Contacts of the helix formed by residues 231 - 241 (chain H) in PDB entry 5UQ9
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 PHE 231 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450G PHE* 3.5 33.0 - + - -
230H SER* 1.3 71.3 + - - +
232H LEU* 1.3 73.1 + - + +
233H ILE 3.0 1.1 - - - -
234H GLU* 2.6 41.4 + - + +
235H ILE* 2.6 50.5 + - + +
366H CYS 4.4 4.3 - - - -
367H ILE* 3.0 31.9 - - + -
369H ARG* 3.2 47.6 - - - +
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Residues in contact with LEU 232 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446G GLN* 3.5 30.7 - - + +
450G PHE* 6.4 0.4 - - + -
191H GLU 4.9 0.9 - - - +
194H ASP* 4.1 22.2 - - + +
195H MET* 3.7 31.0 - - + +
198H ILE* 3.9 13.8 - - + +
230H SER 2.6 10.0 + - - +
231H PHE* 1.3 84.2 - - + +
233H ILE* 1.3 49.7 - - + +
235H ILE* 4.5 4.8 - - + +
236H THR* 2.1 37.9 + - - -
331H LYS* 5.9 1.6 - - - +
367H ILE* 3.5 33.9 - - + +
368H ILE* 4.4 9.0 - - + -
369H ARG 4.4 0.4 + - - +
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Residues in contact with ILE 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198H ILE* 4.1 14.8 - - + -
220H PHE* 4.2 24.3 - - + +
223H TRP* 5.1 0.9 - - + -
224H ASN* 3.2 44.5 + - + +
229H ASP* 3.5 28.5 - - + +
230H SER* 3.3 28.7 - - - +
231H PHE 3.0 0.2 - - - -
232H LEU* 1.3 78.6 - - + +
234H GLU* 1.3 77.4 + - - +
235H ILE 3.3 0.2 - - - -
236H THR* 3.7 7.5 - - - -
237H ALA* 3.2 23.2 + - - +
327H LEU* 6.5 1.3 - - + -
331H LYS* 5.4 4.9 - - - +
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Residues in contact with GLU 234 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224H ASN* 3.4 33.8 + - - +
225H LYS* 5.9 0.9 + - - -
230H SER* 3.1 19.7 + - - -
231H PHE* 2.6 35.1 + - - +
233H ILE* 1.3 76.3 - - - +
235H ILE* 1.3 63.3 + - + +
237H ALA* 3.8 8.9 + - - +
238H ASN* 3.9 12.6 + - - +
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Residues in contact with ILE 235 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446G GLN* 4.9 13.2 - - + +
449G TYR* 3.5 45.1 - - + +
450G PHE* 4.9 8.3 - - + -
231H PHE* 2.6 56.4 + - + +
232H LEU* 4.5 5.8 - - + +
234H GLU* 1.3 73.8 - - + +
236H THR* 1.3 61.3 + - - +
238H ASN* 2.8 24.8 + - - +
239H ILE* 3.1 23.7 + - + +
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Residues in contact with THR 236 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442G LEU* 3.9 23.6 - - + -
446G GLN* 2.6 16.9 + - - +
198H ILE* 3.7 26.0 - - + +
220H PHE* 4.1 19.6 - - + -
232H LEU 2.1 29.9 + - - -
233H ILE* 3.8 9.1 - - - -
234H GLU 3.4 0.8 - - - -
235H ILE* 1.3 76.3 - - - +
237H ALA* 1.3 61.4 + - - +
238H ASN 3.4 0.3 + - - -
239H ILE* 3.4 22.6 + - - +
240H LEU* 3.5 8.6 + - + +
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Residues in contact with ALA 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217H ALA* 3.3 43.1 - - - +
220H PHE* 3.8 16.3 - - + +
221H GLU* 4.1 17.7 - - + +
233H ILE 3.2 16.1 + - - +
234H GLU* 4.0 6.3 - - - +
235H ILE 3.1 0.6 - - - -
236H THR* 1.3 77.0 - - - +
238H ASN* 1.3 61.8 + - - +
241H LYS* 3.4 10.1 + - - +
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Residues in contact with ASN 238 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449G TYR* 4.2 26.5 + - + +
234H GLU 3.9 8.4 + - - +
235H ILE* 2.8 12.6 + - - +
237H ALA* 1.3 80.0 - - - +
239H ILE* 1.3 64.2 + - - +
241H LYS* 3.2 31.7 + - - +
242H PHE* 4.1 17.6 - - + -
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Residues in contact with ILE 239 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442G LEU* 3.5 33.9 - - + +
445G ALA* 3.6 31.2 - - + +
446G GLN* 4.8 7.2 - - + -
449G TYR* 4.5 21.5 - - + -
235H ILE* 3.1 33.0 + - + +
236H THR* 3.5 12.3 - - - +
237H ALA 3.4 0.2 - - - -
238H ASN* 1.3 75.7 - - - +
240H LEU* 1.3 64.6 + - + +
242H PHE* 4.7 8.6 + - - +
251H LEU* 3.1 38.8 - - + +
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Residues in contact with LEU 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442G LEU* 3.6 30.7 - - + -
202H TYR* 3.6 30.5 - - + +
213H GLN* 3.2 50.8 - - + +
216H MET* 4.5 4.5 - - + -
217H ALA* 3.6 23.3 - - + +
220H PHE* 5.9 4.0 - - + -
236H THR* 3.5 10.1 + - + +
238H ASN 3.2 0.6 - - - -
239H ILE* 1.3 87.1 - - + +
241H LYS* 1.3 56.9 + - - +
242H PHE 3.4 7.8 + - - +
249H HIS* 4.6 2.6 + - - +
251H LEU* 4.6 16.2 - - + +
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Residues in contact with LYS 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213H GLN* 5.3 1.1 - - - -
214H ASP* 3.2 30.1 - - + +
217H ALA* 3.6 18.4 - - + -
218H GLN* 5.5 3.4 - - + +
221H GLU* 3.6 23.6 - - - -
237H ALA 3.4 8.6 + - - +
238H ASN* 3.2 19.6 + - - +
240H LEU* 1.3 74.1 - - - +
242H PHE* 1.3 68.6 + - - +
249H HIS* 5.9 1.3 - - - -
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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