
437r GLU* 1.3 57.5 + - + +
439r ASP* 3.4 14.8 + - + +
440r LYS* 3.0 33.0 + - + +
402t ASP* 2.8 20.1 + - + +
403t THR* 4.3 19.7 - - + -
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Residues in contact with GLU 437 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431r ARG* 3.7 21.6 - - + +
432r ARG* 3.5 43.8 + - - +
434r THR* 3.7 13.6 + - - +
435r GLY 3.2 0.8 - - - -
436r LEU* 1.3 78.4 - - + +
438r ARG* 1.3 62.5 + - - +
440r LYS* 2.6 36.0 + - - +
441r ILE* 3.2 27.8 + - - +
404t ASP* 4.8 6.8 - - - +
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Residues in contact with ARG 438 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388r LEU* 3.8 41.9 - - + +
432r ARG 4.4 5.6 - - - +
433r LEU* 3.0 26.7 + - - +
434r THR 3.2 21.9 + - - +
435r GLY* 3.4 22.0 + - - +
436r LEU 3.4 0.2 - - - -
437r GLU* 1.3 76.1 - - - +
439r ASP* 1.3 63.8 + - - +
441r ILE* 3.5 5.2 + - - +
442r GLU* 3.3 21.3 + - - +
399t ARG* 3.5 23.3 + - - +
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Residues in contact with ASP 439 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435r GLY 3.4 16.1 - - - +
436r LEU* 3.4 17.7 + - + +
437r GLU 3.3 0.4 - - - -
438r ARG* 1.3 77.6 + - - +
440r LYS* 1.3 54.4 + - - +
442r GLU* 3.1 6.8 + - - +
443r ALA* 2.9 36.1 + - - +
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Residues in contact with LYS 440 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436r LEU* 3.0 21.3 + - + +
437r GLU* 2.6 43.0 + - - +
439r ASP* 1.3 76.1 - - - +
441r ILE* 1.3 55.8 + - + +
443r ALA* 3.6 7.8 - - - +
444r GLU* 3.1 28.9 + - - +
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Residues in contact with ILE 441 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377r ARG* 6.0 0.2 - - - +
381r LEU* 4.0 25.5 - - + +
384r LEU* 4.2 23.3 - - + -
385r ARG* 4.1 24.2 - - + -
388r LEU* 3.5 28.7 - - + -
428r MET* 5.2 1.3 - - - -
432r ARG* 4.6 22.2 - - + +
437r GLU* 3.2 22.8 + - - +
438r ARG* 3.7 8.1 - - - +
439r ASP 3.2 0.4 - - - -
440r LYS* 1.3 74.6 - - + +
442r GLU* 1.3 60.4 + - - +
444r GLU* 3.5 11.3 + - - +
445r TYR* 3.0 25.5 + - - +
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Residues in contact with GLU 442 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385r ARG* 3.3 39.2 + - + +
438r ARG 3.3 9.2 + - - +
439r ASP* 3.1 9.2 + - - +
441r ILE* 1.3 78.4 - - + +
443r ALA* 1.3 63.5 + - - +
445r TYR* 3.3 4.2 + - + +
446r ASN* 2.8 58.4 + - - +
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Residues in contact with ALA 443 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439r ASP 2.9 17.5 + - - +
440r LYS* 3.6 10.1 - - - +
442r GLU* 1.3 76.5 - - - +
444r GLU* 1.3 61.6 + - - +
446r ASN* 3.3 5.7 + - - +
447r GLU* 3.2 23.3 + - - +
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Residues in contact with GLU 444 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377r ARG* 2.9 46.5 + - - +
381r LEU* 3.7 12.3 - - + +
440r LYS 3.1 16.4 + - - +
441r ILE* 3.7 7.2 - - - +
443r ALA* 1.3 76.5 - - - +
445r TYR* 1.3 58.1 + - - +
447r GLU* 3.6 5.9 + - - +
448r LEU* 3.1 33.7 + - + +
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Residues in contact with TYR 445 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378r ALA* 3.6 29.4 - - + -
381r LEU* 3.6 28.2 - - + +
382r GLU* 2.8 33.5 + - + +
385r ARG* 3.7 41.7 + - - -
441r ILE 3.0 17.7 + - - +
442r GLU* 3.6 6.3 - - - +
443r ALA 3.2 0.2 - - - -
444r GLU* 1.3 76.5 - - - +
446r ASN* 1.3 68.1 + - - +
448r LEU* 3.4 5.0 - - + +
449r LEU* 3.2 55.8 + - + +
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Residues in contact with ASN 446 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385r ARG* 5.6 0.2 + - - -
442r GLU* 2.8 53.9 + - - +
443r ALA* 3.9 5.3 - - - +
445r TYR* 1.3 80.2 - - - +
447r GLU* 1.3 64.3 + - - +
449r LEU* 3.2 21.5 + - - +
450r ASN* 3.3 20.6 + - - +
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Residues in contact with GLU 447 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443r ALA 3.2 15.7 + - - +
444r GLU* 3.9 6.7 - - - +
446r ASN* 1.3 74.6 - - - +
448r LEU* 1.3 56.7 - - - +
450r ASN* 3.3 12.9 + - - +
451r TYR* 2.9 29.0 + - - +
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Residues in contact with LEU 448 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374r ALA* 3.5 37.9 - - + +
377r ARG* 3.4 31.9 - - + -
378r ALA* 3.7 19.7 - - + +
381r LEU* 3.8 17.3 - - + -
444r GLU* 3.1 22.0 + - + +
445r TYR* 3.4 7.6 - - - +
446r ASN 3.2 0.2 - - - -
447r GLU* 1.3 76.3 - - - +
449r LEU* 1.3 51.6 + - - +
451r TYR* 3.3 13.3 + - + +
452r ILE* 2.8 44.3 + - + +
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Residues in contact with LEU 449 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378r ALA* 5.1 3.4 - - + -
382r GLU* 5.2 1.6 - - - +
445r TYR* 3.2 57.9 + - + +
446r ASN* 3.2 16.3 + - - +
448r LEU* 1.3 74.0 - - - +
450r ASN* 1.3 66.8 + - - +
452r ILE* 3.4 17.1 + - + +
453r SER* 3.2 22.7 + - - -
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Residues in contact with ASN 450 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446r ASN 3.3 14.4 + - - +
447r GLU* 3.3 11.9 + - - +
449r LEU* 1.3 77.3 - - - +
451r TYR* 1.3 57.6 + - - +
453r SER* 3.2 9.7 + - - -
454r GLU* 3.0 42.6 + - - +
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Residues in contact with TYR 451 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370r ASN* 3.2 34.5 + - + +
374r ALA* 4.2 19.1 - - + -
447r GLU 2.9 14.3 + - - +
448r LEU* 3.5 15.5 - - + +
450r ASN* 1.3 73.1 - - - +
452r ILE* 1.3 63.4 + - - +
454r GLU* 3.2 21.1 + - + +
455r LEU* 2.9 62.1 + - + +
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Residues in contact with ILE 452 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371r LEU* 3.7 15.7 - - + +
374r ALA* 3.8 29.6 - - + +
375r LYS* 4.2 16.8 - - + -
378r ALA* 4.0 27.8 - - + -
448r LEU* 2.8 28.7 + - + +
449r LEU* 3.8 14.6 - - + +
450r ASN 3.3 0.4 - - - -
451r TYR* 1.3 71.4 - - - +
453r SER* 1.3 55.6 + - - +
455r LEU* 3.4 4.9 + - - +
456r GLU* 3.1 49.9 + - - +
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Residues in contact with SER 453 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449r LEU 3.2 12.5 + - - -
450r ASN* 3.2 11.5 + - - -
452r ILE* 1.3 74.9 - - - +
454r GLU* 1.3 58.4 + - - +
456r GLU* 3.3 14.3 + - - +
457r THR* 2.8 35.0 + - - -
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Residues in contact with GLU 454 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450r ASN* 3.0 33.0 + - + +
451r TYR* 3.5 24.9 - - + +
453r SER* 1.3 74.6 + - - +
455r LEU* 1.3 62.6 + - + +
457r THR* 3.5 10.6 + - - -
458r ILE* 3.4 29.0 + - + +
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Residues in contact with LEU 455 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367r THR* 3.6 29.4 - - + +
370r ASN* 3.8 8.3 - - + +
371r LEU* 3.5 42.2 - - + +
374r ALA* 4.6 1.3 - - + -
451r TYR* 2.9 67.3 + - + +
452r ILE* 3.6 6.3 - - - +
454r GLU* 1.3 74.6 - - + +
456r GLU* 1.3 63.6 + - - +
458r ILE* 3.2 17.6 + - + +
459r LEU* 3.2 20.1 + - - +
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Residues in contact with GLU 456 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371r LEU* 4.0 16.2 - - + -
375r LYS* 3.6 22.8 + - - +
452r ILE* 3.1 35.9 + - - +
453r SER* 3.3 14.2 + - - +
455r LEU* 1.3 73.0 - - - +
457r THR* 1.3 55.9 + - - +
459r LEU* 3.3 7.9 + - + +
460r ALA* 2.9 36.5 + - - +
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Residues in contact with THR 457 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453r SER* 2.8 19.8 + - - -
454r GLU* 3.5 11.3 + - - -
456r GLU* 1.3 76.7 - - - +
458r ILE* 1.3 60.7 + - - +
460r ALA* 3.5 6.9 + - - +
461r ASP* 3.2 24.5 + - + +
464r VAL* 4.1 19.2 - - + +
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Residues in contact with ILE 458 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367r THR* 4.0 18.6 - - + +
454r GLU* 3.4 18.8 + - + +
455r LEU* 3.2 21.4 + - + +
457r THR* 1.3 76.3 - - - +
459r LEU* 1.3 63.7 + - + +
461r ASP 3.3 18.0 - - - +
462r GLU* 4.9 0.2 - - - -
464r VAL* 3.7 20.9 - - + -
465r LEU* 3.6 43.4 - - + +
468r LEU* 3.8 24.7 - - + -
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Residues in contact with LEU 459 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364r ARG* 4.1 22.2 - - + +
367r THR* 3.7 21.5 - - + -
368r GLN* 3.6 37.9 - - + +
371r LEU* 3.6 31.0 - - + -
455r LEU 3.2 15.4 + - - +
456r GLU* 3.3 6.0 + - + +
458r ILE* 1.3 78.3 - - + +
460r ALA* 1.3 60.9 + - - +
461r ASP 5.0 0.9 - - - -
462r GLU* 5.1 1.0 + - - +
465r LEU* 5.9 2.5 - - + -
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Residues in contact with ALA 460 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456r GLU 2.9 18.5 + - - +
457r THR* 3.7 8.1 - - - +
458r ILE 3.3 0.2 - - - -
459r LEU* 1.3 78.0 - - - +
461r ASP* 1.3 58.5 + - + +
462r GLU 4.1 1.7 + - - -
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Residues in contact with ASP 461 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457r THR* 3.2 7.7 + - + +
458r ILE 3.3 8.3 - - - +
460r ALA* 1.3 77.3 - - + +
462r GLU* 1.3 55.4 + - - +
463r GLU* 3.2 22.1 + - - +
464r VAL* 2.9 50.1 + - + +
465r LEU 3.3 8.1 + - - -
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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