Contacts of the helix formed by residues 430 - 454 (chain A) in PDB entry 3NUI
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 430 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348A ASN* 5.6 0.7 - - - -
352A LEU* 4.0 4.3 - - - -
428A ILE 4.0 7.6 - - - +
429A LEU* 1.3 74.3 - - - +
431A GLU* 1.4 55.6 + - - +
432A ALA* 3.5 8.4 + - - +
433A GLN* 3.1 39.8 + - - +
434A MET* 2.7 33.6 + - - +
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Residues in contact with GLU 431 (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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352A LEU* 4.1 11.4 - - + +
355A ARG* 3.7 52.0 - - - +
430A THR* 1.4 73.0 - - - +
432A ALA* 1.3 57.2 + - - +
434A MET* 3.3 12.2 + - - +
435A ASP* 2.8 58.2 + - - +
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Residues in contact with ALA 432 (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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430A THR* 3.2 8.5 + - - +
431A GLU* 1.3 79.6 - - - +
433A GLN* 1.3 59.3 - - + +
435A ASP* 3.4 12.8 + - - +
436A GLU* 2.8 27.8 + - - +
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Residues in contact with GLN 433 (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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39A PRO* 3.7 20.3 - - - +
40A TYR* 3.5 38.1 + - - +
50A LEU* 3.3 12.7 - - + +
428A ILE 4.1 2.3 - - - +
429A LEU* 3.6 23.2 - - + -
430A THR* 3.1 36.6 + - - +
432A ALA* 1.3 76.5 - - + +
434A MET* 1.3 62.3 + - - +
436A GLU* 3.8 10.1 - - - +
437A MET* 2.8 25.1 + - - +
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Residues in contact with MET 434 (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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352A LEU* 3.8 31.9 - - + +
355A ARG* 4.2 12.1 - - - +
356A PHE* 3.6 54.5 - - + -
377A PHE* 3.9 9.6 - - + -
429A LEU* 3.9 18.2 - - + +
430A THR 2.7 13.9 + - - +
431A GLU* 3.3 17.9 + - - +
433A GLN* 1.3 75.2 - - - +
435A ASP* 1.3 63.0 + - - +
437A MET* 3.1 6.1 + - + +
438A PHE* 3.1 44.6 + - + -
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Residues in contact with ASP 435 (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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359A ARG* 3.7 23.2 + - - +
431A GLU* 2.8 48.2 + - - +
432A ALA* 3.5 11.7 - - - +
434A MET* 1.3 68.1 - - - +
436A GLU* 1.3 61.6 + - - +
438A PHE 3.3 0.3 + - - -
439A ASP* 2.8 45.0 + - - +
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Residues in contact with GLU 436 (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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40A TYR* 2.6 41.1 + - - -
50A LEU* 4.0 9.7 - - + +
432A ALA 2.8 20.8 + - - +
433A GLN* 3.4 11.0 - - - +
434A MET 3.3 0.2 - - - -
435A ASP* 1.3 72.2 - - - +
437A MET* 1.3 65.0 + - - +
439A ASP* 3.9 6.5 - - - +
440A LYS* 2.5 67.6 + - + +
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Residues in contact with MET 437 (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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50A LEU* 3.5 26.0 - - + -
52A ALA* 4.3 9.9 - - + -
356A PHE* 4.6 9.2 - - - -
412A LEU* 3.5 22.2 - - + +
423A LEU* 4.1 28.9 - - + -
425A PRO* 3.5 35.4 - - + -
429A LEU* 3.5 21.8 - - + -
433A GLN 2.8 11.3 + - - +
434A MET* 3.1 9.8 + - - +
436A GLU* 1.3 75.5 - - - +
438A PHE* 1.3 68.4 + - + +
440A LYS* 3.8 1.1 - - - +
441A LEU* 2.9 26.3 + - + +
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Residues in contact with PHE 438 (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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356A PHE* 3.4 45.5 - + - -
359A ARG* 3.3 57.0 - - + +
360A LEU* 3.5 24.9 - - + -
363A ILE* 3.7 13.7 - - + -
423A LEU* 5.3 3.8 - - + -
434A MET* 3.1 48.5 + - + +
437A MET* 1.3 82.1 - - + +
439A ASP* 1.3 61.4 + - - +
441A LEU* 4.2 12.6 - - + -
442A GLU* 2.8 34.7 + - - +
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Residues in contact with ASP 439 (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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359A ARG* 3.3 22.1 + - - +
435A ASP* 2.8 32.6 + - - +
436A GLU* 3.9 5.8 + - - +
438A PHE* 1.3 75.6 - - - +
440A LYS* 1.3 64.6 + - + +
442A GLU* 3.5 7.0 + - - +
443A LYS* 3.1 38.6 + - - +
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Residues in contact with LYS 440 (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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48A ARG 4.3 7.3 + - - -
50A LEU* 4.5 1.1 - - + +
407A CYS* 5.2 0.2 - - - -
410A LEU* 3.2 38.5 + - + +
411A GLY* 3.0 28.5 + - - +
412A LEU* 4.1 16.2 - - + -
436A GLU* 2.5 53.8 + - + +
437A MET* 3.8 4.0 - - - +
439A ASP* 1.3 75.1 - - + +
441A LEU* 1.3 66.2 + - - +
443A LYS* 3.3 8.4 + - - +
444A ALA* 3.0 23.0 + - - +
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Residues in contact with LEU 441 (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 ILE* 4.2 12.3 - - + -
381A LEU* 3.5 28.3 - - + -
403A ILE* 4.2 9.9 - - + -
407A CYS* 3.9 20.6 - - - -
412A LEU* 3.8 12.3 - - + +
414A CYS* 5.2 1.3 - - - -
421A VAL* 4.6 9.6 - - + -
423A LEU* 4.3 19.3 - - + -
437A MET* 2.9 18.9 + - + +
438A PHE* 3.1 15.0 + - + +
440A LYS* 1.3 76.4 - - - +
442A GLU* 1.3 58.5 + - - +
444A ALA* 3.2 2.8 + - - +
445A LEU* 2.9 47.0 + - + +
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Residues in contact with GLU 442 (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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359A ARG* 3.1 37.0 + - - -
362A HIS* 4.0 13.9 - - - -
363A ILE* 3.4 36.9 - - + +
366A ARG* 3.6 18.1 + - - +
438A PHE 2.8 18.4 + - - +
439A ASP* 4.0 6.7 - - - +
441A LEU* 1.3 71.7 - - - +
443A LYS* 1.3 58.7 + - + +
445A LEU* 3.5 4.2 + - - -
446A ASP* 3.0 37.8 + - - +
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Residues in contact with LYS 443 (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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410A LEU* 3.9 19.3 - - + -
439A ASP* 3.1 30.9 + - - +
440A LYS* 3.7 7.8 - - - +
442A GLU* 1.3 77.4 - - + +
444A ALA* 1.3 61.7 + - - +
446A ASP* 3.5 12.0 + - - +
447A LYS* 3.1 23.7 + - - +
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Residues in contact with ALA 444 (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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403A ILE* 4.2 5.6 - - + +
406A THR* 3.6 27.8 - - + -
407A CYS* 3.6 27.6 - - - +
410A LEU* 3.5 3.4 - - + +
440A LYS 3.0 13.4 + - - +
441A LEU 3.4 8.3 - - - +
443A LYS* 1.3 74.8 - - - +
445A LEU* 1.3 61.5 + - - +
447A LYS* 3.3 1.6 + - - +
448A VAL* 2.9 35.1 + - - +
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Residues in contact with LEU 445 (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 ILE* 3.7 29.6 - - + -
366A ARG* 3.9 21.8 - - - +
369A ILE* 4.7 5.2 - - + -
381A LEU* 4.7 6.1 - - + -
403A ILE* 3.5 39.7 - - + -
421A VAL* 5.7 1.8 - - + -
441A LEU* 2.9 42.5 + - + +
442A GLU* 3.8 7.2 - - - +
444A ALA* 1.3 68.0 - - - +
446A ASP* 1.3 67.1 + - - +
448A VAL* 4.6 2.9 - - - +
449A PHE* 2.8 45.0 + - + +
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Residues in contact with ASP 446 (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 ARG* 2.8 33.1 + - - +
442A GLU* 3.0 21.7 + - - +
443A LYS* 3.5 14.4 - - - +
444A ALA 3.3 0.2 - - - -
445A LEU* 1.3 76.1 - - - +
447A LYS* 1.3 62.9 + - - +
449A PHE* 4.2 1.6 - - - +
450A ALA* 3.2 23.7 + - - +
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Residues in contact with LYS 447 (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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406A THR* 3.4 35.2 - - + -
409A ASP* 5.6 3.4 - - - -
443A LYS 3.1 14.7 + - - +
444A ALA 3.7 2.9 - - - +
446A ASP* 1.3 79.0 - - - +
448A VAL* 1.3 65.5 + - - +
450A ALA* 3.9 3.2 - - - +
451A GLU* 3.0 52.7 + - + +
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Residues in contact with VAL 448 (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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399A VAL* 4.1 15.5 - - + -
402A ARG* 3.5 49.1 - - + +
403A ILE* 3.8 23.8 - - + -
406A THR* 3.5 13.5 - - - +
444A ALA 2.9 21.0 + - - +
445A LEU* 4.2 0.9 - - - +
447A LYS* 1.3 80.3 - - - +
449A PHE* 1.3 61.1 + - + +
451A GLU* 3.3 7.4 + - - +
452A VAL* 2.9 36.3 + - + +
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Residues in contact with PHE 449 (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 ARG* 4.4 12.3 - - + +
368A ASN* 3.6 51.0 - - + +
369A ILE* 3.7 26.7 - - + -
383A ALA* 4.2 8.3 - - + -
393A PHE* 4.3 9.9 - + - -
399A VAL* 4.0 24.9 - - + -
403A ILE* 4.2 8.1 - - + -
445A LEU* 2.8 52.1 + - + +
446A ASP* 4.4 1.8 - - - +
448A VAL* 1.3 74.0 - - + +
450A ALA* 1.3 57.7 + - - +
452A VAL* 3.6 5.5 - - + +
453A ALA* 3.0 29.3 + - - +
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Residues in contact with ALA 450 (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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446A ASP 3.2 19.3 + - - +
447A LYS* 3.9 4.3 - - - +
448A VAL 3.2 0.4 - - - -
449A PHE* 1.3 75.0 - - - +
451A GLU* 1.3 64.8 + - - +
453A ALA* 3.2 15.5 + - - +
454A ALA* 3.2 13.9 + - - +
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Residues in contact with GLU 451 (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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402A ARG* 3.5 26.9 + - - +
447A LYS* 3.0 49.1 + - + +
448A VAL* 3.8 6.8 - - - +
450A ALA* 1.3 78.3 - - - +
452A VAL* 1.3 65.8 + - + +
453A ALA 3.4 0.2 + - - -
454A ALA* 3.5 19.7 - - - +
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Residues in contact with VAL 452 (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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393A PHE* 3.8 37.4 - - + -
397A LEU* 4.6 17.6 - - + +
399A VAL* 4.3 13.9 - - + -
402A ARG* 3.6 37.2 - - - +
448A VAL* 2.9 28.8 + - + +
449A PHE* 3.6 13.5 - - + +
451A GLU* 1.3 70.1 - - + +
453A ALA* 1.3 71.3 + - - +
454A ALA 3.3 7.2 - - - -
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Residues in contact with ALA 453 (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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393A PHE* 6.1 0.9 - - - -
449A PHE 3.0 20.7 + - - +
450A ALA* 3.2 10.2 + - - +
452A VAL* 1.3 75.0 - - - +
454A ALA* 1.3 70.1 + - - +
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Residues in contact with ALA 454 (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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450A ALA 3.2 7.1 + - - +
451A GLU* 3.5 17.0 - - - +
452A VAL* 3.3 10.5 - - - -
453A ALA* 1.3 85.3 - - - +
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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