Contacts of the helix formed by residues 488 - 496 (chain F) in PDB entry 5UHE
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 THR 488 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478F ARG* 5.5 0.2 - - - +
486F PRO 3.8 3.0 + - - +
487F ARG* 1.3 72.2 - - - +
489F LEU* 1.3 61.1 + - - +
490F ASP* 3.2 4.7 + - - +
491F GLU* 2.8 49.8 + - - +
492F ILE* 3.1 9.2 + - - +
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Residues in contact with LEU 489 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478F ARG* 3.9 37.5 - - - +
487F ARG 3.4 2.2 + - - -
488F THR* 1.3 75.5 - - - +
490F ASP* 1.3 70.7 + - + +
491F GLU 3.1 0.4 - - - -
492F ILE* 3.7 10.5 - - + +
493F GLY* 3.3 20.8 + - - -
501F GLU* 5.9 2.1 - - - +
503F ILE* 4.6 6.0 - - + +
504F ARG* 3.3 51.6 - - + +
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Residues in contact with ASP 490 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488F THR* 3.2 4.7 - - - +
489F LEU* 1.3 87.8 - - + +
491F GLU* 1.3 60.5 + - + +
493F GLY* 4.5 2.0 - - - -
494F GLN* 3.5 31.0 + - - +
501F GLU* 4.3 7.3 - - - +
504F ARG* 4.1 17.8 + - - -
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Residues in contact with GLU 491 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487F ARG* 5.4 4.5 - - + -
488F THR* 2.8 27.8 + - - +
490F ASP* 1.3 82.7 - - + +
492F ILE* 1.3 58.4 + - - +
493F GLY 3.4 0.4 - - - -
494F GLN* 3.3 13.3 + - - +
495F VAL* 2.8 35.9 + - + +
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Residues in contact with ILE 492 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474F VAL* 4.5 3.8 - - + -
477F LEU* 3.5 38.4 - - + +
478F ARG* 3.5 41.1 - - + +
487F ARG* 3.3 38.4 - - + +
488F THR 3.1 6.7 + - - +
489F LEU* 3.3 9.4 + - - +
491F GLU* 1.3 77.1 - - - +
493F GLY* 1.3 58.9 + - - +
494F GLN 3.1 0.9 - - - -
495F VAL* 3.3 7.2 - - + +
496F TYR* 3.1 30.1 + - - +
503F ILE* 3.7 20.4 - - + -
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Residues in contact with GLY 493 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489F LEU 3.3 9.9 + - - -
490F ASP 5.2 0.7 - - - -
491F GLU 3.4 0.2 - - - -
492F ILE* 1.3 80.7 - - - +
494F GLN* 1.3 61.5 + - - +
496F TYR* 3.6 3.0 - - - +
498F VAL 2.8 24.2 - - - +
499F THR* 3.5 12.0 - - - -
501F GLU* 4.9 10.5 - - - -
503F ILE* 3.5 23.3 - - - -
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Residues in contact with GLN 494 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490F ASP* 3.5 21.7 + - - +
491F GLU* 3.3 16.2 + - - +
492F ILE 3.1 0.2 - - - -
493F GLY* 1.3 82.4 - - - +
495F VAL* 1.3 61.1 + - - +
496F TYR 3.3 7.1 - - - +
499F THR* 5.1 10.9 + - - +
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Residues in contact with VAL 495 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477F LEU* 4.8 12.1 - - + -
487F ARG* 4.4 25.1 - - - +
491F GLU* 2.8 23.1 + - + +
492F ILE* 3.3 16.2 - - + +
494F GLN* 1.3 76.2 - - - +
496F TYR* 1.3 66.8 + - - +
497F GLY 3.8 1.2 + - - -
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Residues in contact with TYR 496 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469F GLU 5.2 1.3 + - - -
470F ARG* 3.4 36.1 + - + +
473F GLY* 6.2 3.1 - - - -
477F LEU* 4.8 11.7 - - + -
492F ILE 3.1 18.3 + - - +
493F GLY 3.6 6.5 - - - +
494F GLN* 3.7 6.1 - - - +
495F VAL* 1.3 80.7 - - + +
497F GLY* 1.3 72.3 + - - +
498F VAL* 2.9 53.7 + - + +
499F THR* 5.5 0.5 - - - -
503F ILE* 3.5 33.9 - - + -
506F ILE* 4.8 2.2 - - + -
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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