Contacts of the helix formed by residues 5088 - 5095 (chain c) in PDB entry 3A0B
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 LEU5088 (chain c).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5063c TRP* 3.6 16.4 - - + -
5064c ALA 3.5 14.4 - - - +
5067c MET* 3.5 32.8 - - + -
5068c THR* 3.3 24.9 - - + +
5071c GLU* 2.8 20.8 + - - +
5087c ILE* 1.3 77.4 - - - +
5089c ILE* 1.3 57.2 + - - +
5090c PRO 3.1 1.1 - - - -
5091c HIS* 2.6 31.9 + - - +
5092c ILE* 3.2 12.8 + - + +
5118c HIS* 6.5 0.4 - - + -
6027c CLA 3.0 52.7 - - + -
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Residues in contact with ILE5089 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5068c THR* 4.9 7.6 - - + +
5071c GLU* 2.6 54.5 + - + +
5072c LEU* 3.4 11.4 - - + +
5075c PHE* 4.5 8.7 - - + -
5081c MET* 4.0 15.5 - - + -
5086c LEU* 3.4 20.9 - - + -
5088c LEU* 1.3 72.8 - - - +
5090c PRO* 1.3 69.7 - - + +
5092c ILE* 2.7 33.5 - - + +
5093c ALA* 3.2 4.0 + - - +
5111c PHE* 3.3 35.2 - - + -
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Residues in contact with PRO5090 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5081c MET* 3.7 22.0 - - + -
5086c LEU* 3.1 28.7 - - + +
5087c ILE 3.5 9.2 - - - +
5088c LEU 3.4 3.1 - - - -
5089c ILE* 1.3 96.8 - - + +
5091c HIS* 1.3 60.8 + - - +
5093c ALA* 3.3 10.2 + - - +
5094c THR* 3.3 18.7 - - - +
5301c PHE* 3.2 30.6 - - + +
5302c TYR* 3.4 22.2 - - + -
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Residues in contact with HIS5091 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5087c ILE 3.0 20.2 + - - -
5088c LEU 2.6 18.4 + - - +
5090c PRO* 1.3 73.9 - - - +
5092c ILE* 1.3 50.5 + - - +
5094c THR* 2.6 24.7 + - - -
5095c LEU* 2.7 15.8 - - - +
5297c TYR* 4.7 2.7 + + - -
5302c TYR* 3.3 26.9 + + - -
5426c LEU* 4.6 9.0 - - + -
6025c CLA 3.8 22.8 + - - -
6026c CLA 3.5 65.7 + + + +
6027c CLA 3.4 28.0 - - + +
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Residues in contact with ILE5092 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5068c THR* 5.6 7.6 - - + +
5088c LEU* 3.2 18.4 + - + +
5089c ILE* 2.7 22.0 + - + +
5091c HIS* 1.3 75.8 - - + +
5093c ALA* 1.3 62.7 + - - +
5095c LEU* 3.4 18.4 + - - +
5096c GLY 3.6 0.5 + - - -
5097c TRP* 2.8 55.6 + - + +
5111c PHE* 3.2 39.9 - - + -
5114c VAL* 5.0 22.4 - - + -
6027c CLA 3.9 16.8 - - + +
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Residues in contact with ALA5093 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5081c MET* 4.4 5.8 - - + -
5089c ILE 3.8 7.2 - - - +
5090c PRO* 3.4 10.5 - - + +
5092c ILE* 1.3 90.1 - - + +
5094c THR* 1.3 55.0 + - - +
5095c LEU 3.0 0.2 - - - -
5096c GLY* 2.7 27.2 + - - -
5097c TRP 3.8 8.2 + - - +
5098c GLY 6.1 0.2 - - - -
5099c VAL* 3.8 2.6 - - - +
5111c PHE* 5.2 2.5 - - + -
5186c TYR* 3.8 2.9 - - - +
5301c PHE* 3.2 45.2 - - + -
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Residues in contact with THR5094 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5090c PRO 3.3 16.6 - - - +
5091c HIS 2.6 17.4 + - - +
5093c ALA* 1.3 74.3 - - - +
5095c LEU* 1.3 65.8 + - - +
5185c LEU* 3.5 10.7 - - - +
5186c TYR* 3.0 24.3 + - - +
5296c VAL* 4.0 6.3 - - - +
5298c PRO* 3.5 35.7 - - + -
5301c PHE* 3.7 6.5 - - - -
5302c TYR* 3.6 13.2 - - - +
6025c CLA 3.4 16.5 - - - -
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Residues in contact with LEU5095 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5091c HIS 2.7 26.7 - - - +
5092c ILE 3.4 9.6 - - - +
5093c ALA 3.0 0.2 - - - -
5094c THR* 1.3 82.0 - - - +
5096c GLY* 1.3 55.0 + - - +
5097c TRP* 4.3 3.1 - - + -
5175c LEU* 3.3 35.2 - - + -
5178c LYS* 3.0 30.8 + - + +
5183c GLY 3.2 0.3 - - - +
5184c GLY 2.6 28.7 - - - +
5185c LEU* 3.4 14.7 - - + +
6025c CLA 4.0 12.8 - - + +
6027c CLA 3.4 35.0 - - + -
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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