Contacts of the helix formed by residues 225 - 238 (chain B) in PDB entry 1OE4
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 GLY 225 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223B GLY 3.7 1.3 - - - +
224B VAL* 1.3 77.2 - - - +
226B ARG* 1.3 66.1 + - - -
227B PHE 3.4 3.3 + - - -
228B SER 3.5 1.7 + - - -
229B GLU* 3.2 23.8 + - - +
248B ILE 3.0 19.2 + - - -
249B MET* 5.2 0.2 - - - -
250B HIS* 3.7 22.6 - - - +
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Residues in contact with ARG 226 (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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225B GLY* 1.3 68.9 - - - -
227B PHE* 1.3 66.4 + - - +
229B GLU* 3.1 29.2 + - - +
230B GLN* 3.0 48.8 + - - +
247B GLY* 5.8 2.4 - - - -
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Residues in contact with PHE 227 (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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95B MET* 3.4 43.3 - - + -
175B HIS* 4.3 13.9 - + - -
190B PRO* 4.8 2.9 - - + -
191B THR* 3.5 33.4 - - + -
202B LEU* 3.9 29.8 - - + -
225B GLY* 3.4 0.8 - - - -
226B ARG* 1.3 78.0 - - - +
228B SER* 1.3 64.7 + - - +
230B GLN* 3.8 4.2 - - - +
231B ARG* 2.9 58.1 + - + +
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Residues in contact with SER 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 3.3 33.3 - - - +
94B GLY* 3.0 28.3 + - - -
95B MET* 3.1 11.8 + - - +
175B HIS* 5.0 1.9 - - - +
223B GLY* 4.0 3.0 - - - -
224B VAL 3.9 12.5 + - - -
225B GLY 3.5 2.2 + - - -
226B ARG 3.3 0.4 - - - -
227B PHE* 1.3 79.8 - - - +
229B GLU* 1.3 64.7 + - - +
231B ARG* 4.1 3.3 - - - +
232B ALA* 3.1 26.7 + - - +
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Residues in contact with GLU 229 (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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223B GLY* 3.7 11.8 - - - +
225B GLY 3.2 16.8 + - - +
226B ARG* 3.1 37.1 + - - +
228B SER* 1.3 78.0 - - - +
230B GLN* 1.3 60.1 + - - +
233B ARG* 3.0 56.4 + - - +
245B VAL* 3.4 10.0 - - + +
246B LYS* 3.3 19.3 - - - +
247B GLY* 3.7 22.9 + - - -
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Residues in contact with GLN 230 (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* 3.0 41.7 + - - +
227B PHE* 4.0 4.0 - - - +
229B GLU* 1.3 79.0 - - + +
231B ARG* 1.3 65.2 + - - +
233B ARG* 3.5 18.4 + - - +
234B LYS* 3.2 23.9 + - - +
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Residues in contact with ARG 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 6.2 0.2 - - + -
175B HIS* 3.6 27.6 - - + +
199B ASP* 5.1 5.5 + - - +
202B LEU* 3.6 38.7 - - - +
203B GLU* 4.1 9.9 + - - +
206B ASP* 2.8 34.1 + - - +
209B LEU* 5.2 0.7 - - - -
227B PHE* 2.9 43.6 + - + +
228B SER* 4.1 3.8 - - - +
230B GLN* 1.3 73.8 - - - +
232B ALA* 1.3 60.9 + - - +
234B LYS* 3.6 32.6 + - - +
235B ALA* 3.0 28.1 + - - +
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Residues in contact with ALA 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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93B LEU* 3.9 18.8 - - + +
209B LEU* 4.0 15.7 - - + +
221B VAL* 4.2 11.2 - - + -
228B SER 3.1 19.8 + - - +
229B GLU 3.9 3.1 - - - +
231B ARG* 1.3 75.9 - - - +
233B ARG* 1.3 65.5 + - - +
235B ALA* 3.9 0.2 - - - -
236B LEU* 3.0 34.2 + - + +
245B VAL* 4.1 13.9 - - + -
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Residues in contact with ARG 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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229B GLU* 3.0 57.5 + - - +
230B GLN* 3.7 18.6 - - - +
231B ARG 3.4 0.2 - - - -
232B ALA* 1.3 76.6 - - - +
234B LYS* 1.3 55.8 + - - +
236B LEU* 4.0 1.2 - - - +
237B MET* 3.1 36.6 + - + +
245B VAL* 2.8 46.0 + - + +
246B LYS* 4.3 2.0 - - - +
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Residues in contact with LYS 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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206B ASP* 4.7 2.7 - - - +
230B GLN 3.2 15.4 + - - +
231B ARG* 3.9 40.5 - - - +
233B ARG* 1.3 79.2 - - - +
235B ALA* 1.3 65.3 + - - +
237B MET* 3.5 16.1 + - + +
238B ALA* 3.1 25.9 + - + +
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Residues in contact with ALA 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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206B ASP* 3.5 45.3 - - + +
209B LEU* 4.6 8.1 - - + -
210B CYS* 3.4 16.8 - - - -
231B ARG 3.0 19.2 + - - +
232B ALA* 3.4 5.1 + - - +
234B LYS* 1.3 76.1 - - - +
236B LEU* 1.3 62.5 + - + +
238B ALA* 3.4 14.1 + - - +
239B GLU* 3.5 6.9 + - - +
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Residues in contact with LEU 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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209B LEU* 4.8 6.7 - - + -
210B CYS* 3.9 16.6 - - - +
213B VAL* 4.1 20.9 - - + -
221B VAL* 4.3 13.7 - - + -
232B ALA* 3.0 21.2 + - + +
233B ARG* 4.2 2.7 - - - +
235B ALA* 1.3 73.6 - - - +
237B MET* 1.3 64.8 + - - +
239B GLU 3.4 1.9 + - - -
240B GLY 3.1 17.2 + - - -
241B ILE* 3.1 44.8 + - + +
243B VAL* 4.2 25.1 - - + +
245B VAL* 3.8 26.2 - - + -
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Residues in contact with MET 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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233B ARG* 3.1 24.1 + - + +
234B LYS* 3.9 14.6 - - + +
236B LEU* 1.3 77.1 - - - +
238B ALA* 1.3 63.3 + - + +
240B GLY* 3.1 14.7 + - - +
241B ILE 5.2 2.0 - - - -
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Residues in contact with ALA 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 LYS* 3.1 19.6 + - + +
235B ALA* 3.7 8.1 - - - +
236B LEU 3.3 0.6 - - - -
237B MET* 1.3 79.1 - - + +
239B GLU* 1.3 61.2 + - + +
240B GLY 3.6 0.2 - - - -
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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