Contacts of the helix formed by residues 463 - 483 (chain A) in PDB entry 4DGX
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 ILE 463 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A ASP 3.4 20.6 - - - +
62A TYR* 4.8 0.4 - - - -
72A ALA* 3.8 26.5 - - + -
282A ILE* 4.3 18.8 - - + -
459A CYS* 3.9 2.6 - - - -
461A ALA* 3.3 12.7 - - + +
462A GLY* 1.3 86.3 - - - +
464A GLY* 1.3 66.1 + - - +
465A ARG 3.9 0.2 - - - -
466A THR* 4.5 0.2 - - - -
467A GLY 3.3 10.2 + - - -
501A ARG* 3.8 17.5 - - + +
502A SER 3.4 20.4 - - - +
503A GLY 4.3 4.0 - - - +
504A MET* 3.4 7.6 - - - +
505A VAL 3.0 23.7 + - - -
506A GLN* 3.5 25.1 - - - +
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Residues in contact with GLY 464 (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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60A GLY 3.4 19.1 - - - -
61A ASP* 4.4 2.8 + - - +
459A CYS* 4.6 1.2 - - - -
463A ILE* 1.3 81.3 - - - +
465A ARG* 1.3 65.8 + - - +
468A THR* 3.1 26.0 + - - -
505A VAL* 3.9 1.7 - - - -
506A GLN* 3.4 19.9 - - - +
510A GLN* 3.4 7.5 - - - +
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Residues in contact with ARG 465 (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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60A GLY 4.0 2.2 + - - -
61A ASP* 4.3 20.0 + - - +
356A THR* 2.8 43.4 + - - +
357A THR* 3.6 6.3 + - - +
361A GLU* 2.6 45.5 + - - -
423A TRP* 3.3 58.7 - - + +
424A PRO 3.6 6.9 + - - -
425A ASP 4.3 5.9 + - - -
459A CYS* 3.8 15.3 - - + -
464A GLY* 1.3 73.9 - - - +
466A THR* 1.3 64.1 + - - +
468A THR* 3.2 4.7 + - - -
469A PHE* 2.9 30.6 + - + -
510A GLN* 3.6 8.8 - - - +
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Residues in contact with THR 466 (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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329A ALA* 3.7 19.5 - - + -
356A THR* 4.7 2.0 - - - -
457A VAL* 3.8 20.0 - - + +
458A HIS* 3.2 7.8 + - - -
459A CYS* 2.9 34.0 + - - -
462A GLY* 3.5 23.6 - - - +
464A GLY 3.3 0.6 - - - -
465A ARG* 1.3 80.0 - - - +
467A GLY* 1.3 57.4 + - - +
469A PHE* 3.6 1.9 + - - +
470A ILE* 3.1 46.9 + - + +
504A MET* 4.1 1.3 - - + -
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Residues in contact with GLY 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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463A ILE 3.3 15.9 + - - -
465A ARG 3.2 0.4 - - - -
466A THR* 1.3 77.5 - - - +
468A THR* 1.3 60.5 + - - +
470A ILE* 4.0 0.6 - - - +
471A VAL* 2.9 37.1 + - - +
504A MET* 3.5 26.2 - - - -
505A VAL* 3.5 12.8 - - - -
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Residues in contact with THR 468 (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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423A TRP* 4.0 25.4 - - + -
464A GLY 3.1 18.9 + - - -
465A ARG* 3.4 8.3 - - - +
467A GLY* 1.3 76.0 - - - +
469A PHE* 1.3 64.4 + - + +
471A VAL* 3.9 1.9 - - - +
472A ILE* 3.1 41.7 + - + +
505A VAL* 3.7 11.9 - - - +
510A GLN* 3.3 29.5 + - + +
513A PHE* 4.2 7.9 - - + -
514A ILE* 4.2 9.2 - - + +
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Residues in contact with PHE 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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354A VAL* 4.4 2.7 - - + -
356A THR* 3.8 29.6 - - + -
420A PHE* 4.0 22.7 - + - -
423A TRP* 3.5 33.9 - + - -
435A VAL* 4.2 21.5 - - + -
438A PHE* 3.6 30.5 - + - -
439A LEU* 3.8 25.8 - - + +
457A VAL* 4.5 11.9 - - + -
465A ARG* 2.9 25.8 + - + +
466A THR 3.8 4.7 - - - +
468A THR* 1.3 79.8 - - + +
470A ILE* 1.3 57.2 + - - +
472A ILE* 3.4 7.8 + - - +
473A ASP* 2.9 29.6 + - - +
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Residues in contact with ILE 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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310A ILE* 4.2 11.7 - - + -
327A TYR* 3.9 38.8 - - + -
329A ALA* 4.0 9.9 - - + -
457A VAL* 3.9 21.5 - - + -
466A THR* 3.1 40.5 + - + +
467A GLY* 4.0 4.5 - - - +
469A PHE* 1.3 76.0 - - - +
471A VAL* 1.3 58.8 + - - +
473A ASP* 3.1 8.1 + - - +
474A ILE* 3.0 45.5 + - + +
497A VAL* 4.7 7.4 - - + -
504A MET* 3.8 10.5 - - + -
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Residues in contact with VAL 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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467A GLY 2.9 21.5 + - - +
468A THR 3.9 2.7 - - - +
470A ILE* 1.3 74.1 - - - +
472A ILE* 1.3 67.1 + - - +
474A ILE* 3.0 7.5 + - - +
475A LEU* 3.0 44.3 + - + +
493A THR* 4.6 6.7 - - + +
494A ILE* 3.9 27.6 - - + +
497A VAL* 4.1 27.6 - - + -
505A VAL* 3.9 13.7 - - + -
514A ILE* 4.0 14.6 - - + -
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Residues in contact with ILE 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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435A VAL* 4.5 9.4 - - + -
436A LEU* 4.5 7.9 - - + -
439A LEU* 3.7 15.3 - - + -
468A THR* 3.1 25.1 + - + +
469A PHE* 3.7 5.2 - - - +
471A VAL* 1.3 76.5 - - - +
473A ASP* 1.3 62.9 + - - +
475A LEU* 3.9 4.6 - - - +
476A ILE* 3.0 46.2 + - + +
513A PHE* 3.8 33.9 - - + -
514A ILE* 3.8 24.7 - - + +
517A ALA* 4.0 13.9 - - + -
518A VAL* 5.4 2.5 - - + -
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Residues in contact with ASP 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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325A LYS* 3.2 22.6 + - - -
327A TYR* 2.5 33.2 + - + +
439A LEU* 3.7 39.2 - - + +
442A VAL* 5.7 3.0 - - - +
443A HIS* 4.9 1.0 + - - +
469A PHE 2.9 18.5 + - - +
470A ILE* 3.1 8.0 + - - +
472A ILE* 1.3 78.4 - - - +
474A ILE* 1.3 57.2 + - - +
476A ILE* 3.9 3.0 - - - +
477A ASP* 3.0 37.2 + - - +
480A ARG* 4.7 4.7 + - - -
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Residues in contact with ILE 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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310A ILE* 5.0 3.4 - - + -
312A PRO* 4.3 27.1 - - + -
327A TYR* 3.7 25.8 - - + +
470A ILE* 3.0 33.6 + - + +
471A VAL* 3.0 8.5 + - - +
473A ASP* 1.3 75.3 - - - +
475A LEU* 1.3 68.0 + - - +
477A ASP* 3.0 16.0 + - - +
478A ILE* 3.1 26.0 + - + +
493A THR* 4.0 17.9 - - + -
496A MET* 4.7 6.3 - - + -
497A VAL* 4.0 22.0 - - + -
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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
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471A VAL* 3.0 33.8 + - + +
472A ILE 3.9 1.3 - - - +
474A ILE* 1.3 75.5 - - - +
476A ILE* 1.3 64.1 + - - +
478A ILE* 3.2 24.1 + - + +
479A ILE* 3.2 20.1 + - + +
488A ILE* 4.6 22.2 - - + +
489A ASP 4.6 3.8 - - - +
490A VAL* 3.9 20.0 - - + -
493A THR* 3.7 29.4 - - + +
514A ILE* 3.8 18.6 - - + -
518A VAL* 3.9 21.8 - - + -
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Residues in contact with ILE 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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436A LEU* 3.4 33.4 - - + -
439A LEU* 5.5 4.7 - - + -
440A GLU* 4.9 1.8 - - - +
472A ILE* 3.0 31.4 + - + +
473A ASP* 4.3 3.6 - - - +
475A LEU* 1.3 75.0 - - - +
477A ASP* 1.3 59.2 + - - +
478A ILE 3.1 1.6 - - - -
479A ILE* 3.9 5.8 - - + +
480A ARG* 2.9 42.7 + - - +
517A ALA 4.5 2.9 - - - +
518A VAL* 4.5 11.7 - - + -
521A TYR* 3.4 48.9 - - + +
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Residues in contact with ASP 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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325A LYS* 2.9 38.2 + - - +
327A TYR* 3.6 6.2 + - - -
443A HIS* 3.6 6.4 + - - -
473A ASP* 3.0 24.9 + - - +
474A ILE* 3.0 8.6 + - - +
476A ILE* 1.3 77.1 - - - +
478A ILE* 1.3 60.6 + - + +
480A ARG* 2.6 39.3 + - - +
481A GLU* 3.4 22.9 + - - +
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Residues in contact with ILE 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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474A ILE* 3.1 25.7 + - + +
475A LEU* 3.3 19.1 - - + +
476A ILE 3.1 0.2 - - - -
477A ASP* 1.3 77.7 - - + +
479A ILE* 1.3 56.0 + - - +
481A GLU* 3.3 8.4 + - - +
482A LYS* 2.8 49.5 + - + +
486A CYS* 3.9 18.4 - - - -
487A ASP 4.3 7.6 - - - +
488A ILE* 4.1 13.2 - - + -
493A THR* 5.6 2.9 - - + +
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Residues in contact with ILE 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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223A ALA* 4.2 13.7 - - + -
475A LEU 3.4 17.3 - - - +
476A ILE* 3.9 5.8 - - - +
478A ILE* 1.3 73.2 - - - +
480A ARG* 1.3 62.6 + - - +
483A GLY* 2.7 48.1 + - - +
484A VAL 4.5 0.2 - - - +
486A CYS* 4.1 5.2 - - - -
488A ILE* 4.1 13.5 - - + -
518A VAL* 3.7 30.5 - - + -
521A TYR* 3.5 26.2 - - + -
522A ILE* 3.7 24.0 - - + -
525A LEU* 4.0 12.8 - - + +
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Residues in contact with ARG 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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439A LEU* 5.3 1.8 + - - +
440A GLU* 3.0 40.1 + - - -
443A HIS* 3.3 47.9 + - - +
444A HIS* 5.3 3.4 - - - -
473A ASP* 4.7 5.5 + - - -
476A ILE* 2.9 31.7 + - - +
477A ASP* 2.6 31.9 + - - +
479A ILE* 1.3 77.1 - - - +
481A GLU* 1.3 62.3 + - - +
483A GLY* 4.9 0.5 + - - -
521A TYR* 3.5 20.7 + - - +
525A LEU* 5.3 3.6 - - - -
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Residues in contact with GLU 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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477A ASP 3.4 17.2 + - - +
478A ILE* 3.3 4.8 + - - +
479A ILE 3.1 1.4 - - - -
480A ARG* 1.3 82.8 - - - +
482A LYS* 1.3 85.2 + - + +
483A GLY* 3.4 1.4 + - - -
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Residues in contact with LYS 482 (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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478A ILE* 2.8 35.8 + - + +
481A GLU* 1.3 91.9 - - + +
483A GLY* 1.3 59.6 + - - +
485A ASP* 3.7 11.6 - - - +
486A CYS* 3.8 21.8 - - + +
487A ASP 5.8 1.0 - - - +
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Residues in contact with GLY 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A ILE* 2.7 27.1 + - - +
480A ARG 5.3 0.7 - - - -
481A GLU 3.3 3.1 - - - -
482A LYS* 1.3 74.5 - - - +
484A VAL* 1.3 59.8 + - - -
485A ASP 2.9 12.1 + - - -
486A CYS* 3.1 22.2 - - - -
525A LEU* 5.7 1.6 - - - -
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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
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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