Contacts of the helix formed by residues 233 - 241 (chain B) in PDB entry 1BGB
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 ILE 233 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179B ASP* 2.8 27.3 + - + +
205B ILE* 4.3 15.7 - - + +
206B PHE* 3.6 34.3 - - + -
211B GLU* 4.3 0.7 - - - +
215B TYR* 4.1 5.4 - - + -
232B ASN* 1.3 70.2 - - + +
234B SER* 1.3 74.8 + - - +
236B TYR* 3.3 20.8 + - + +
237B ARG* 3.2 64.7 + - - +
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Residues in contact with SER 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ASN* 2.8 15.8 + - - -
233B ILE* 1.3 81.4 - - - +
235B GLU* 1.3 65.4 + - - +
237B ARG* 3.2 8.3 + - - +
238B ASN* 3.1 22.3 + - - +
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Residues in contact with GLU 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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226B ARG 4.7 2.3 - - - +
227B ASN* 5.4 3.8 - - - +
229B LYS 4.5 3.0 - - - +
230B TYR* 3.4 19.9 - - + -
231B ASN* 3.0 27.6 + - - +
232B ASN* 2.7 35.0 + - - +
234B SER* 1.3 80.6 - - - +
236B TYR* 1.3 56.7 + - - +
238B ASN* 3.3 6.3 + - + +
239B TRP* 2.9 30.0 + - - +
242B ARG* 3.3 8.4 + - - +
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Residues in contact with TYR 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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211B GLU* 3.6 31.8 + - + +
214B ASP* 2.6 40.7 + - - +
215B TYR* 3.5 41.7 + + + -
230B TYR* 3.4 33.5 - + + +
232B ASN 3.1 5.1 + - - -
233B ILE* 3.5 23.3 - - + +
235B GLU* 1.3 74.2 - - - +
237B ARG* 1.3 69.9 + - + +
239B TRP* 3.5 7.6 + + - +
240B ILE* 3.1 46.6 + - + +
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Residues in contact with ARG 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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205B ILE 3.6 16.2 + - - -
207B ASP* 3.2 22.9 + - - -
211B GLU* 2.9 38.4 + - - +
233B ILE* 3.2 34.9 + - - +
234B SER* 3.5 11.2 - - - +
236B TYR* 1.3 91.6 - - + +
238B ASN* 1.3 60.9 + - - +
240B ILE* 3.3 8.2 + - - +
241B TYR* 3.1 21.8 + - - +
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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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234B SER 3.1 14.0 + - - +
235B GLU* 3.7 10.1 - - + +
237B ARG* 1.3 74.9 - - - +
239B TRP* 1.3 57.2 + - - +
241B TYR* 3.5 18.8 + - - +
242B ARG* 3.0 48.4 + - - +
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Residues in contact with TRP 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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218B ASN* 4.0 18.2 - - + -
228B ASP 5.5 0.4 - - - -
229B LYS* 3.7 40.1 - - + +
230B TYR* 3.8 23.1 - + + -
235B GLU 2.9 17.6 + - - +
236B TYR* 3.5 16.2 - + - +
237B ARG 3.2 0.2 - - - -
238B ASN* 1.3 74.9 - - - +
240B ILE* 1.3 87.2 + - + +
242B ARG* 3.1 41.0 + - - +
243B GLY 3.3 4.2 + - - -
244B ARG* 2.6 81.4 + - + -
245B LYS* 3.2 20.5 - - - +
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Residues in contact with ILE 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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214B ASP* 3.8 6.3 - - - +
236B TYR* 3.1 37.3 + - + +
237B ARG* 3.3 8.7 + - - +
239B TRP* 1.3 89.8 - - + +
241B TYR* 1.3 60.2 + - - +
243B GLY* 2.8 26.0 + - - -
244B ARG* 3.0 42.7 + - + +
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Residues in contact with TYR 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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237B ARG 3.1 11.0 + - - +
238B ASN* 3.6 25.8 - - - +
240B ILE* 1.3 81.7 - - - +
242B ARG* 1.3 68.0 + - + +
243B GLY* 3.0 5.9 + - - -
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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