Contacts of the helix formed by residues 469 - 494 (chain A) in PDB entry 6RKU
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 LEU 469 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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467A THR* 3.0 7.7 + - - +
468A GLY* 1.3 87.1 - - - +
470A GLU* 1.3 66.3 + - + +
471A HIS 3.3 1.8 - - - -
472A GLU* 3.3 13.7 + - - +
473A LYS* 3.0 52.4 + - + +
401C PRO* 3.4 26.0 - - + +
402C THR* 5.1 6.1 - - - +
403C PRO* 5.2 4.7 - - + -
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Residues in contact with GLU 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A LEU* 5.4 0.9 - - + -
464A GLN* 3.6 24.2 - - - +
465A LYS* 3.7 46.2 - - + +
467A THR* 3.7 10.7 + - - +
469A LEU* 1.3 77.6 - - - +
471A HIS* 1.3 58.9 + - - +
473A LYS* 3.7 29.7 + - - +
474A LEU* 2.9 45.5 + - + +
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Residues in contact with HIS 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A LEU* 3.9 29.3 - - + +
420A VAL* 5.4 15.0 + - + +
421A ALA* 6.3 2.0 - - - -
467A THR 4.3 9.1 + - - +
468A GLY* 5.5 3.4 - - - -
469A LEU 3.3 1.5 - - - +
470A GLU* 1.3 78.9 - - - +
472A GLU* 1.3 65.4 + - + +
474A LEU* 3.3 8.2 + - - +
475A LEU* 3.0 41.8 + - + +
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Residues in contact with GLU 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A GLY 4.6 14.3 - - - +
469A LEU* 3.3 13.5 + - - +
471A HIS* 1.3 82.6 - - + +
473A LYS* 1.3 61.4 + - + +
475A LEU* 3.3 7.1 + - - +
476A ASP* 2.9 43.5 + - - +
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Residues in contact with LYS 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A LEU* 3.0 41.0 + - + +
470A GLU* 3.7 31.4 + - - +
471A HIS 3.3 0.2 - - - -
472A GLU* 1.3 78.1 - - + +
474A LEU* 1.3 58.4 + - + +
476A ASP* 3.3 8.6 + - - +
477A GLU* 2.9 30.4 + - - +
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Residues in contact with LEU 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ARG* 6.1 1.3 - - - +
380A LEU* 3.9 32.1 - - + +
383A LEU* 3.6 33.0 - - + -
384A ALA* 5.2 10.8 - - + +
387A LEU* 4.2 19.1 - - + -
465A LYS* 5.7 8.3 - - + -
470A GLU* 2.9 30.2 + - + +
471A HIS* 3.7 4.9 - - - +
473A LYS* 1.3 74.1 - - + +
475A LEU* 1.3 60.6 + - - +
477A GLU* 3.3 11.6 + - - +
478A TYR* 2.9 30.7 + - - +
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Residues in contact with LEU 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A HIS* 3.0 32.2 + - + +
472A GLU* 3.3 7.6 + - - +
474A LEU* 1.3 77.3 - - - +
476A ASP* 1.3 68.8 + - - +
478A TYR* 3.3 8.7 + - + +
479A LYS* 3.0 37.1 + - + +
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Residues in contact with ASP 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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472A GLU* 2.9 31.2 + - - +
473A LYS* 3.6 6.5 - - - +
475A LEU* 1.3 85.2 - - - +
477A GLU* 1.3 65.6 + - - +
479A LYS* 3.3 7.4 + - - +
480A GLU* 2.9 26.0 + - - +
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Residues in contact with GLU 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ARG* 3.1 39.1 + - - +
380A LEU* 3.4 22.5 - - + +
473A LYS 2.9 17.0 + - - +
474A LEU* 3.7 13.7 - - - +
476A ASP* 1.3 74.9 - - - +
478A TYR* 1.3 57.9 + - - +
480A GLU* 3.3 10.3 + - + +
481A LEU* 2.9 44.5 + - + +
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Residues in contact with TYR 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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377A ALA* 4.6 14.6 - - + -
380A LEU* 3.7 24.6 - - + +
381A GLU* 3.1 41.4 + - + -
427A ALA* 3.8 19.4 - - + +
432A ALA* 4.9 1.2 - - - +
474A LEU 2.9 16.6 + - - +
475A LEU* 3.6 8.3 - - + +
477A GLU* 1.3 78.0 - - - +
479A LYS* 1.3 64.3 + - + +
481A LEU* 3.3 6.4 + - + +
482A LEU* 3.0 59.4 + - + +
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Residues in contact with LYS 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 LEU* 3.0 25.5 + - + +
476A ASP* 3.8 7.2 - - - +
478A TYR* 1.3 78.1 - - + +
480A GLU* 1.3 63.5 + - - +
482A LEU* 3.3 14.3 + - + +
483A ASP* 3.0 23.3 + - + +
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Residues in contact with GLU 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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476A ASP 2.9 17.4 + - - +
477A GLU* 3.7 9.6 - - - +
479A LYS* 1.3 76.4 - - - +
481A LEU* 1.3 60.5 + - + +
483A ASP* 3.3 8.1 + - + +
484A GLN* 2.9 34.7 + - + +
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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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373A ALA* 4.5 16.2 - - + +
376A ARG* 3.8 29.4 - - + -
377A ALA* 4.1 29.6 - - + +
380A LEU* 4.8 4.9 - - + -
477A GLU* 2.9 37.6 + - + +
478A TYR* 3.8 6.5 - - - +
479A LYS 3.3 0.2 - - - -
480A GLU* 1.3 75.9 - - + +
482A LEU* 1.3 65.6 + - - +
484A GLN* 3.7 18.7 - - - +
485A ILE* 2.9 32.9 + - + +
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Residues in contact with LEU 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ALA* 5.9 3.4 - - + -
427A ALA* 3.8 28.7 - - + -
428A GLY* 4.9 3.4 - - - +
432A ALA* 4.6 9.4 - - + -
478A TYR* 3.0 56.8 + - + +
479A LYS* 3.5 12.8 - - + +
481A LEU* 1.3 76.6 - - - +
483A ASP* 1.3 63.7 + - - +
485A ILE* 3.0 21.5 - - + +
486A ALA* 3.0 24.1 + - - +
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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
----------------------------------------------------------
479A LYS* 3.0 15.5 + - + +
480A GLU* 3.6 10.5 - - + +
482A LEU* 1.3 76.0 - - - +
484A GLN* 1.3 56.9 + - - +
486A ALA* 3.3 7.1 + - - +
487A GLU* 3.0 31.9 + - - +
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Residues in contact with GLN 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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369A GLU* 4.9 13.3 + - - +
373A ALA* 4.8 11.4 - - + +
480A GLU* 2.9 22.1 + - + +
481A LEU* 3.7 22.3 - - - +
482A LEU 3.2 0.2 - - - -
483A ASP* 1.3 77.9 - - - +
485A ILE* 1.3 58.7 + - + +
487A GLU* 3.3 7.6 + - + +
488A LEU* 2.9 52.3 + - + +
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Residues in contact with ILE 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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370A LEU* 4.1 23.3 - - + +
373A ALA* 3.8 33.9 - - + +
374A ARG* 4.6 6.1 - - - +
377A ALA* 5.8 6.5 - - + -
430A ASP 5.7 0.4 - - - +
431A ALA* 3.5 31.4 - - + +
432A ALA* 4.4 5.8 - - + -
481A LEU* 2.9 21.4 + - + +
482A LEU* 3.0 35.4 - - + +
484A GLN* 1.3 72.1 - - - +
486A ALA* 1.3 62.2 + - + +
488A LEU* 3.3 2.8 + - + +
489A LEU* 2.9 30.7 + - - +
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Residues in contact with ALA 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 3.0 18.1 + - - +
483A ASP* 3.6 8.3 - - - +
485A ILE* 1.3 79.1 - - - +
487A GLU* 1.3 62.7 + - - +
489A LEU* 3.3 7.1 + - - +
490A ARG* 3.0 23.8 + - - +
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Residues in contact with GLU 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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483A ASP* 3.0 21.5 + - - +
484A GLN* 3.3 7.6 + - + +
486A ALA* 1.3 75.6 - - - +
488A LEU* 1.3 62.2 + - + +
490A ARG* 3.2 19.2 + - - +
491A ILE* 2.9 32.3 + - + +
497A ARG* 3.7 34.4 + - - +
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Residues in contact with LEU 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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366A THR* 3.9 20.6 - - + +
369A GLU* 4.1 22.0 - - + +
370A LEU* 3.7 46.9 - - + +
373A ALA* 5.3 2.0 - - + -
484A GLN* 2.9 38.9 + - + +
485A ILE* 3.8 4.5 - - - +
486A ALA 3.2 0.2 - - - -
487A GLU* 1.3 78.6 - - + +
489A LEU* 1.3 65.1 + - - +
491A ILE* 3.0 11.6 - - + +
492A LEU* 2.9 28.8 + - - +
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Residues in contact with LEU 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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370A LEU* 4.9 9.5 - - + +
374A ARG* 5.6 3.1 - - - +
430A ASP* 6.0 0.7 - - - +
431A ALA* 4.1 26.0 - - + -
485A ILE 2.9 17.3 + - - +
486A ALA* 3.7 7.0 - - - +
488A LEU* 1.3 76.1 - - - +
490A ARG* 1.3 62.3 + - - +
492A LEU* 3.3 10.7 + - + +
493A GLY* 2.9 25.0 + - - -
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Residues in contact with ARG 490 (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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486A ALA 3.0 13.8 + - - +
487A GLU* 3.6 22.7 - - - +
489A LEU* 1.3 81.2 - - - +
491A ILE* 1.3 57.2 + - - +
493A GLY* 3.1 1.8 + - - -
494A SER* 3.0 42.7 + - - +
497A ARG* 5.0 9.3 - - + +
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Residues in contact with ILE 491 (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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362A VAL* 5.8 6.1 - - + -
366A THR* 3.8 24.0 - - + +
487A GLU* 2.9 20.7 + - + +
488A LEU* 3.0 30.1 - - + +
490A ARG* 1.3 77.1 - - - +
492A LEU* 1.3 62.2 + - + +
494A SER 3.1 15.6 - - - +
497A ARG* 3.6 28.0 - - + +
498A LEU* 4.5 18.7 - - + +
501A VAL* 3.7 32.1 - - + -
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Residues in contact with LEU 492 (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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363A THR* 4.5 15.3 - - + +
366A THR* 3.7 30.7 - - + -
367A ILE* 4.3 24.0 - - + -
370A LEU* 4.0 26.2 - - + -
488A LEU 2.9 19.7 + - - +
489A LEU* 3.7 7.0 - - + +
491A ILE* 1.3 78.8 - - - +
493A GLY* 1.3 63.4 + - - +
494A SER 4.7 1.0 - - - +
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Residues in contact with GLY 493 (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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489A LEU* 2.9 16.0 + - - -
490A ARG* 3.1 3.5 + - - -
492A LEU* 1.3 80.9 - - - +
494A SER* 1.3 59.9 + - - +
495A ALA 3.8 1.4 + - - -
667B ARG* 5.4 5.7 + - - -
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Residues in contact with SER 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A ARG* 3.0 28.7 + - - +
491A ILE 3.1 17.0 - - - +
492A LEU 4.8 1.1 - - - -
493A GLY* 1.3 75.9 - - - +
495A ALA* 1.3 62.9 + - - +
496A ASP* 4.5 4.0 - - - -
497A ARG* 3.7 17.7 + - - +
498A LEU* 3.6 9.4 + - - +
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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
------------------------------------------------------------
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