Contacts of the helix formed by residues 489 - 496 (chain Z) in PDB entry 5WTI
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 489 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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488Z PHE* 1.3 71.9 - - - +
490Z ARG* 1.3 62.1 + - - +
491Z ASP* 3.1 25.0 + - - +
492Z HIS* 3.1 28.8 + - + +
493Z LEU* 3.1 17.2 + - - +
505Z VAL 5.5 1.4 + - - +
506Z GLY* 5.3 1.1 - - - -
507Z ARG* 3.5 48.0 + - + +
509Z TYR* 4.5 11.4 - - + -
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Residues in contact with ARG 490 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B G 3.1 34.7 + - - +
107B G 2.5 45.4 + - - -
383Z ILE 4.6 4.0 + - - +
384Z ASN 2.7 20.4 + - - -
385Z HIS* 4.2 1.6 + - - -
386Z PRO* 3.2 31.3 - - + +
388Z TRP* 4.7 4.0 - - + -
488Z PHE 3.2 7.8 + - - +
489Z ASP* 1.3 69.2 + - - +
491Z ASP* 1.3 67.5 + - - +
492Z HIS 3.1 1.6 - - - -
493Z LEU* 4.1 11.4 - - + -
494Z ARG* 2.9 29.1 + - + +
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Residues in contact with ASP 491 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489Z ASP* 3.1 15.9 + - - +
490Z ARG* 1.3 77.4 - - - +
492Z HIS* 1.3 61.5 + - - +
494Z ARG* 4.2 6.1 - - - +
495Z ARG* 3.2 27.0 + - - +
775Z ARG* 5.1 6.9 + - - +
782Z ASN* 4.0 30.4 + - - +
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Residues in contact with HIS 492 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B U 3.4 39.8 + + - -
489Z ASP* 3.1 29.0 + - + +
490Z ARG 3.1 0.6 - - - -
491Z ASP* 1.3 77.4 - - - +
493Z LEU* 1.3 60.2 + - - +
494Z ARG 3.2 0.2 - - - -
495Z ARG 3.1 0.2 + - - -
496Z TYR* 2.8 63.1 + + + +
499Z LYS* 4.5 0.2 - - - +
500Z VAL* 3.8 12.1 - - + +
504Z ASN* 2.7 26.3 + - - -
505Z VAL 3.0 26.5 + - - +
506Z GLY* 3.7 6.3 + - - -
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Residues in contact with LEU 493 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21Z TRP* 3.6 28.9 - - + -
382Z PRO 3.8 20.6 - - - +
383Z ILE* 3.4 39.5 - - + +
386Z PRO* 4.6 6.1 - - + -
388Z TRP* 4.8 2.5 - - + -
488Z PHE* 4.2 18.2 - - + -
489Z ASP 3.1 14.7 + - - +
490Z ARG* 3.3 17.0 + - + +
492Z HIS* 1.3 77.1 - - - +
494Z ARG* 1.3 62.2 + - - +
497Z PRO* 3.6 13.9 - - - +
500Z VAL* 3.8 23.3 - - + -
505Z VAL 4.3 11.2 - - - +
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Residues in contact with ARG 494 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E C 2.6 32.6 + - - -
383Z ILE* 5.1 2.9 + - - -
384Z ASN* 5.5 5.2 - - - +
490Z ARG* 2.9 18.8 + - + +
491Z ASP* 4.2 4.9 - - - +
493Z LEU* 1.3 81.3 - - - +
495Z ARG* 1.3 62.1 + - - +
497Z PRO* 3.7 8.8 - - - +
773Z GLY 5.8 0.6 + - - -
775Z ARG* 3.6 46.3 - - - +
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Residues in contact with ARG 495 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B A 4.4 6.1 + - - -
63B C 2.9 42.0 + - - +
491Z ASP 3.2 17.6 + - - +
492Z HIS 3.1 1.6 + - - -
494Z ARG* 1.3 82.7 - - - +
496Z TYR* 1.3 101.9 + - + +
497Z PRO* 3.3 6.9 - - - +
775Z ARG* 4.4 7.0 - - - +
778Z ILE* 3.5 41.7 - - + +
779Z ASP* 2.9 35.2 + - - -
782Z ASN* 5.1 2.2 - - - +
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Residues in contact with TYR 496 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B U 4.8 8.3 - + - -
63B C 4.2 9.8 + - - -
64B U 3.4 36.6 + - - -
492Z HIS* 2.8 47.4 + + + +
495Z ARG* 1.3 126.3 + - + +
497Z PRO* 1.3 63.3 - - - +
498Z HIS 3.2 3.6 - - - +
499Z LYS* 3.6 29.8 - - + +
500Z VAL* 3.2 24.9 + - - +
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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