Contacts of the helix formed by residues 458 - 471 (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 LEU 458 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110D LEU* 4.0 28.9 - - + +
208D PHE* 3.2 37.7 - - + -
211D ASP* 4.9 2.7 - - + -
212D ALA* 4.5 9.2 - - - +
215D ALA* 4.0 10.1 - - + -
456D PRO 3.7 6.7 + - - +
457D GLU* 1.3 73.9 - - - +
459D PRO* 1.3 75.8 - - + +
460D GLN* 4.8 2.2 - - + +
461D ALA* 3.3 25.5 + - + +
462D LYS* 3.3 8.1 + - - +
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Residues in contact with PRO 459 (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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211D ASP* 3.4 54.5 - - + +
214D ARG* 4.0 14.8 - - + -
215D ALA* 4.4 2.7 - - + +
457D GLU 3.3 5.1 - - - +
458D LEU* 1.3 81.0 - - + +
460D GLN* 1.3 68.5 + - - +
462D LYS* 2.8 25.7 + - + +
463D VAL* 3.2 5.6 + - - +
481D VAL* 4.2 23.3 - - + +
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Residues in contact with GLN 460 (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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207D LYS* 3.7 27.8 - - - +
211D ASP* 5.2 6.8 - - - +
458D LEU* 3.5 2.8 - - + +
459D PRO* 1.3 81.1 - - - +
461D ALA* 1.3 66.1 + - - +
463D VAL* 2.7 22.1 + - - +
464D GLU* 2.8 32.2 + - + +
478D GLN* 2.7 33.9 + - - +
482D ASP* 5.7 1.2 + - - -
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Residues in contact with ALA 461 (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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457D GLU* 5.2 3.6 - - + -
458D LEU* 3.3 26.2 + - + +
459D PRO 3.2 0.2 - - - -
460D GLN* 1.3 77.6 - - - +
462D LYS* 1.3 62.5 + - - +
464D GLU* 3.2 12.9 + - - +
465D ARG* 3.0 22.8 + - - +
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Residues in contact with LYS 462 (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* 4.8 14.3 - - - +
457D GLU* 2.9 54.6 + - + +
458D LEU 3.3 2.4 + - - +
459D PRO* 2.8 14.1 + - + +
461D ALA* 1.3 76.7 - - - +
463D VAL* 1.3 58.7 + - - +
465D ARG* 2.6 41.1 + - - +
466D TYR* 2.8 41.5 + - + +
481D VAL* 4.6 5.4 - - + -
486D ASP* 4.0 30.7 + - + +
487D GLU* 5.4 0.2 - - - +
490D GLU* 5.2 5.2 - - - +
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Residues in contact with VAL 463 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459D PRO 3.2 4.9 + - - +
460D GLN* 2.7 21.0 + - - +
462D LYS* 1.3 76.7 - - - +
464D GLU* 1.3 67.4 + - + +
465D ARG 3.2 0.3 + - - -
466D TYR* 3.3 9.0 + - - +
467D VAL* 3.3 21.4 + - + +
474D ARG* 5.1 4.7 - - + +
477D ALA* 3.7 24.7 - - + +
478D GLN* 3.6 42.0 - - + +
481D VAL* 3.6 30.9 - - + +
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Residues in contact with GLU 464 (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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460D GLN* 2.8 34.8 + - + +
461D ALA* 3.5 12.6 - - - +
463D VAL* 1.3 82.2 - - + +
465D ARG* 1.3 56.8 + - - +
467D VAL* 4.2 7.8 - - - +
468D LYS* 3.4 25.5 + - - +
474D ARG* 4.5 14.7 + - - -
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Residues in contact with ARG 465 (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 ALA 3.0 10.3 + - - +
462D LYS* 2.6 28.5 + - - +
464D GLU* 1.3 72.5 - - - +
466D TYR* 1.3 92.1 + - - +
467D VAL 3.2 1.3 - - - -
468D LYS* 4.6 2.2 - - - -
469D GLU* 2.5 52.5 + - + +
470D TYR* 4.3 21.0 + - - -
490D GLU* 5.6 4.4 - - - +
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Residues in contact with TYR 466 (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* 2.8 33.6 + - + +
463D VAL* 3.6 7.4 - - - +
465D ARG* 1.3 108.8 + - - +
467D VAL* 1.3 58.4 + - - +
470D TYR* 2.8 32.3 + + - -
471D LYS 3.1 0.7 + - - -
472D LEU* 2.8 30.2 - - + +
477D ALA* 4.2 12.6 - - + -
480D LEU* 4.1 13.2 - - + -
481D VAL* 4.0 25.4 - - + -
486D ASP 3.3 22.9 + - - -
489D PHE* 3.5 37.6 - + - -
490D GLU* 4.1 7.9 - - + +
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Residues in contact with VAL 467 (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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463D VAL* 3.3 9.7 + - + +
464D GLU* 4.6 5.6 - - - +
465D ARG 3.2 0.4 - - - -
466D TYR* 1.3 78.2 - - - +
468D LYS* 1.3 64.3 + - + +
471D LYS* 2.9 32.2 + - - +
472D LEU 3.4 25.4 - - - +
474D ARG* 3.7 32.1 - - + +
477D ALA* 3.8 18.6 - - + -
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Residues in contact with LYS 468 (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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464D GLU 3.4 18.8 + - - +
465D ARG* 3.4 3.2 + - + +
467D VAL* 1.3 85.4 - - + +
469D GLU* 1.3 60.4 + - + +
471D LYS* 3.5 23.4 + - - +
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Residues in contact with GLU 469 (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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465D ARG* 2.5 36.3 + - + +
468D LYS* 1.3 75.4 - - + +
470D TYR* 1.3 69.8 + - + +
471D LYS* 3.2 15.8 + - - +
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Residues in contact with TYR 470 (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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465D ARG* 4.3 24.3 + - - -
466D TYR* 2.8 46.9 + + + +
469D GLU* 1.3 83.3 - - + +
471D LYS* 1.3 70.9 + - - +
472D LEU* 3.2 13.1 + - + +
489D PHE* 4.8 6.7 - + - -
493D VAL* 4.6 17.2 - - + +
499D PRO 3.6 20.2 - - - +
500D SER* 3.5 17.3 - - - -
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Residues in contact with LYS 471 (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 3.1 0.2 + - - -
467D VAL* 2.9 20.6 + - - +
468D LYS* 3.5 21.3 + - - +
469D GLU 3.8 8.7 - - - +
470D TYR* 1.3 80.4 - - - +
472D LEU* 1.3 60.9 + - - +
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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