Contacts of the helix formed by residues 466 - 489 (chain A) in PDB entry 5UNJ
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 ASN 466 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368A GLU 5.5 3.0 + - - -
369A LEU* 4.0 10.2 - - + +
370A LYS 6.3 0.2 - - - +
373A ASP* 3.1 12.1 + - - +
464A LEU* 3.2 3.1 - - - -
465A GLU* 1.3 90.3 + - - +
467A PHE* 1.3 60.5 + - - +
468A GLN* 3.6 10.3 + - - +
469A LEU* 2.9 50.8 + - - +
470A VAL* 3.4 14.8 + - - +
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Residues in contact with PHE 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459A LEU* 4.1 39.9 - - + -
461A VAL 4.7 5.2 - - - -
464A LEU* 3.9 39.0 + - + +
465A GLU 3.8 2.4 + - - -
466A ASN* 1.3 76.3 - - - +
468A GLN* 1.3 64.1 + - + +
470A VAL* 4.4 2.7 - - + -
471A GLU* 2.8 61.7 + - + +
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Residues in contact with GLN 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A ASN* 3.1 8.7 - - - +
467A PHE* 1.3 83.7 - - + +
469A LEU* 1.3 57.5 + - - +
471A GLU* 3.6 18.5 - - - +
472A GLY* 2.9 26.2 + - - -
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Residues in contact with LEU 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A PHE* 3.8 27.6 - - + +
368A GLU* 4.0 21.3 - - + +
369A LEU* 3.7 26.7 - - + +
457A PHE* 5.1 1.6 - - + -
466A ASN* 2.9 33.3 + - - +
468A GLN* 1.3 73.7 - - - +
470A VAL* 1.3 59.1 + - - +
472A GLY* 3.2 1.3 + - - -
473A VAL* 2.8 50.0 + - + +
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Residues in contact with VAL 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A LEU* 4.2 16.4 - - + -
377A LEU* 4.3 12.8 - - + -
457A PHE* 3.9 34.7 - - + +
458A SER 3.4 25.6 - - - +
459A LEU* 4.4 4.7 - - + -
464A LEU* 4.0 24.9 - - + -
466A ASN 3.4 12.1 + - - +
467A PHE* 3.3 9.2 + - + +
469A LEU* 1.3 74.4 - - - +
471A GLU* 1.3 65.3 + - - +
473A VAL* 3.3 2.1 + - - +
474A GLN* 2.9 22.7 + - - +
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Residues in contact with GLU 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459A LEU* 3.7 19.6 - - + +
467A PHE* 2.8 49.3 + - + +
468A GLN* 3.6 17.7 - - - +
470A VAL* 1.3 73.4 - - - +
472A GLY* 1.3 58.9 + - - +
474A GLN* 3.3 2.9 + - - +
475A GLU* 3.0 35.9 + - + +
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Residues in contact with GLY 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468A GLN 2.9 18.2 + - - -
469A LEU* 3.7 0.9 - - - -
471A GLU* 1.3 75.6 - - - +
473A VAL* 1.3 64.8 + - - +
475A GLU* 3.3 16.6 + - - +
476A GLN* 3.0 31.9 + - - +
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Residues in contact with VAL 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A PHE* 3.9 39.7 - - + -
453A PHE* 5.0 2.5 - - + +
457A PHE* 3.6 39.3 - - + -
469A LEU* 2.8 35.3 + - + +
470A VAL 3.7 3.6 - - - +
472A GLY* 1.3 72.0 - - - +
474A GLN* 1.3 64.0 + - - +
476A GLN* 3.3 3.8 + - - -
477A VAL* 2.9 44.4 + - + +
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Residues in contact with GLN 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A LEU* 3.5 36.2 + - - +
457A PHE* 2.6 28.7 - - - +
458A SER* 4.5 0.6 - - - -
459A LEU* 3.9 36.0 - - + +
470A VAL 2.9 18.0 + - - +
471A GLU 3.5 4.9 - - - +
473A VAL* 1.3 78.7 - - - +
475A GLU* 1.3 62.4 + - - +
477A VAL* 4.8 0.4 - - - -
478A ASN* 3.0 49.0 + - - +
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Residues in contact with GLU 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471A GLU* 3.0 21.6 + - + +
472A GLY* 3.3 22.0 - - - +
473A VAL 3.2 0.2 - - - -
474A GLN* 1.3 78.2 - - - +
476A GLN* 1.3 82.4 + - + +
478A ASN* 3.8 5.9 - - - +
479A ALA* 3.1 27.5 + - - +
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Residues in contact with GLN 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A LEU* 3.3 23.6 - - + +
472A GLY 3.0 21.5 + - - +
473A VAL* 4.0 3.8 - - - +
475A GLU* 1.3 96.3 + - + +
477A VAL* 1.3 60.0 + - + +
479A ALA* 3.4 9.1 + - - +
480A ALA* 2.9 23.0 + - - +
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Residues in contact with VAL 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A LEU* 4.1 17.7 - - + -
308A LEU* 4.5 12.3 - - + -
365A PHE* 5.4 0.9 - - + -
450A CYS* 3.6 40.7 - - + +
453A PHE* 4.4 15.5 - - + -
454A LEU* 3.7 17.5 - - + -
473A VAL* 2.9 36.5 + - + +
474A GLN* 4.8 0.2 - - - -
476A GLN* 1.3 73.9 - - - +
478A ASN* 1.3 59.9 + - - +
480A ALA* 3.2 2.5 + - - +
481A LEU* 2.9 28.4 + - - +
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Residues in contact with ASN 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A LEU* 3.5 22.0 - - - +
474A GLN* 3.0 46.9 + - - +
475A GLU* 3.8 6.8 - - - +
477A VAL* 1.3 77.7 - - - +
479A ALA* 1.3 57.0 + - - +
481A LEU* 3.3 2.3 + - - -
482A LEU* 2.9 26.3 + - - +
496A PHE* 3.5 30.6 - - + -
500A LEU* 3.9 8.4 - - - +
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Residues in contact with ALA 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475A GLU 3.1 18.9 + - - +
476A GLN* 3.8 11.9 - - - +
477A VAL 3.3 0.2 - - - -
478A ASN* 1.3 75.8 - - - +
480A ALA* 1.3 58.6 + - - +
482A LEU* 3.5 8.2 + - - +
483A ASP* 2.9 29.6 + - - +
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Residues in contact with ALA 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A PRO* 3.9 10.9 - - + +
304A LEU* 3.8 21.8 - - + -
305A ILE* 3.6 23.7 - - + +
308A LEU* 6.5 0.2 - - + -
450A CYS* 5.2 0.7 - - - -
476A GLN 2.9 17.3 + - - +
477A VAL* 3.7 4.3 - - - +
479A ALA* 1.3 77.1 - - - +
481A LEU* 1.3 57.6 + - - +
483A ASP* 3.5 6.3 + - - +
484A TYR* 2.9 30.3 + - - +
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Residues in contact with LEU 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447A GLU* 3.8 33.9 - - + +
450A CYS* 3.8 27.9 - - + -
451A LEU* 4.0 26.5 - - + -
454A LEU* 4.2 12.8 - - + -
477A VAL 2.9 17.4 + - - +
478A ASN* 3.7 4.0 - - - +
480A ALA* 1.3 74.3 - - - +
482A LEU* 1.3 60.7 + - - +
484A TYR* 3.8 4.7 - - + +
485A THR* 2.9 40.5 + - + +
496A PHE* 3.9 21.8 - - + -
499A LEU* 4.3 8.3 - - + -
500A LEU* 4.3 4.3 - - + -
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Residues in contact with LEU 482 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478A ASN 2.9 16.9 + - - +
479A ALA* 3.8 7.0 - - - +
481A LEU* 1.3 75.1 - - - +
483A ASP* 1.3 64.3 + - - +
485A THR* 3.1 2.4 + - - -
486A MET* 2.9 56.8 + - + +
496A PHE* 3.6 44.3 - - + -
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Residues in contact with ASP 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A SER 5.6 0.9 - - - +
302A PRO* 4.1 15.0 - - + +
479A ALA 2.9 18.3 + - - +
480A ALA* 3.8 7.2 - - - +
482A LEU* 1.3 77.9 - - - +
484A TYR* 1.3 63.6 + - - +
486A MET* 4.0 3.2 - - - +
487A CYS* 3.0 46.0 + - - +
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Residues in contact with TYR 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A SER 4.3 1.1 - - - -
301A ILE* 4.1 13.0 - - + -
302A PRO* 4.0 21.3 - - + +
305A ILE* 3.8 14.4 - - + -
444A ASP* 2.6 33.9 + - - -
446A ARG* 2.9 41.5 + - + -
447A GLU* 3.7 26.5 - - + -
480A ALA 2.9 18.8 + - - +
481A LEU* 3.8 3.8 - - + +
482A LEU 3.2 0.2 - - - -
483A ASP* 1.3 78.5 + - - +
485A THR* 1.3 59.7 + - + +
487A CYS* 4.9 0.2 - - - -
488A ASN* 2.8 70.0 + - + +
489A TYR* 4.0 7.5 + + - -
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Residues in contact with THR 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447A GLU* 3.5 26.2 - - + +
481A LEU* 2.9 40.0 + - + +
482A LEU* 3.1 5.7 + - - +
484A TYR* 1.3 77.7 - - + +
486A MET* 1.3 61.2 + - - +
489A TYR* 2.8 37.3 + - - +
495A LYS* 4.4 10.3 - - + -
496A PHE* 3.5 28.3 + - - +
499A LEU* 4.1 11.7 - - + -
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Residues in contact with MET 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482A LEU* 2.9 46.1 + - + +
483A ASP* 4.0 4.0 - - - +
485A THR* 1.3 78.6 + - - +
487A CYS* 1.3 65.1 + - - +
489A TYR 5.0 0.4 - - - -
490A PRO* 3.3 28.6 - - - +
496A PHE* 5.8 0.4 - - + -
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Residues in contact with CYS 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A SER 5.2 8.5 - - - +
483A ASP* 3.0 39.0 + - - +
484A TYR* 4.1 1.8 - - - +
486A MET* 1.3 81.6 - - - +
488A ASN* 1.3 69.3 + - - +
490A PRO* 3.9 8.7 - - - +
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Residues in contact with ASN 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A SER* 3.3 26.6 + - - +
301A ILE* 5.6 1.0 - - - +
484A TYR* 2.8 58.3 + - + +
487A CYS* 1.3 84.0 - - - +
489A TYR* 1.3 84.6 + - + +
490A PRO* 3.4 6.2 - - - +
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Residues in contact with TYR 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442A GLN* 3.7 40.4 + - + -
444A ASP* 2.7 30.3 + - - +
446A ARG* 4.6 2.6 + - - -
447A GLU* 3.3 13.5 - - - -
484A TYR* 4.0 3.0 + + - -
485A THR* 2.8 20.9 + - - +
486A MET* 5.0 0.3 - - - -
488A ASN* 1.3 96.2 - - + +
490A PRO* 1.3 65.5 - - - +
491A GLN 3.2 2.5 - - - -
492A GLN* 3.1 25.8 + - + +
495A LYS* 3.3 42.0 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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