Contacts of the helix formed by residues 485 - 494 (chain D) in PDB entry 1ZQ1
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 ARG 485 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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479D THR 5.1 1.6 - - - +
480D LEU* 3.0 20.5 + - + +
483D ASP* 2.6 15.3 + - + +
484D GLU* 1.3 69.7 - - - +
486D ASP* 1.3 53.1 + - - +
487D GLU 2.7 18.4 + - - -
488D LEU* 3.0 12.0 + - + +
489D PHE* 3.0 23.6 + - - +
507D VAL* 3.7 30.1 - - + -
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Residues in contact with ASP 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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217D LYS* 6.4 2.0 - - + -
462D LYS* 4.0 21.8 + - + +
466D TYR* 3.3 22.3 + - - -
480D LEU 2.9 9.0 + - - -
481D VAL* 3.9 36.3 - - + +
484D GLU* 2.9 6.4 - - - +
485D ARG* 1.3 75.1 - - - +
487D GLU* 1.3 58.7 + - - +
489D PHE* 4.4 2.2 - - - +
490D GLU* 3.6 9.4 + - - +
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Residues in contact with GLU 487 (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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217D LYS* 4.0 29.3 - - + +
462D LYS* 5.4 0.9 - - - +
484D GLU 3.8 7.9 + - - +
485D ARG 2.7 4.9 + - - -
486D ASP* 1.3 72.7 - - - +
488D LEU* 1.3 67.0 + - - +
489D PHE 3.1 1.3 - - - -
490D GLU* 2.9 8.6 + - - +
491D GLU* 2.8 25.0 + - - +
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Residues in contact with LEU 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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485D ARG* 3.0 17.7 + - + +
487D GLU* 1.3 78.4 - - - +
489D PHE* 1.3 53.4 + - - +
491D GLU* 3.2 7.9 + - - +
492D LEU* 2.8 36.1 + - - +
507D VAL* 5.2 11.4 - - + -
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Residues in contact with PHE 489 (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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466D TYR* 3.5 41.7 - + - -
470D TYR* 4.8 9.6 - + - -
472D LEU* 4.1 5.4 - - + -
480D LEU* 3.1 39.9 - - + -
485D ARG* 3.0 14.4 + - - +
486D ASP 4.5 2.2 - - - +
488D LEU* 1.3 76.9 - - - +
490D GLU* 1.3 64.5 + - - +
492D LEU* 3.1 6.0 + - - +
493D VAL* 2.9 35.6 + - + +
500D SER* 3.5 46.0 - - - -
503D ALA* 3.6 23.1 - - + -
504D SER* 3.8 4.7 - - - -
507D VAL* 5.4 5.1 - - + +
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Residues in contact with GLU 490 (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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462D LYS* 5.2 5.8 - - - +
465D ARG* 5.6 4.7 - - - +
466D TYR* 4.1 9.4 - - + +
486D ASP 3.6 12.7 + - - +
487D GLU* 2.9 10.3 + - - +
489D PHE* 1.3 84.0 - - - +
491D GLU* 1.3 53.4 + - - +
493D VAL* 4.0 3.6 - - - +
494D SER* 2.8 36.1 + - - -
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Residues in contact with GLU 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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487D GLU 2.8 13.2 + - - +
488D LEU* 3.4 12.3 - - - +
490D GLU* 1.3 73.8 - - - +
492D LEU* 1.3 66.6 + - - +
494D SER* 3.2 17.8 - - - -
495D MET* 3.7 4.9 + - - +
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Residues in contact with LEU 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 LEU 2.8 20.4 + - - +
489D PHE* 3.1 6.5 + - - +
491D GLU* 1.3 68.4 - - - +
493D VAL* 1.3 56.9 + - - +
495D MET* 2.6 37.3 + - - +
497D VAL* 4.0 7.5 - - + +
498D LYS* 5.4 3.6 - - + -
503D ALA* 4.3 18.4 - - + -
507D VAL* 6.2 2.5 - - + -
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Residues in contact with VAL 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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470D TYR* 4.6 18.4 - - + +
489D PHE* 2.9 30.8 + - + +
490D GLU* 4.0 5.4 - - - +
492D LEU* 1.3 67.1 - - - +
494D SER* 1.3 51.6 + - - +
495D MET 2.8 5.6 - - - -
496D GLY* 2.5 32.3 + - - +
497D VAL 3.6 10.5 + - - +
498D LYS 4.8 5.4 - - - +
499D PRO 4.6 15.0 - - - +
503D ALA* 5.1 1.0 - - - +
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Residues in contact with SER 494 (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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490D GLU 2.8 21.4 + - - -
491D GLU* 3.2 15.5 - - - -
492D LEU 3.0 0.4 + - - -
493D VAL* 1.3 76.1 - - - +
495D MET* 1.3 55.7 + - - +
496D GLY* 2.9 4.9 + - - -
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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