Contacts of the helix formed by residues 238 - 248 (chain B) in PDB entry 3BUN
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 VAL 238 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168B ILE* 4.0 13.0 - - + -
176B GLY 4.3 2.7 - - - +
179B PHE* 3.7 33.5 - - + +
181B ILE* 3.8 32.5 - - + -
190B TRP* 3.8 35.2 - - + +
197B LYS 4.2 2.7 - - - +
198B THR* 2.8 25.1 + - + +
237B SER* 1.3 70.7 - - - +
239B PHE* 1.3 59.8 + - - +
241B PHE* 3.5 4.0 - - - +
242B ASP* 2.9 28.2 + - - +
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Residues in contact with PHE 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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160B HIS* 4.5 1.8 - - + -
163B ALA* 3.7 29.6 - - + -
164B GLU* 3.6 36.1 - - + -
167B GLY* 4.2 12.1 - - - -
168B ILE* 4.2 11.9 - - + -
179B PHE* 3.9 29.4 - + + -
230B LEU* 5.6 0.4 - - + -
237B SER* 3.5 8.7 - - - +
238B VAL* 1.3 79.3 - - - +
240B GLU* 1.3 71.6 + - + +
242B ASP* 3.1 6.4 + - - +
243B ILE* 3.0 54.4 + - + +
300B LEU* 4.0 9.4 - - + -
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Residues in contact with GLU 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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164B GLU* 3.6 14.6 - - - +
199B ILE* 6.0 0.2 - - - +
228B ILE* 3.6 28.8 - - + +
229B ASP* 3.6 3.3 - - - +
230B LEU* 3.3 15.5 + - + +
231B THR* 2.8 41.0 + - + +
233B ASN* 4.7 0.5 + - - +
235B TYR 3.3 15.4 - - - +
236B ILE* 3.5 1.5 - - + -
237B SER* 2.9 35.0 + - - +
239B PHE* 1.3 81.3 - - + +
241B PHE* 1.3 67.2 + - - +
243B ILE* 3.2 8.6 + - - +
244B PHE* 3.0 24.6 + - - +
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Residues in contact with PHE 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ILE* 3.8 20.6 - - + -
186B ALA* 3.4 36.6 - - + -
189B PHE* 3.6 18.8 - + - -
190B TRP* 3.4 26.9 - + + -
205B PHE* 3.5 36.6 - + - -
209B LEU* 5.6 0.4 - - + -
228B ILE* 4.7 2.5 - - + -
236B ILE* 4.3 5.5 - - + +
237B SER 2.8 15.3 + - - +
238B VAL 3.5 3.8 - - - +
240B GLU* 1.3 79.1 - - - +
242B ASP* 1.3 62.2 + - - +
244B PHE* 3.4 5.0 + + + +
245B THR* 2.8 44.4 + - + +
251B TRP* 3.7 19.5 - + - -
254B LEU* 6.0 0.4 - - + -
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Residues in contact with ASP 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B PHE* 3.7 23.3 - - + -
180B ARG 4.4 0.4 - - - +
181B ILE* 3.6 7.2 - - - +
182B THR* 2.7 41.7 + - - -
183B LYS* 4.5 0.7 + - - +
238B VAL 2.9 15.3 + - - +
239B PHE* 3.1 10.4 + - - +
241B PHE* 1.3 79.3 - - - +
243B ILE* 1.3 64.6 + - - +
245B THR* 3.2 6.9 + - - -
246B ARG* 3.0 47.3 + - - +
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Residues in contact with ILE 243 (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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230B LEU* 3.7 26.5 - - + -
239B PHE* 3.0 48.1 + - + +
240B GLU* 3.2 6.9 + - - +
242B ASP* 1.3 80.4 - - - +
244B PHE* 1.3 64.4 + - - +
246B ARG* 3.3 6.1 + - - +
247B LEU* 3.0 49.0 + - + +
295B LEU* 4.5 3.4 - - + -
300B LEU* 3.5 33.9 - - + +
301B GLY* 4.0 17.9 - - - +
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Residues in contact with PHE 244 (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 PHE* 6.1 0.2 - + - -
209B LEU* 5.9 0.4 - - + -
224B LEU* 3.4 22.7 - - + -
227B THR* 3.6 17.5 - - + -
228B ILE* 3.0 47.1 - - + -
240B GLU 3.0 16.5 + - - +
241B PHE* 3.8 4.5 - + - +
243B ILE* 1.3 77.8 - - - +
245B THR* 1.3 67.5 + - + +
247B LEU* 3.3 6.7 + - + -
248B PHE* 3.0 63.6 + + - +
254B LEU* 3.8 28.9 - - + -
255B LEU* 4.6 1.8 - - + -
258B TRP* 3.9 14.6 - + + -
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Residues in contact with THR 245 (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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181B ILE* 4.7 2.3 - - - +
183B LYS* 3.8 9.1 - - - +
186B ALA* 3.6 19.5 - - - +
241B PHE* 2.8 35.4 + - + +
242B ASP* 3.2 10.6 + - - -
244B PHE* 1.3 82.9 - - + +
246B ARG* 1.3 61.2 + - - +
249B GLN* 3.2 24.9 + - - +
251B TRP* 3.6 36.2 + - + -
254B LEU* 4.3 12.6 - - + +
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Residues in contact with ARG 246 (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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182B THR* 4.0 26.3 + - + +
183B LYS* 4.3 12.7 - - + +
242B ASP* 3.0 38.4 + - - +
243B ILE* 3.8 6.9 - - - +
245B THR* 1.3 78.2 + - - +
247B LEU* 1.3 63.9 + - - +
249B GLN* 2.8 44.0 + - - +
300B LEU 3.3 24.7 + - - -
301B GLY* 3.5 23.1 - - - +
302B GLN* 4.3 15.6 - - - +
303B TRP* 5.8 0.2 - - - -
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Residues in contact with LEU 247 (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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243B ILE* 3.0 40.4 + - + +
244B PHE* 3.7 7.4 - - + +
246B ARG* 1.3 78.7 - - - +
248B PHE* 1.3 72.5 + - + +
249B GLN* 3.8 2.8 + - - +
261B LEU* 4.7 4.7 - - - +
295B LEU* 3.5 32.1 - - + -
301B GLY* 3.3 28.9 - - - +
302B GLN 3.7 14.4 - - - +
303B TRP* 3.0 49.9 + - + +
324B LEU* 5.3 1.0 + - - +
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Residues in contact with PHE 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B THR* 3.9 11.7 - - + -
244B PHE* 3.0 56.8 + + + +
245B THR 4.0 2.7 - - - -
247B LEU* 1.3 92.8 - - + +
249B GLN* 1.3 62.1 + - - +
254B LEU* 3.5 27.4 - - + +
257B ASN* 2.8 25.3 + - - +
258B TRP* 3.5 41.7 - + + +
261B LEU* 4.1 19.3 - - + -
262B ALA* 4.4 7.2 - - + -
268B TYR* 5.0 2.9 - + - -
295B LEU* 5.2 1.3 - - + -
303B TRP* 3.5 31.6 - + - -
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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