Contacts of the helix formed by residues 237 - 247 (chain B) in PDB entry 3EU9
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 237 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198B ALA 3.6 17.6 + - - +
199B TYR 5.3 0.4 - - - -
200B ARG 5.2 0.2 - - - +
201B THR 2.7 31.5 + - - +
202B HIS* 3.0 33.1 + - + +
232B ALA* 2.9 13.5 + - - +
235B ALA* 4.4 1.1 - - + -
236B GLY* 1.3 73.3 - - - +
238B THR* 1.3 56.4 + - - +
239B THR* 3.6 0.5 - - - -
240B VAL* 2.9 36.8 + - + +
241B ILE* 3.0 31.0 + - - +
273B MET* 4.9 0.2 - - - +
322B SO4 3.4 10.2 + - - -
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Residues in contact with THR 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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236B GLY 4.2 7.2 - - - +
237B ASN* 1.3 68.8 - - - +
239B THR* 1.3 65.7 + - - +
241B ILE* 3.8 9.2 - - - -
242B SER* 3.3 10.7 + - - -
270B ASN* 4.8 6.3 - - - +
272B TRP* 3.3 55.2 - - + -
273B MET* 4.4 15.9 - - + -
322B SO4 2.7 27.5 + - - +
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Residues in contact with THR 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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202B HIS 4.7 1.0 + - - -
203B SER* 3.4 35.4 + - - +
204B VAL* 3.5 19.3 - - + +
237B ASN* 3.2 4.6 - - - -
238B THR* 1.3 80.5 + - - +
240B VAL* 1.3 62.2 + - - +
242B SER* 3.7 5.9 + - - -
243B LEU* 3.5 20.1 + - - +
322B SO4 2.8 30.2 + - - -
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Residues in contact with VAL 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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198B ALA* 3.7 22.7 - - + -
201B THR 3.5 11.2 - - - +
203B SER 4.1 7.6 - - - +
207B THR* 3.6 18.4 - - - +
232B ALA* 3.8 4.0 - - + -
237B ASN* 2.9 40.6 + - + +
239B THR* 1.3 74.2 - - - +
241B ILE* 1.3 66.9 + - - +
243B LEU* 3.1 8.4 + - - +
244B LEU* 2.9 52.1 + - + +
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Residues in contact with ILE 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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229B LEU* 3.7 14.8 - - + +
232B ALA* 3.4 25.6 - - + -
233B VAL* 3.6 28.9 - - + +
237B ASN 3.0 20.0 + - - +
238B THR* 3.7 9.9 - - - +
240B VAL* 1.3 77.8 - - - +
242B SER* 1.3 64.2 + - - +
244B LEU* 3.1 2.0 + - - +
245B LEU* 2.9 38.8 + - + +
272B TRP* 3.7 14.6 - - + -
273B MET* 4.8 8.3 - - + -
277B LEU* 3.6 27.8 - - + -
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Residues in contact with SER 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 THR 3.3 3.5 + - - -
239B THR* 3.7 10.7 - - - -
240B VAL 3.2 0.4 - - - -
241B ILE* 1.3 80.4 - - - +
243B LEU* 1.3 64.3 + - - +
245B LEU* 3.3 8.1 + - - +
246B GLU* 3.0 25.7 + - - +
272B TRP* 3.2 29.0 - - - -
276B HIS* 5.1 2.3 - - - -
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Residues in contact with LEU 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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203B SER 4.5 0.2 - - - +
204B VAL* 3.3 43.1 - - + +
207B THR* 3.9 15.0 - - + -
208B ARG* 4.0 28.7 - - + +
211B LEU* 3.8 17.5 - - + +
239B THR* 3.5 16.6 + - + +
240B VAL* 3.1 9.3 + - - +
242B SER* 1.3 78.6 - - - +
244B LEU* 1.3 65.0 + - - +
246B GLU* 3.4 17.2 + - - +
247B ALA* 3.1 21.5 + - - +
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Residues in contact with LEU 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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194B LEU* 4.8 10.3 - - + -
198B ALA* 4.5 0.2 - - + -
207B THR* 3.6 20.4 - - + -
211B LEU* 4.6 6.1 - - + -
217B VAL* 5.7 3.8 - - + -
228B ALA* 3.6 42.2 - - + +
229B LEU* 3.6 19.1 - - + +
232B ALA* 4.2 1.6 - - + -
240B VAL* 2.9 42.6 + - + +
241B ILE 3.6 3.1 - - - +
243B LEU* 1.3 72.0 - - - +
245B LEU* 1.3 61.5 + - - +
247B ALA* 2.9 27.3 + - - +
249B ALA* 3.1 27.1 + - + +
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Residues in contact with LEU 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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229B LEU* 4.3 27.1 - - + -
241B ILE* 2.9 38.9 + - + +
242B SER* 3.6 7.4 - - - +
244B LEU* 1.3 73.9 - - - +
246B GLU* 1.3 56.6 + - - +
248B GLY* 2.7 25.8 + - - -
249B ALA* 3.8 10.6 + - + +
251B VAL* 5.1 6.1 - - + -
272B TRP* 5.6 0.2 - - + -
276B HIS* 3.7 35.2 - - + +
277B LEU* 4.3 13.2 - - + +
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Residues in contact with GLU 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 SER 3.0 14.2 + - - +
243B LEU* 3.8 17.3 - - - +
245B LEU* 1.3 78.7 - - - +
247B ALA* 1.3 57.8 + - - +
248B GLY 3.2 1.1 + - - -
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Residues in contact with ALA 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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211B LEU* 3.8 30.5 - - + -
217B VAL* 3.9 17.6 - - + +
243B LEU 3.1 12.5 + - - +
244B LEU* 2.9 13.5 + - - +
246B GLU* 1.3 79.3 - - - +
248B GLY* 1.3 58.4 - - - +
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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