Contacts of the helix formed by residues 235 - 246 (chain M) in PDB entry 3J8B
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 GLU 235 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232M LEU 3.4 14.8 - - - +
233M GLU 2.6 12.6 + - - +
234M GLY* 1.3 70.2 - - - +
236M LEU* 1.3 61.5 + - - +
238M HIS* 3.2 7.4 + - - +
239M ASP* 2.9 29.9 + - - +
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Residues in contact with LEU 236 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234M GLY 3.3 0.4 - - - -
235M GLU* 1.3 78.9 - - - +
237M ILE* 1.3 57.9 + - - +
239M ASP* 3.2 8.4 + - - +
240M LEU* 2.9 28.7 + - - +
258M ASN 5.9 2.7 - - - +
259M ASN* 6.5 0.9 - - - -
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Residues in contact with ILE 237 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204M ALA* 5.3 4.3 - - + +
205M HIS* 4.8 16.4 - - + +
208M ILE* 4.7 19.9 - - + +
229M VAL 5.8 2.9 - - - +
234M GLY* 3.2 15.3 + - - +
235M GLU 3.2 0.2 - - - -
236M LEU* 1.3 80.2 - - - +
238M HIS* 1.3 57.3 + - - +
240M LEU* 3.2 8.5 + - - +
241M LEU* 2.9 28.1 + - - +
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Residues in contact with HIS 238 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229M VAL 5.0 9.3 + - - +
230M LYS 5.4 3.4 - - - +
231M PHE 4.9 7.2 - - - +
232M LEU* 5.6 1.3 - - - +
234M GLY 2.9 13.6 + - - +
235M GLU* 3.2 11.6 + - - +
237M ILE* 1.3 76.9 - - - +
239M ASP* 1.3 58.0 + - - +
241M LEU* 3.2 8.2 + - - +
242M THR* 2.9 28.6 + - - -
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Residues in contact with ASP 239 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235M GLU 2.9 13.3 + - - +
236M LEU* 3.4 11.2 - - - +
238M HIS* 1.3 78.0 - - - +
240M LEU* 1.3 57.6 + - - +
242M THR* 3.2 7.3 + - - -
243M ILE* 2.9 30.2 + - - +
258M ASN 5.2 9.6 - - - +
259M ASN* 5.7 6.7 - - + -
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Residues in contact with LEU 240 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208M ILE* 5.2 10.3 - - + +
236M LEU 2.9 13.5 + - - +
237M ILE* 3.2 11.9 + - - +
239M ASP* 1.3 77.2 - - - +
241M LEU* 1.3 52.6 + - - +
243M ILE* 3.2 8.5 + - - +
244M PHE* 2.7 38.0 + - - +
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Residues in contact with LEU 241 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220M PHE* 5.8 3.6 - - + +
224M LEU* 4.1 27.1 - - + -
229M VAL* 6.5 0.2 - - + -
237M ILE 2.9 13.4 + - - +
238M HIS* 3.2 12.1 + - - +
240M LEU* 1.3 74.5 - - - +
242M THR* 1.3 53.0 + - - +
244M PHE* 4.4 2.2 - - - +
245M VAL* 2.5 44.2 + - - +
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Residues in contact with THR 242 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238M HIS 2.9 12.6 + - - -
239M ASP* 3.2 11.2 + - - -
241M LEU* 1.3 75.0 - - - +
243M ILE* 1.3 58.0 + - - +
245M VAL* 4.5 2.9 - - - -
246M SER* 2.8 32.9 + - - +
247M ALA* 3.1 9.6 + - - +
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Residues in contact with ILE 243 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239M ASP 2.9 17.7 + - - +
240M LEU* 3.4 9.2 - - - +
242M THR* 1.3 78.8 - - - +
244M PHE* 1.3 59.6 + - - +
247M ALA* 3.4 35.7 + - + +
248M LYS 5.2 1.0 - - - +
251M SER 6.3 0.4 - - - -
252M TYR* 5.8 11.0 - - + -
277M MET* 5.8 3.6 - - - +
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Residues in contact with PHE 244 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212M LEU* 4.7 20.0 - - + -
218M PHE 5.0 6.9 - - - +
220M PHE* 4.3 13.2 - - + +
240M LEU 2.7 19.4 + - - +
241M LEU* 4.5 1.3 - - - +
243M ILE* 1.3 73.7 - - + +
245M VAL* 1.3 63.9 + - - +
246M SER 3.5 0.2 - - - -
247M ALA 5.2 1.5 - - - +
277M MET* 6.5 0.9 - - - -
280M LEU* 5.1 11.7 - - - +
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Residues in contact with VAL 245 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220M PHE* 4.0 30.2 - - + +
221M ASP* 4.7 4.7 - - + +
224M LEU* 4.7 8.7 - - + -
241M LEU 2.5 26.6 + - - +
242M THR* 4.4 2.0 - - - +
244M PHE* 1.3 76.7 - - - +
246M SER* 1.3 58.4 + - - +
247M ALA 4.0 0.2 - - - -
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Residues in contact with SER 246 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242M THR* 2.8 22.8 + - - -
245M VAL* 1.3 77.4 - - - +
247M ALA* 1.3 60.1 + - - +
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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