Contacts of the helix formed by residues 235 - 246 (chain B) in PDB entry 1OFU
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 ASN 235 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233B GLY 3.4 0.8 - - - -
234B PRO* 1.3 90.7 + - - +
236B ARG* 1.3 63.6 + - - +
237B ALA* 3.0 5.3 + - - -
238B ARG* 3.1 17.2 + - + +
239B GLU* 2.9 40.7 + - + +
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Residues in contact with ARG 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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231B ALA* 3.7 32.5 - - - +
232B SER 3.8 3.6 + - - -
233B GLY 3.2 18.8 + - - +
234B PRO 3.5 0.2 - - - -
235B ASN* 1.3 76.5 - - - +
237B ALA* 1.3 58.8 + - - +
239B GLU* 4.1 0.4 - - - -
240B ALA* 2.8 36.9 + - - +
267B ALA* 5.1 1.5 - - - +
270B ASP* 2.5 45.8 + - - +
271B LEU* 3.6 3.8 - - - +
275B GLU* 2.6 40.9 + - - +
305B ASP* 2.8 39.5 + - - +
306B GLU 3.7 7.3 + - - -
307B LEU* 3.6 19.5 - - + +
125Y ARG* 4.6 2.4 - - - +
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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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234B PRO 5.4 0.2 + - - -
235B ASN* 3.0 2.1 + - - -
236B ARG* 1.3 84.2 - - - +
238B ARG* 1.3 59.0 + - - +
240B ALA* 4.2 0.9 - - - +
241B THR* 2.7 31.4 + - - -
275B GLU* 3.8 44.9 - - + +
278B ASP* 4.1 15.5 - - + +
279B VAL* 4.2 4.0 - - + +
282B ILE* 4.6 1.5 - - - +
307B LEU* 4.0 12.8 - - + -
309B VAL* 4.8 0.2 - - - +
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Residues in contact with ARG 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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235B ASN* 3.1 19.3 + - + +
237B ALA* 1.3 77.0 - - - +
239B GLU* 1.3 61.7 + - + +
241B THR* 3.4 0.9 + - - -
242B GLU* 2.9 65.3 + - - +
278B ASP* 5.2 3.5 + - + +
282B ILE* 3.6 33.8 - - + +
285B GLN* 5.4 7.9 + - - +
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Residues in contact with GLU 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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230B CYS 5.4 0.2 - - - -
231B ALA* 3.5 24.3 - - + +
232B SER 4.5 8.1 - - - +
235B ASN* 2.9 36.4 + - + +
236B ARG 4.4 1.1 + - - -
238B ARG* 1.3 79.2 - - + +
240B ALA* 1.3 57.1 + - - +
242B GLU* 3.9 7.1 - - - +
243B ALA* 2.9 31.4 + - - +
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Residues in contact with ALA 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B GLY* 3.5 4.9 - - - +
230B CYS* 4.0 12.8 - - - +
231B ALA* 3.7 9.3 - - - +
236B ARG 2.8 22.4 + - - +
237B ALA 4.2 0.2 - - - +
239B GLU* 1.3 73.9 - - - +
241B THR* 1.3 56.7 - - - +
243B ALA* 3.4 2.6 + - - +
244B ALA* 2.9 28.4 + - - +
307B LEU* 3.3 28.7 - - + +
309B VAL* 3.7 17.3 - - + +
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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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237B ALA 2.7 22.5 + - - -
238B ARG 3.8 2.9 - - - -
240B ALA* 1.3 76.5 - - - +
242B GLU* 1.3 64.6 + - - +
244B ALA* 3.3 3.0 + - + +
245B ILE* 3.1 31.3 + - + +
279B VAL* 3.5 23.7 - - + +
282B ILE* 3.5 33.9 - - + -
283B ILE* 4.1 23.3 - - + -
309B VAL* 3.7 14.9 - - + +
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Residues in contact with GLU 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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238B ARG* 2.9 62.0 + - + +
239B GLU* 3.9 5.5 - - - +
241B THR* 1.3 75.4 - - - +
243B ALA* 1.3 58.9 + - - +
245B ILE* 3.1 10.5 + - + +
246B ARG* 2.8 64.7 + - - +
282B ILE* 4.7 11.0 - - + -
286B PHE* 6.4 2.2 - - + -
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Residues in contact with ALA 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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228B THR 3.7 2.0 - - - +
229B GLY* 3.8 13.9 - - - -
230B CYS 4.4 7.0 - - - +
239B GLU 2.9 20.0 + - - +
240B ALA* 3.5 7.4 - - - +
242B GLU* 1.3 78.0 - - - +
244B ALA* 1.3 60.9 + - - +
246B ARG* 3.4 13.7 + - - +
247B ASN* 3.0 24.1 + - - +
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Residues in contact with ALA 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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227B GLY* 3.4 23.2 - - - +
228B THR 3.5 11.4 - - - -
229B GLY* 3.5 1.5 - - - +
240B ALA 2.9 14.7 + - - +
241B THR 3.6 4.9 - - - +
242B GLU 3.2 0.4 - - - -
243B ALA* 1.3 76.5 - - - +
245B ILE* 1.3 62.6 + - + +
247B ASN* 3.4 15.2 - - - +
250B LEU* 3.7 3.8 - - - +
309B VAL* 3.4 33.7 - - + +
311B VAL* 3.9 10.3 - - + -
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Residues in contact with ILE 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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241B THR* 3.1 22.2 + - + +
242B GLU* 3.6 9.4 - - - +
244B ALA* 1.3 80.3 - - + +
246B ARG* 1.3 58.5 + - + +
247B ASN 3.2 1.5 + - - +
250B LEU* 3.8 25.2 - - + +
251B GLU* 5.7 0.3 - - - -
255B LEU* 4.2 23.4 - - + +
282B ILE* 4.1 23.8 - - + +
283B ILE* 5.1 7.9 - - + -
286B PHE* 4.1 40.6 - - + -
311B VAL* 4.9 11.2 - - + -
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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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242B GLU* 2.8 60.2 + - - +
243B ALA* 3.6 12.6 - - - +
245B ILE* 1.3 75.8 - - + +
247B ASN* 1.3 64.8 + - - +
248B PRO* 3.2 8.1 - - - +
251B GLU* 5.1 4.2 - - - +
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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