Contacts of the helix formed by residues 230 - 242 (chain B) 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 SER 230 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198B ILE* 4.9 0.7 - - - +
224B ASN* 2.9 22.6 - - - +
228B LEU 3.0 7.4 + - - -
229B ASP* 1.3 75.7 - - - +
231B PHE* 1.3 63.1 + - - +
232B LEU* 3.6 8.2 + - - +
233B ILE* 3.2 29.1 + - - +
234B GLU* 3.2 11.8 + - - +
331B LYS* 4.1 12.9 + - - -
367B ILE 5.9 0.2 - - - -
368B ILE 5.5 1.3 - - - -
369B ARG 3.6 14.4 - - - -
370B SER* 3.8 9.9 - - - +
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Residues in contact with PHE 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A TYR* 4.6 8.5 - + - -
450A PHE* 3.8 26.5 - - + -
230B SER* 1.3 72.1 - - - +
232B LEU* 1.3 61.0 + - - +
234B GLU* 3.3 20.7 + - + -
235B ILE* 3.0 62.6 + - + +
367B ILE* 4.0 24.5 - - + +
369B ARG* 3.1 57.9 + - + +
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Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A GLN* 4.1 7.5 + - - +
450A PHE* 4.5 2.7 - - + -
191B GLU 4.7 1.8 - - - +
194B ASP* 3.7 33.0 - - + +
195B MET* 3.7 31.2 - - + +
198B ILE* 3.7 13.0 - - + -
230B SER* 3.3 7.2 + - - +
231B PHE* 1.3 78.4 - - + +
233B ILE* 1.3 52.9 + - - +
235B ILE* 3.2 24.6 - - + +
236B THR* 2.4 36.6 + - - -
367B ILE* 3.7 37.6 + - + +
368B ILE* 4.8 6.5 - - + -
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Residues in contact with ILE 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ILE* 3.6 22.0 - - + -
220B PHE* 3.6 40.2 - - + +
223B TRP* 4.7 2.5 - - + +
224B ASN* 3.3 20.6 - - + +
228B LEU* 3.2 45.8 - - + +
230B SER* 3.2 14.4 + - - +
231B PHE 3.2 0.2 - - - -
232B LEU* 1.3 75.0 - - - +
234B GLU* 1.3 63.9 + - - +
236B THR* 3.5 5.2 - - - -
237B ALA* 3.0 23.4 + - - +
327B LEU* 4.7 9.4 - - + -
331B LYS* 6.0 2.0 - - - +
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Residues in contact with GLU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B ASN* 3.0 34.9 + - - +
230B SER 3.2 8.3 + - - +
231B PHE* 3.3 27.8 + - + +
233B ILE* 1.3 78.0 - - - +
235B ILE* 1.3 58.1 + - + +
237B ALA* 3.4 3.6 + - - +
238B ASN* 2.3 40.2 + - - +
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Residues in contact with ILE 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A GLN* 3.9 33.4 - - + +
449A TYR* 3.5 35.0 - - + -
450A PHE* 4.0 15.3 - - + -
231B PHE* 3.0 39.2 + - + +
232B LEU* 3.2 31.2 - - + +
234B GLU* 1.3 74.6 - - + +
236B THR* 1.3 64.9 + - - +
238B ASN* 3.3 7.1 + - - +
239B ILE* 2.7 36.3 + - + +
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Residues in contact with THR 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442A LEU* 3.9 20.0 - - + -
446A GLN* 3.0 18.9 + - - -
198B ILE* 3.7 17.2 - - + +
220B PHE* 3.7 31.4 - - + -
232B LEU 2.4 25.2 + - - -
233B ILE* 3.5 9.2 - - - -
234B GLU 3.2 0.4 - - - -
235B ILE* 1.3 77.9 - - - +
237B ALA* 1.3 61.7 + - - +
239B ILE* 3.3 7.5 + - - +
240B LEU* 3.0 30.1 + - + +
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Residues in contact with ALA 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B ALA* 3.2 38.2 - - - +
220B PHE* 3.7 16.6 - - + +
221B GLU* 4.0 15.7 - - + +
233B ILE 3.0 13.1 + - - +
234B GLU* 3.9 4.5 - - - +
236B THR* 1.3 77.1 - - - +
238B ASN* 1.3 65.8 + - - +
240B LEU 3.3 0.3 + - - -
241B LYS* 3.1 26.8 + - - +
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Residues in contact with ASN 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A TYR* 3.8 28.8 + - + +
469A TRP* 4.5 0.7 - - - -
234B GLU* 2.3 40.3 + - - +
235B ILE 3.8 2.9 - - - +
237B ALA* 1.3 79.7 - - - +
239B ILE* 1.3 61.7 + - - +
241B LYS* 3.4 22.1 - - - +
242B PHE* 3.2 24.9 + - - +
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Residues in contact with ILE 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442A LEU* 4.1 13.0 - - + -
445A ALA* 3.3 43.7 - - + +
446A GLN* 3.7 20.0 - - + +
449A TYR* 3.5 16.2 - - + -
469A TRP* 3.5 31.4 - - + -
235B ILE* 2.7 28.3 + - + +
236B THR* 3.7 4.9 - - - +
237B ALA 3.2 0.4 - - - -
238B ASN* 1.3 72.5 - - - +
240B LEU* 1.3 65.8 + - - +
242B PHE* 3.3 14.6 + - - +
250B LEU* 3.9 8.3 - - - +
251B LEU* 4.4 16.0 - - + +
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Residues in contact with LEU 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A LEU* 4.8 6.1 - - + -
202B TYR* 3.5 29.6 - - + -
213B GLN* 3.4 25.7 - - - +
214B ASP* 4.5 0.2 - - - -
216B MET* 3.7 20.9 - - + -
217B ALA* 3.6 17.7 - - + +
220B PHE* 3.5 38.4 - - + -
236B THR* 3.0 20.5 + - + +
237B ALA 3.3 0.2 + - - -
239B ILE* 1.3 78.7 - - - +
241B LYS* 1.3 56.6 + - - +
242B PHE 4.1 0.2 - - - +
249B HIS* 3.2 23.7 - - - +
251B LEU* 3.6 22.2 - - + -
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Residues in contact with LYS 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B ASP* 3.3 18.1 + - - +
217B ALA* 3.7 20.3 + - + +
218B GLN* 4.5 13.5 + - - -
221B GLU* 5.4 12.5 + - - +
237B ALA* 3.1 18.7 + - - +
238B ASN* 3.4 32.8 - - - +
240B LEU* 1.3 75.6 - - - +
242B PHE* 1.3 67.0 + - - +
243B GLN* 2.9 27.0 + - - +
249B HIS* 4.1 0.4 - - - -
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Residues in contact with PHE 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A TYR* 6.1 0.2 - + - -
467A THR* 3.6 20.0 - - + -
468A ASN 4.2 4.9 - - - -
469A TRP* 3.5 49.1 - + + -
238B ASN 3.2 13.8 + - - +
239B ILE 3.5 12.8 - - - +
240B LEU 3.3 2.1 - - - +
241B LYS* 1.3 75.8 - - - +
243B GLN* 1.3 78.1 + - - +
244B ASP* 4.3 7.0 - - - -
249B HIS* 3.4 18.4 - - - +
250B LEU* 3.4 41.9 - - + +
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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