Contacts of the helix formed by residues 479 - 494 (chain D) in PDB entry 1Z6T
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 479 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396D PRO* 4.1 8.5 - - + -
398D LYS* 3.3 30.6 - - + +
399D VAL* 3.7 18.6 - - + -
402D ILE* 3.5 4.2 - - - +
468D HIS* 3.2 25.2 + - - -
477D GLN* 3.8 13.9 - - - +
478D GLU* 1.3 76.4 + - - +
480D CYS* 1.3 64.8 + - - +
481D MET 3.4 2.5 - - - -
482D TYR* 3.0 15.2 + - - +
483D TRP* 3.1 34.4 + - - +
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Residues in contact with CYS 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473D LEU* 3.5 18.0 - - + +
474D SER 3.4 19.5 - - - +
475D PRO* 3.6 27.4 - - + -
477D GLN* 3.2 19.6 + - + +
478D GLU 3.4 1.0 - - - -
479D ASP* 1.3 79.4 + - - +
481D MET* 1.3 68.9 + - + +
483D TRP 3.2 2.6 + - - -
484D TYR* 3.1 47.5 + - - -
516D LEU* 4.5 4.3 - - - -
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Residues in contact with MET 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D GLN* 5.5 1.6 - - - +
216D LEU* 5.3 6.5 - - + -
475D PRO* 5.7 3.8 - - + -
478D GLU 5.0 2.1 + - - +
479D ASP 3.4 0.4 - - - -
480D CYS* 1.3 84.1 - - + +
482D TYR* 1.3 66.0 + - - +
484D TYR* 3.9 8.1 - - + +
485D ASN* 3.0 56.0 + - - +
516D LEU* 4.4 24.9 - - - -
517D VAL* 3.7 28.0 - - + -
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Residues in contact with TYR 482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388D ILE* 5.0 2.1 + - - +
389D LEU* 5.3 5.0 - - - +
390D GLN* 4.2 6.1 + - - -
393D VAL* 4.1 7.9 - - + -
394D LYS 5.5 0.2 - - - -
395D VAL* 3.7 31.9 - - + +
396D PRO* 4.5 9.9 - - + -
399D VAL* 3.7 32.9 - - + +
460D ILE* 4.6 2.9 - - + +
478D GLU 5.5 0.4 + - - -
479D ASP* 3.0 15.6 + - - +
481D MET* 1.3 79.2 - - - +
483D TRP* 1.3 80.6 + + - +
485D ASN* 4.6 0.4 - - - +
486D PHE* 2.8 59.5 + + + -
490D HIS* 2.6 39.8 + + - -
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Residues in contact with TRP 483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399D VAL* 4.2 20.4 - - + -
402D ILE* 4.0 21.8 - - + -
460D ILE* 3.7 36.3 - - + -
461D ILE* 5.3 0.2 - - + -
464D PHE* 3.5 50.7 - + + -
468D HIS* 4.0 3.5 - + - -
473D LEU* 4.0 21.5 - - + -
479D ASP* 3.1 46.7 + - - +
480D CYS 3.2 4.0 + - - +
482D TYR* 1.3 92.7 - + - +
484D TYR* 1.3 62.4 + - - +
487D LEU* 2.8 55.8 + - + +
490D HIS* 4.7 5.4 - + - -
509D TRP* 4.6 1.6 - - - -
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Residues in contact with TYR 484 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470D PRO 4.5 2.8 + - - -
473D LEU* 3.0 49.5 + - + +
474D SER* 5.8 0.2 - - - -
480D CYS* 3.1 24.9 + - - +
481D MET* 4.1 12.8 - - + +
483D TRP* 1.3 77.0 - - - +
485D ASN* 1.3 64.8 + - - +
487D LEU* 4.7 0.9 + - - +
488D ALA 5.6 0.5 + - - -
509D TRP* 3.4 34.2 - + - -
512D ALA* 3.4 20.9 + - + +
513D LYS* 2.8 68.5 + - + +
516D LEU* 3.4 31.4 - - + +
517D VAL* 5.6 2.5 - - + -
525D GLU* 4.2 1.7 - - - +
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Residues in contact with ASN 485 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D MET* 3.6 32.8 - - - +
200D GLN* 5.7 0.3 - - - +
481D MET* 3.0 49.0 + - - +
482D TYR 3.6 3.4 - - - +
484D TYR* 1.3 81.2 - - - +
486D PHE* 1.3 88.1 + - + +
489D TYR* 4.8 2.8 - - - +
513D LYS* 5.5 1.2 - - - -
517D VAL* 5.2 4.5 - - - +
521D HIS* 3.1 27.0 + - - -
525D GLU* 3.9 6.1 - - - +
529D TYR* 5.3 0.3 + - - -
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Residues in contact with PHE 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D MET* 4.0 24.9 - - + -
390D GLN* 3.5 27.6 - - - +
393D VAL* 3.7 34.8 - - + -
482D TYR* 2.8 59.8 + + + +
483D TRP* 3.8 0.7 - - - -
485D ASN* 1.3 102.1 - - + +
487D LEU* 1.3 64.2 + - - +
488D ALA 3.4 2.0 - - - -
489D TYR* 3.8 13.7 - + + +
490D HIS* 3.0 33.4 + - + +
521D HIS* 6.2 0.2 - + - -
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Residues in contact with LEU 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461D ILE* 3.4 29.6 - - + +
464D PHE* 3.9 36.3 - - + -
470D PRO* 4.5 5.6 - - + -
473D LEU* 6.4 0.2 - - + -
483D TRP* 2.8 45.2 + - + +
484D TYR 4.7 0.4 - - - +
485D ASN 3.9 0.4 - - - -
486D PHE* 1.3 72.5 - - - +
488D ALA* 1.3 62.8 + - - +
490D HIS 3.3 0.3 + - - -
491D MET* 3.0 40.8 + - + +
503D LEU* 3.8 33.7 - - + -
509D TRP* 4.6 11.4 - - + -
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Residues in contact with ALA 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484D TYR 5.6 0.4 + - - -
486D PHE* 4.4 0.2 - - - +
487D LEU* 1.3 77.1 - - - +
489D TYR* 1.3 65.2 + - - +
491D MET* 3.4 0.4 + - - -
492D ALA* 2.9 27.0 + - - +
500D LEU* 3.5 21.8 - - + +
503D LEU* 4.2 11.2 - - + -
504D MET* 4.0 13.2 - - + -
509D TRP* 6.0 3.1 - - + +
525D GLU* 3.3 23.5 + - - +
529D TYR* 3.7 12.8 - - + -
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Residues in contact with TYR 489 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388D ILE 4.8 0.7 + - - -
390D GLN* 3.5 49.2 - - + +
457D HIS* 3.7 28.1 + + - -
485D ASN 4.8 1.6 - - - +
486D PHE* 3.4 21.6 + + + +
488D ALA* 1.3 78.5 - - - +
490D HIS* 1.3 69.0 + + - +
492D ALA* 3.4 1.7 + - - +
493D SER* 2.7 49.8 + - - -
525D GLU* 4.6 0.6 + - - -
529D TYR* 3.2 32.1 + + - +
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Residues in contact with HIS 490 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388D ILE* 3.8 31.6 - - + -
390D GLN* 4.5 0.9 + - - -
457D HIS* 3.0 33.7 + + - +
460D ILE* 3.7 20.7 - - + +
461D ILE* 3.6 21.5 - - + -
482D TYR* 2.6 40.5 + + - -
483D TRP* 4.7 4.7 - + - -
486D PHE* 3.0 31.6 + - + +
489D TYR* 1.3 82.7 - + - +
491D MET* 1.3 61.1 + - - +
493D SER 3.4 0.7 + - - -
494D ALA* 2.8 29.8 + - - +
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Residues in contact with MET 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461D ILE* 3.7 28.9 - - + +
464D PHE* 5.8 1.6 - - + -
465D GLN* 4.5 7.4 - - + +
470D PRO* 5.9 2.2 - - + -
487D LEU* 3.0 37.0 + - + +
488D ALA 3.6 4.5 - - - +
490D HIS* 1.3 75.9 - - - +
492D ALA* 1.3 60.4 + - - +
494D ALA* 3.2 4.8 + - - +
495D LYS 3.1 4.0 + - - -
496D MET* 2.8 34.7 + - + +
499D GLU* 3.5 42.4 - - + +
500D LEU* 3.7 18.2 - - + -
503D LEU* 3.9 26.9 - - + -
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Residues in contact with ALA 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488D ALA 2.9 17.5 + - - +
489D TYR 3.9 2.5 - - - +
491D MET* 1.3 74.2 - - - +
493D SER* 1.3 64.1 + - - +
495D LYS* 3.1 18.7 + - - +
500D LEU* 4.2 6.5 - - + -
529D TYR* 3.7 39.0 - - + -
531D HIS* 6.2 0.2 - - - +
532D ILE* 3.9 27.2 - - + +
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Residues in contact with SER 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454D GLN* 3.5 17.7 - - - +
457D HIS* 3.5 33.4 - - - -
489D TYR* 2.7 41.7 + - - -
490D HIS 3.7 0.7 - - - -
492D ALA* 1.3 78.8 - - - +
494D ALA* 1.3 55.1 + - - +
495D LYS* 3.1 7.8 + - - +
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Residues in contact with ALA 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454D GLN* 3.3 32.1 + - - +
457D HIS* 3.6 0.8 - - - +
458D LYS* 3.3 31.4 - - + +
490D HIS 2.8 17.5 + - - +
491D MET 3.2 6.0 + - - +
493D SER* 1.3 74.1 - - - +
495D LYS* 1.3 64.2 + - - +
496D MET* 3.2 25.2 + - + +
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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