Contacts of the helix formed by residues 433 - 455 (chain A) in PDB entry 4Z1H
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 ASP 433 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327A TYR* 4.9 1.1 + - - +
429A GLN* 2.8 26.7 + - - +
430A SER 3.3 4.7 - - - +
431A LYS 5.1 0.2 - - - -
432A LYS* 1.3 83.6 - - + +
434A ALA* 1.3 64.0 + - - +
435A GLU* 3.4 4.7 + - - +
436A LYS* 3.1 43.1 + - + +
437A TYR* 3.4 15.4 + - - +
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Residues in contact with ALA 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A SER* 3.9 10.3 - - - +
431A LYS 6.0 0.2 - - - +
433A ASP* 1.3 73.4 + - - +
435A GLU* 1.3 67.2 + - + +
436A LYS 3.4 1.1 - - - -
437A TYR* 3.6 5.0 + - - +
438A ALA* 2.9 25.8 + - - +
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Residues in contact with GLU 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A ASP* 3.4 4.3 + - - +
434A ALA* 1.3 80.0 - - + +
436A LYS* 1.3 60.2 + - - +
438A ALA* 3.1 12.1 + - - +
439A LYS* 2.9 28.6 + - - +
478A GLY 5.3 6.0 - - - +
479A GLN* 5.8 5.5 - - - +
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Residues in contact with LYS 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ARG* 3.2 39.5 + - - +
327A TYR* 3.7 24.5 - - + +
429A GLN* 5.3 2.3 + - - +
433A ASP* 3.1 32.9 + - + +
435A GLU* 1.3 79.0 - - - +
437A TYR* 1.3 57.5 + - - +
438A ALA 3.3 0.2 + - - -
439A LYS* 3.3 7.6 + - - +
440A PHE* 2.9 25.6 + - - +
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Residues in contact with TYR 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A TYR* 3.6 16.2 + + - +
426A PHE* 3.4 19.4 - - + +
429A GLN* 4.3 2.2 - - + +
430A SER* 3.2 35.4 - - - -
433A ASP 3.4 20.0 + - - +
434A ALA* 4.0 4.3 - - - +
435A GLU 3.3 0.4 - - - -
436A LYS* 1.3 75.4 - - - +
438A ALA* 1.3 60.4 + - - +
440A PHE* 3.4 32.0 - + - +
441A PHE* 2.9 27.2 + - + +
448A MET* 4.2 3.3 - - - +
467A LEU* 2.6 50.3 + - - +
469A ARG* 3.7 27.6 - - + -
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Residues in contact with ALA 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A ALA 2.9 16.6 + - - +
435A GLU* 3.2 22.7 - - - +
436A LYS 3.1 0.4 - - - -
437A TYR* 1.3 76.6 - - - +
439A LYS* 1.3 59.8 + - - +
441A PHE* 3.0 9.1 + - - +
442A GLU* 2.9 38.8 + - - +
469A ARG* 5.7 1.1 - - - -
480A LEU* 4.0 25.2 - - + +
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Residues in contact with LYS 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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326A ARG* 3.6 10.6 - - - +
347A ASP* 3.9 18.8 + - - +
349A LYS* 5.0 6.6 - - - +
435A GLU 2.9 12.0 + - - +
436A LYS* 3.7 9.0 - - - +
438A ALA* 1.3 76.0 - - - +
440A PHE* 1.3 62.2 + - - +
442A GLU* 3.2 16.4 + - - +
443A ASP* 3.0 57.4 + - - +
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Residues in contact with PHE 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ARG* 3.7 12.7 - - - +
327A TYR* 3.8 20.6 - + + -
345A VAL* 3.6 28.7 - - + -
386A PHE* 3.8 17.5 - + - -
426A PHE* 3.4 39.0 - + - -
436A LYS 2.9 14.6 + - - +
437A TYR* 3.4 35.2 - + - +
438A ALA 3.2 0.2 - - - -
439A LYS* 1.3 77.9 - - - +
441A PHE* 1.3 56.8 + - - +
443A ASP 3.3 0.5 + - - -
444A TYR* 2.9 50.7 + + + +
448A MET* 4.2 18.6 - - - -
467A LEU* 5.8 0.2 - - + -
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Residues in contact with PHE 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A TYR* 2.9 22.3 + - + +
438A ALA* 3.0 10.5 + - - +
440A PHE* 1.3 78.3 - - - +
442A GLU* 1.3 69.3 + - + +
445A GLY* 2.9 30.2 + - - +
448A MET* 3.3 33.0 - - + -
449A ARG* 4.3 16.4 + - - -
467A LEU 3.6 8.1 - - - -
468A LEU* 3.5 18.6 - - + -
469A ARG* 3.2 47.6 - - + -
470A TYR* 4.0 17.5 - + - -
480A LEU* 5.4 4.0 - - + -
532A ASP* 5.2 0.2 - - - -
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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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438A ALA* 2.9 28.0 + - + +
439A LYS* 3.2 19.1 + - - +
441A PHE* 1.3 84.6 - - + +
443A ASP* 1.3 66.5 + - - +
445A GLY* 4.4 1.7 + - - -
446A LEU 5.4 0.7 + - - -
449A ARG* 5.9 1.2 + - - -
480A LEU* 5.8 3.9 - - + +
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Residues in contact with ASP 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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326A ARG* 2.8 28.0 + - - +
349A LYS* 3.2 35.4 - - + +
350A PRO* 3.9 14.7 - - - +
439A LYS* 3.0 32.6 + - - +
442A GLU* 1.3 88.3 - - - +
444A TYR* 1.3 80.7 + - + +
445A GLY 3.8 0.2 - - - -
446A LEU* 5.3 3.8 + - - +
447A PHE* 4.7 0.7 - - - -
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Residues in contact with TYR 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ARG* 3.8 19.5 - - - -
345A VAL* 3.8 17.9 - - + -
346A PRO* 3.9 18.8 - - + +
348A MET 2.9 19.1 + - - -
349A LYS 4.5 0.2 - - - -
350A PRO* 3.6 25.8 - - + +
386A PHE* 3.5 32.0 - + + -
440A PHE* 2.9 43.0 + + + +
443A ASP* 1.3 87.3 - - + +
445A GLY* 1.3 62.4 + - - +
446A LEU 3.0 8.3 + - - +
447A PHE* 3.1 38.5 + + + +
448A MET* 3.6 13.0 + - - +
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Residues in contact with GLY 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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441A PHE* 2.9 28.3 + - - -
442A GLU 4.4 1.0 + - - -
443A ASP 3.8 0.8 - - - -
444A TYR* 1.3 75.4 - - - +
446A LEU* 1.3 57.2 + - - +
447A PHE 3.4 0.2 - - - -
448A MET* 3.3 20.8 + - - +
449A ARG* 2.9 45.7 + - - +
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Residues in contact with LEU 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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385A ARG* 5.2 2.5 - - - +
442A GLU 5.4 1.0 + - - -
443A ASP 5.3 3.3 - - - +
444A TYR* 4.6 3.4 - - - +
445A GLY* 1.3 77.3 - - - +
447A PHE* 1.3 89.4 + - + +
448A MET 3.3 0.3 + - - -
449A ARG* 3.3 24.7 + - - +
450A GLU* 2.9 42.7 + - + +
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Residues in contact with PHE 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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350A PRO* 3.8 26.9 - - + -
383A TRP* 3.1 36.2 - - - +
385A ARG* 3.7 44.0 - - + -
386A PHE* 3.7 26.7 - + + -
443A ASP 4.7 0.7 - - - -
444A TYR* 3.1 46.3 + + - +
446A LEU* 1.3 95.1 - - + +
448A MET* 1.3 57.7 + - - +
450A GLU* 3.7 5.2 - - - +
451A GLY 2.9 22.3 + - - -
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Residues in contact with MET 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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383A TRP* 3.7 28.3 - - + -
386A PHE* 5.4 2.7 - - + -
437A TYR* 4.2 0.4 - - - +
440A PHE* 4.2 24.2 - - - -
441A PHE* 3.3 26.0 - - + -
444A TYR 3.7 8.7 - - - +
445A GLY* 3.3 18.6 + - - +
446A LEU 3.2 0.6 - - - -
447A PHE* 1.3 77.5 - - + +
449A ARG* 1.3 59.8 + - - +
451A GLY 3.4 0.3 + - - -
452A ILE* 2.9 36.9 + - - +
464A ILE* 3.6 10.1 - - + +
467A LEU* 3.2 44.9 - - + +
468A LEU* 4.1 5.4 - - + +
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Residues in contact with ARG 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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441A PHE* 4.3 15.2 + - - -
442A GLU 5.9 1.2 + - - -
445A GLY* 2.9 28.7 + - - +
446A LEU* 3.4 29.9 - - - +
448A MET* 1.3 75.9 - - - +
450A GLU* 1.3 63.3 + - - +
452A ILE* 3.0 6.6 + - - +
453A VAL* 2.9 27.8 + - - +
468A LEU* 4.3 11.9 - - + -
470A TYR* 4.2 0.9 - - - +
531A PHE* 3.2 45.1 - - - +
532A ASP* 3.2 27.2 + - - +
535A THR* 3.3 36.7 - - + +
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Residues in contact with GLU 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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382A LYS* 3.4 23.2 - - + +
383A TRP* 4.5 3.8 - - + -
385A ARG* 2.7 39.1 + - - -
446A LEU* 2.9 27.7 + - + +
447A PHE* 3.7 8.1 - - - +
449A ARG* 1.3 75.0 - - - +
451A GLY* 1.3 55.6 + - - +
453A VAL* 3.3 7.4 + - - +
454A THR* 2.3 45.1 + - - +
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Residues in contact with GLY 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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383A TRP* 3.5 31.3 - - - -
447A PHE 2.9 12.4 + - - -
448A MET 3.8 1.1 - - - -
450A GLU* 1.3 73.5 - - - +
452A ILE* 1.3 65.2 + - - +
454A THR* 3.8 7.0 - - - -
455A ALA* 3.1 25.6 + - - +
464A ILE* 3.8 10.2 - - - +
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Residues in contact with ILE 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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448A MET 2.9 19.3 + - - +
449A ARG 3.3 6.7 - - - +
451A GLY* 1.3 78.1 - - - +
453A VAL* 1.3 63.8 + - - +
454A THR 3.3 0.2 + - - -
455A ALA* 3.4 1.9 + - - -
461A LYS* 3.2 34.3 + - + +
464A ILE* 3.7 22.7 - - + -
465A ALA* 3.6 16.8 - - + +
468A LEU* 3.6 37.2 - - + -
535A THR* 4.1 22.9 - - + +
538A HIS* 3.9 5.6 + - + -
539A LEU* 4.1 22.2 - - + -
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Residues in contact with VAL 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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449A ARG 2.9 18.7 + - - +
450A GLU* 3.7 8.5 - - - +
452A ILE* 1.3 75.7 - - + +
454A THR* 1.3 60.8 + - - +
455A ALA 3.5 1.6 + - - +
461A LYS* 3.9 1.6 + - - -
534A LEU* 5.4 1.6 - - + +
535A THR* 4.5 22.2 - - + +
538A HIS* 3.0 49.4 + - + +
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Residues in contact with THR 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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382A LYS* 5.5 11.4 - - + -
450A GLU* 2.3 38.4 + - - +
451A GLY* 3.9 7.0 - - - -
452A ILE 3.2 0.2 - - - -
453A VAL* 1.3 75.7 - - - +
455A ALA* 1.3 68.3 + - - +
456A THR* 4.7 3.5 - - - +
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Residues in contact with ALA 455 (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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451A GLY 3.1 16.5 + - - +
452A ILE* 3.7 4.3 - - - +
453A VAL 3.3 3.6 - - - +
454A THR* 1.3 83.2 - - - +
456A THR* 1.3 66.3 + - - +
460A VAL* 3.7 24.5 - - + -
461A LYS* 2.9 33.9 + - + +
464A ILE* 4.9 0.4 - - + -
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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
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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