Contacts of the helix formed by residues 234 - 246 (chain B) in PDB entry 1JQE
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 234 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228B ASP* 4.4 6.9 - - - +
231B ILE* 2.6 39.1 + - - +
232B ASP 3.3 1.0 + - - -
233B GLY* 1.3 67.1 - - - +
235B GLU* 1.3 66.8 + - - +
236B ASN 3.4 2.2 - - - -
237B GLY* 3.1 4.5 + - - +
238B ASP* 3.0 20.6 + - - -
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Residues in contact with GLU 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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233B GLY 3.0 8.8 + - - -
234B ASN* 1.3 71.5 - - - +
236B ASN* 1.3 62.6 + - - +
238B ASP* 3.2 8.7 + - - -
239B LEU* 3.3 10.2 + - - +
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Residues in contact with ASN 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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228B ASP* 3.6 20.4 - - + +
234B ASN 3.4 0.4 - - - -
235B GLU* 1.3 74.2 - - - +
237B GLY* 1.3 59.7 + - - +
239B LEU* 2.8 30.5 + - - +
240B LEU* 3.1 13.9 + - + +
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Residues in contact with GLY 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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228B ASP* 3.3 41.1 - - - +
229B CYS* 3.4 7.8 - - - -
234B ASN 3.1 6.8 + - - -
236B ASN* 1.3 78.6 - - - +
238B ASP* 1.3 59.8 + - - +
240B LEU* 3.1 12.1 + - - -
241B TRP* 3.2 21.4 + - - -
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Residues in contact with ASP 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 ASN 3.0 12.9 + - - -
235B GLU 3.2 3.6 + - - -
236B ASN 3.2 0.4 - - - -
237B GLY* 1.3 75.2 - - - +
239B LEU* 1.3 54.8 + - - +
240B LEU 3.2 0.4 + - - -
241B TRP* 3.6 19.8 + - - +
242B ASP* 2.6 27.9 + - - +
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Residues in contact with LEU 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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18B SER* 6.0 1.9 - - - -
21B ARG* 5.9 5.9 - - - +
235B GLU 3.3 7.5 + - - +
236B ASN* 2.8 20.1 + - - +
238B ASP* 1.3 79.9 - - - +
240B LEU* 1.3 63.5 + - + +
242B ASP* 3.9 9.7 + - - +
243B PHE* 3.7 15.9 + - - +
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Residues in contact with LEU 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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21B ARG 4.1 20.0 - - - +
22B PHE* 4.9 1.6 - - - -
25B HIS* 5.1 9.0 - - - -
224B MET* 3.7 25.1 - - + -
225B ASP 3.4 25.8 - - - +
226B ILE* 3.8 17.7 - - + -
228B ASP* 4.8 6.5 - - + +
229B CYS* 3.4 16.8 - - - -
236B ASN* 3.5 15.7 - - + +
237B GLY* 3.1 4.9 + - - +
239B LEU* 1.3 78.4 - - + +
241B TRP* 1.3 59.2 + - - +
242B ASP 3.1 2.0 - - - -
243B PHE* 3.1 6.1 + - + +
244B LEU* 2.9 38.7 + - + +
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Residues in contact with TRP 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 CYS* 3.1 40.6 + - + +
237B GLY 3.2 26.1 + - - -
238B ASP* 3.7 13.5 - - - +
239B LEU 3.4 0.4 - - - -
240B LEU* 1.3 80.2 - - - +
242B ASP* 1.3 53.1 + - - +
244B LEU* 4.1 5.5 - - + +
245B THR* 2.5 42.7 + - + +
250B PHE* 3.7 36.5 - + + +
251B ASN* 5.1 6.5 - - - +
259B ARG* 3.3 45.6 - - - +
262B LEU* 3.8 17.7 - - + -
263B GLY* 3.7 18.2 - - - -
266B LEU* 3.7 30.3 - - + -
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Residues in contact with ASP 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 ASP 2.6 22.8 - - - +
239B LEU* 4.0 9.8 - - - +
240B LEU 3.1 0.4 - - - -
241B TRP* 1.3 77.2 - - - +
243B PHE* 1.3 59.8 + - - +
245B THR* 3.7 0.2 - - - -
246B GLU* 3.0 23.9 + - - -
247B THR 2.8 20.9 + - - +
248B CYS* 4.5 1.8 - - - -
249B ASN* 2.6 34.6 + - - -
250B PHE* 2.7 17.7 + - - -
251B ASN 5.5 0.7 - - - -
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Residues in contact with PHE 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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18B SER* 4.1 18.4 - - - +
19B PHE* 4.1 25.8 - - + -
21B ARG 6.4 0.4 - - - -
22B PHE* 4.4 14.4 - - - -
179B TRP* 3.9 24.0 - + - -
224B MET* 3.2 29.8 - - + -
239B LEU 3.7 10.4 + - - +
240B LEU* 3.1 12.6 + - + +
242B ASP* 1.3 76.9 - - - +
244B LEU* 1.3 60.3 + - - +
245B THR 3.2 0.7 + - - -
246B GLU* 2.7 35.9 + - - +
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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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179B TRP* 3.6 20.6 - - + -
182B LEU* 3.1 30.5 - - + +
224B MET* 3.4 30.1 - - - -
226B ILE* 3.9 21.3 - - + -
229B CYS* 4.5 5.8 - - - -
240B LEU 2.9 24.5 + - - +
241B TRP* 4.1 6.5 - - + +
243B PHE* 1.3 77.0 - - - +
245B THR* 1.3 62.3 + - + +
246B GLU* 3.5 9.5 - - - +
266B LEU* 4.0 31.0 - - + -
281B PHE* 4.1 18.2 - - + -
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Residues in contact with THR 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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182B LEU* 6.0 2.2 - - + -
190B PHE* 4.3 15.0 - - - +
241B TRP* 2.5 27.3 + - + +
242B ASP 3.5 3.8 + - - -
244B LEU* 1.3 80.8 - - + +
246B GLU* 1.3 72.2 + - - +
247B THR* 2.7 29.0 + - - +
250B PHE* 3.4 39.3 - - + +
262B LEU* 3.8 16.6 - - + -
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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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179B TRP* 4.4 8.5 - - - -
183B TRP* 3.8 23.4 + - - -
191B PRO* 4.3 9.5 - - + +
196B CYS* 5.5 9.0 - - - -
198B TYR* 4.5 20.1 + - + +
242B ASP 3.0 8.8 + - - -
243B PHE* 2.7 30.3 + - - +
244B LEU 3.5 13.7 - - - +
245B THR* 1.3 78.4 - - - +
247B THR* 1.3 64.3 + - - +
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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