Contacts of the helix formed by residues 489 - 498 (chain A) in PDB entry 1ASZ
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 HIS 489 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487A HIS 3.1 7.1 + - - -
488A ASP* 1.3 72.6 - - - +
490A ALA* 1.3 60.9 + - - +
492A LEU* 3.4 6.3 - - + +
493A GLN* 2.7 61.1 + - - +
512A CYS* 2.9 45.3 + - - -
513A ASP* 3.7 12.2 - - + +
515A PHE* 3.9 16.8 - + + -
516A SER* 3.9 21.9 + - - +
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Residues in contact with ALA 490 (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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488A ASP* 2.8 15.0 + - - +
489A HIS* 1.3 78.1 + - - +
491A LEU* 1.3 66.2 + - - +
492A LEU 3.2 0.7 + - - -
493A GLN* 3.2 7.7 + - - +
494A GLU* 3.2 19.4 + - - +
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Residues in contact with LEU 491 (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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458A MET* 3.7 31.0 - - + -
459A PRO* 4.6 7.6 - - + -
486A ILE* 3.6 20.0 - - + -
488A ASP* 3.1 17.3 + - + +
490A ALA* 1.3 78.0 - - - +
492A LEU* 1.3 62.9 + - - +
494A GLU* 3.1 20.0 + - + +
495A ARG* 3.0 37.8 + - + +
80B LEU* 5.1 9.6 - - + -
82B GLN* 5.3 5.4 - - - +
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Residues in contact with LEU 492 (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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455A PHE* 4.3 18.1 - - + +
456A TYR* 4.3 12.6 - - + -
486A ILE* 3.1 34.0 - - + +
488A ASP 2.8 17.2 + - - +
489A HIS* 3.4 5.6 - - - +
491A LEU* 1.3 74.5 - - - +
493A GLN* 1.3 58.3 + - - +
495A ARG* 3.2 6.8 + - - +
496A MET* 3.0 45.0 + - + +
511A TYR* 4.4 6.7 - - + +
512A CYS* 4.6 10.8 - - - -
515A PHE* 3.3 38.8 - - + -
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Residues in contact with GLN 493 (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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489A HIS* 2.7 60.4 + - - +
490A ALA* 3.2 5.2 + - - +
492A LEU* 1.3 77.1 - - - +
494A GLU* 1.3 66.0 + - - +
496A MET* 3.1 10.0 + - - +
497A LYS* 2.9 40.5 + - - +
503A PRO* 3.9 27.8 - - + +
512A CYS* 3.6 16.1 - - - -
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Residues in contact with GLU 494 (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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490A ALA 3.2 10.9 + - - +
491A LEU* 3.1 24.1 + - + +
493A GLN* 1.3 78.5 - - - +
495A ARG* 1.3 60.9 + - + +
497A LYS* 3.2 10.6 + - - +
498A ALA* 3.0 24.9 + - + +
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Residues in contact with ARG 495 (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 LEU* 3.3 33.1 - - - +
451A GLU* 2.9 26.2 + - - -
454A PRO 5.4 1.2 + - - -
455A PHE* 3.6 20.3 + - - +
457A THR 4.6 3.1 + - - -
459A PRO* 4.1 17.5 - - - +
486A ILE* 3.3 20.4 - - + -
491A LEU* 3.0 25.4 + - + +
492A LEU 3.5 7.2 - - - +
494A GLU* 1.3 75.8 - - + +
496A MET* 1.3 61.8 + - - +
498A ALA* 2.9 45.9 - - - +
499A HIS* 3.0 25.8 + - - -
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Residues in contact with MET 496 (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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455A PHE* 3.6 42.4 - - + +
492A LEU* 3.0 25.7 + - + +
493A GLN* 3.3 13.7 - - + +
495A ARG* 1.3 77.1 - - - +
497A LYS* 1.3 64.6 + - + +
499A HIS* 2.9 13.5 + - - +
501A LEU* 3.0 23.8 + - + -
502A SER* 4.2 13.5 - - - +
503A PRO* 3.9 29.6 - - + -
508A LEU* 4.2 15.7 - - + -
511A TYR* 4.2 11.9 - - + -
512A CYS* 4.1 23.1 - - + -
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Residues in contact with LYS 497 (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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493A GLN* 2.9 24.8 + - - +
494A GLU* 3.4 9.6 - - + +
496A MET* 1.3 75.0 - - - +
498A ALA* 1.3 55.8 + - - +
500A GLY* 2.7 26.1 + - - +
501A LEU 4.5 11.2 - - - +
502A SER* 4.5 3.1 - - - +
503A PRO* 3.5 34.7 - - + +
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Residues in contact with ALA 498 (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 GLU* 5.1 4.9 - - - +
494A GLU 3.0 10.3 + - - +
495A ARG* 2.9 47.5 + - - +
497A LYS* 1.3 78.2 - - - +
499A HIS* 1.3 57.6 + - + +
500A GLY* 3.0 5.2 + - - -
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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
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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