Contacts of the helix formed by residues 230 - 241 (chain B) in PDB entry 5BOU
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 LYS 230 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59B ASP* 4.7 13.7 + - - +
228B ILE 4.6 4.9 + - - +
229B PHE* 1.3 75.8 - - - +
231B PRO* 1.3 78.5 - - + +
232B GLN* 3.2 5.6 - - + +
233B GLU* 2.7 32.8 + - + +
234B ILE* 2.9 22.5 + - - +
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Residues in contact with PRO 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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58B GLN* 3.8 37.5 - - + +
59B ASP* 3.9 35.4 - - + +
207B TYR* 3.4 22.5 - - + -
229B PHE 4.6 1.3 - - - +
230B LYS* 1.3 93.6 - - + +
232B GLN* 1.3 56.0 + - - +
234B ILE* 3.5 7.0 + - + +
235B LYS* 3.1 21.5 + - - +
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Residues in contact with GLN 232 (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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207B TYR* 5.5 0.4 - - - -
230B LYS* 3.2 3.9 - - + +
231B PRO* 1.3 80.5 - - - +
233B GLU* 1.3 61.1 + - + +
235B LYS* 3.3 25.4 + - - +
236B ASP* 3.0 59.8 + - - +
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Residues in contact with GLU 233 (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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227B LYS* 3.1 28.5 + - - +
228B ILE 4.2 1.4 - - - +
229B PHE* 3.6 17.5 - - + -
230B LYS* 2.7 49.7 + - + +
232B GLN* 1.3 76.8 - - + +
234B ILE* 1.3 64.1 + - - +
236B ASP* 3.5 10.8 + - - +
237B ILE* 3.2 24.4 + - - +
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Residues in contact with ILE 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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58B GLN* 4.7 2.2 - - - +
193B LEU* 5.9 0.2 - - + -
207B TYR* 3.9 23.8 - - + +
210B LEU* 3.5 46.0 - - + +
211B GLU* 4.2 1.1 - - - -
212B PHE* 4.0 23.8 - - + +
229B PHE* 3.7 26.0 - - + +
230B LYS 2.9 19.9 + - - +
231B PRO* 3.7 10.1 - - + +
233B GLU* 1.3 74.3 - - - +
235B LYS* 1.3 65.2 + - - +
237B ILE* 3.3 10.8 - - + +
238B LEU* 3.1 24.8 + - + +
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Residues in contact with LYS 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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207B TYR* 3.8 43.7 + - + +
231B PRO 3.1 14.3 + - - +
232B GLN* 3.4 32.2 - - - +
233B GLU 3.3 0.2 - - - -
234B ILE* 1.3 77.7 - - - +
236B ASP* 1.3 61.2 + - - +
238B LEU* 3.6 4.8 + - - +
239B VAL* 3.3 29.1 + - + +
244B THR* 4.5 1.7 + - - +
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Residues in contact with ASP 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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232B GLN* 3.0 43.4 + - - +
233B GLU* 3.8 10.4 - - - +
234B ILE 3.3 0.2 - - - -
235B LYS* 1.3 76.4 - - - +
237B ILE* 1.3 59.8 + - - +
239B VAL* 3.2 8.8 + - - +
240B LYS* 2.9 28.0 + - - +
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Residues in contact with ILE 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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189B ILE* 3.7 37.2 - - + -
193B LEU* 4.0 15.8 - - + +
212B PHE* 5.2 6.5 - - + -
229B PHE* 4.7 19.1 - - + -
233B GLU 3.2 12.4 + - - +
234B ILE* 3.3 19.3 - - + +
236B ASP* 1.3 76.4 - - - +
238B LEU* 1.3 59.4 + - + +
240B LYS* 3.7 31.4 - - + -
241B THR* 2.7 37.2 + - + +
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Residues in contact with LEU 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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193B LEU* 3.8 34.8 - - + -
205B LEU* 4.2 9.0 - - + +
206B THR* 3.7 12.1 - - - -
207B TYR* 3.5 34.1 - - + +
210B LEU* 3.8 13.7 - - + -
234B ILE* 3.1 22.0 + - + +
235B LYS* 3.7 4.9 - - - +
237B ILE* 1.3 78.8 - - + +
239B VAL* 1.3 59.4 + - - +
241B THR* 3.5 3.1 + - - -
242B GLY 3.3 2.8 + - - -
243B ILE* 2.9 42.8 + - + -
244B THR* 3.4 20.2 + - + +
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Residues in contact with VAL 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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235B LYS* 3.3 20.8 + - + +
236B ASP* 3.2 10.6 + - - +
238B LEU* 1.3 75.6 - - - +
240B LYS* 1.3 66.7 + - - +
242B GLY* 3.1 13.5 + - - -
244B THR* 3.7 27.1 - - - +
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Residues in contact with LYS 240 (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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186B ASP* 4.9 21.1 + - - +
189B ILE* 5.8 1.1 - - - -
190B GLU* 5.5 3.8 + - - -
236B ASP 2.9 16.6 + - - +
237B ILE* 3.7 30.7 - - + +
238B LEU 3.4 0.2 - - - -
239B VAL* 1.3 80.1 - - - +
241B THR* 1.3 71.7 + - - +
242B GLY* 3.5 0.9 + - - -
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Residues in contact with THR 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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186B ASP 5.7 0.9 - - - +
189B ILE* 4.6 3.4 - - + -
190B GLU* 4.0 42.0 - - + +
193B LEU* 3.9 10.1 - - + +
194B LYS* 3.5 19.5 + - - -
237B ILE* 2.7 25.8 + - + +
238B LEU* 3.5 7.8 + - - -
240B LYS* 1.3 90.3 - - - +
242B GLY* 1.3 61.0 + - - +
243B ILE* 3.5 20.7 - - - +
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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