Contacts of the helix formed by residues 232 - 239 (chain B) in PDB entry 3E8R
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 ASP 232 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230B VAL 3.9 1.0 + - - -
231B ALA* 1.3 75.2 - - - +
233B HIS* 1.3 60.7 + - - +
234B ARG* 3.1 15.7 + - - -
235B PHE* 2.8 20.8 + - - +
236B TYR* 3.0 24.6 + - - +
285B LEU* 3.6 7.6 - - - -
298B TYR* 4.6 13.5 - - + +
299B ASN* 3.7 15.3 - - + +
337B LEU* 4.0 16.0 - - + +
338B PHE 3.1 9.3 + - - -
339B THR* 2.5 36.9 + - - -
341B GLN* 3.9 3.8 + - - -
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Residues in contact with HIS 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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232B ASP* 1.3 76.0 - - - +
234B ARG* 1.3 86.7 + - + +
236B TYR* 4.0 3.9 - - - +
237B ARG* 3.2 56.5 + - - +
285B LEU 3.0 19.9 + - - +
286B LYS 4.0 3.8 - - - +
287B SER* 3.6 17.3 - - - -
288B PRO* 3.4 18.4 - - + +
299B ASN* 2.8 44.3 + - - +
300B MET 3.3 15.3 - - - -
301B ALA* 4.0 8.7 + - - +
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Residues in contact with ARG 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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232B ASP* 3.1 11.3 + - - +
233B HIS* 1.3 96.5 - - + +
235B PHE* 1.3 61.0 + - - +
237B ARG* 6.0 0.2 - - - +
238B TYR* 2.9 49.4 + - + -
298B TYR 5.4 3.0 + - - -
300B MET 3.9 5.5 + - - -
301B ALA 3.2 26.6 + - - -
302B LYS 3.6 12.5 + - - -
303B SER* 3.5 15.9 + - - +
310B ASP* 3.0 30.5 + - - -
312B TRP* 4.4 5.1 - - - +
339B THR* 3.7 0.2 - - - -
340B TYR* 3.4 29.0 + - - +
341B GLN* 3.5 33.0 - - - +
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Residues in contact with PHE 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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231B ALA* 3.8 15.5 - - + -
232B ASP* 2.8 12.7 + - - +
234B ARG* 1.3 76.4 - - - +
236B TYR* 1.3 61.1 + - - +
239B MET* 2.8 53.9 + - + +
240B GLY 3.0 2.5 + - - -
247B THR* 4.1 15.3 - - + -
250B TYR* 3.6 31.4 - + + -
251B LEU* 3.9 24.7 - - + -
338B PHE* 3.4 34.5 - + + +
339B THR* 3.6 18.8 - - - -
340B TYR* 3.9 6.7 - - - +
387B THR* 3.7 26.9 - - + -
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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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231B ALA* 5.0 0.2 - - - +
232B ASP 3.0 15.2 + - - +
233B HIS 4.0 4.0 - - - +
235B PHE* 1.3 77.4 - - - +
237B ARG* 1.3 62.2 + - + +
240B GLY* 3.0 15.2 + - - -
242B GLY* 2.6 49.8 + - - -
243B GLU* 3.4 23.2 - - - -
244B GLU* 3.6 6.4 + - - -
247B THR* 3.4 20.4 - - + -
284B ILE* 3.4 27.4 - - + -
285B LEU 4.2 3.8 - - - +
286B LYS* 3.4 60.8 + - + +
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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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233B HIS* 3.2 43.0 + - - +
234B ARG 4.2 0.9 - - - +
236B TYR* 1.3 86.6 - - + +
238B TYR* 1.3 106.8 + - + +
239B MET 3.5 0.2 - - - -
241B ARG* 4.2 5.2 + - - -
242B GLY* 4.1 15.4 + - - +
286B LYS 5.5 3.0 + - - +
288B PRO* 4.4 14.3 - - - +
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Residues in contact with TYR 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 ARG* 2.9 41.4 + - + +
237B ARG* 1.3 126.4 + - + +
239B MET* 1.3 67.9 + - - +
241B ARG 4.9 0.9 - - - -
340B TYR* 3.4 39.4 - + + -
393B THR* 4.7 2.9 + - - -
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Residues in contact with MET 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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235B PHE* 2.8 35.4 + - + +
238B TYR* 1.3 81.4 - - - +
240B GLY* 1.3 57.1 + - - +
241B ARG* 3.3 6.0 + - - +
246B THR* 4.3 9.2 - - - +
250B TYR* 3.4 51.2 - - + +
340B TYR* 3.6 20.9 - - + -
387B THR* 3.1 29.6 - - - +
393B THR* 3.6 28.7 - - + -
394B ILE 5.7 0.4 - - - +
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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