Contacts of the helix formed by residues 228 - 245 (chain B) in PDB entry 1JXH
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 SER 228 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B ARG* 4.0 10.1 - - - +
226B HIS* 3.9 1.6 - - - +
227B ARG* 1.3 79.7 - - - +
229B TRP* 1.3 56.5 + - - +
230B GLY* 3.6 5.1 + - - -
231B GLU* 3.4 26.4 + - - +
232B THR* 2.7 33.0 + - - +
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Residues in contact with TRP 229 (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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101B ASN* 5.1 4.0 - - - -
103B VAL* 3.6 23.3 - - + -
134B SER* 4.0 21.6 + - - -
135B LEU* 3.6 37.9 - - + -
171B GLU* 3.1 28.0 + - - -
172B ALA* 3.9 19.1 - - + -
189B LEU* 3.8 20.9 - - + -
191B THR* 5.1 6.1 - - + +
219B LEU* 3.8 18.6 - - + -
223B ARG* 3.4 46.2 - - + +
228B SER* 1.3 72.2 - - - +
230B GLY* 1.3 56.9 + - - +
232B THR* 3.2 15.9 - - + -
233B VAL* 2.7 44.2 + - + +
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Residues in contact with GLY 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B LEU* 3.6 18.9 - - - +
196B GLN* 4.1 20.3 + - - -
198B PHE* 3.7 9.2 - - - -
228B SER* 3.2 7.0 + - - -
229B TRP* 1.3 78.6 - - - +
231B GLU* 1.3 57.0 + - - +
234B ASN* 3.0 27.7 + - - +
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Residues in contact with GLU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B HIS* 3.7 24.7 + - + +
227B ARG* 3.2 49.0 + - - +
228B SER* 3.4 17.8 + - - +
229B TRP 3.3 0.2 - - - -
230B GLY* 1.3 72.7 - - - +
232B THR* 1.3 65.9 + - - +
234B ASN* 3.1 8.2 + - - +
235B GLU* 3.0 23.4 + - - +
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Residues in contact with THR 232 (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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219B LEU* 3.6 23.2 + - - +
222B LEU* 4.1 4.4 - - - +
223B ARG* 3.6 18.7 + - - -
226B HIS* 3.5 27.1 - - + -
228B SER 2.7 29.1 + - - +
229B TRP* 3.2 33.9 - - + +
231B GLU* 1.3 75.3 - - - +
233B VAL* 1.3 55.0 + - - +
235B GLU* 4.1 0.3 - - - +
236B ALA* 2.9 30.5 + - - +
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Residues in contact with VAL 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 5.1 2.2 - - + -
174B LEU* 4.3 19.7 - - + -
189B LEU* 4.2 20.0 - - + -
198B PHE* 3.7 34.5 - - + -
219B LEU* 3.7 22.7 - - + -
229B TRP* 2.7 37.9 + - + +
230B GLY 3.7 3.8 - - - +
232B THR* 1.3 71.9 - - - +
234B ASN* 1.3 63.6 + - - +
236B ALA* 3.8 0.7 - - - +
237B LYS* 3.1 35.2 + - + +
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Residues in contact with ASN 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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196B GLN* 5.9 0.2 - - - +
198B PHE* 4.2 21.4 - - + -
230B GLY 3.0 14.6 + - - +
231B GLU* 3.1 12.1 + - - +
233B VAL* 1.3 79.1 - - - +
235B GLU* 1.3 63.5 + - - +
237B LYS* 3.6 3.2 + - - +
238B ALA* 3.2 22.9 + - - +
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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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30B LEU* 5.0 4.9 - - - +
222B LEU* 3.8 24.6 - - + +
225B ARG* 5.6 1.0 - - - +
226B HIS* 2.4 46.5 + - + +
231B GLU 3.0 10.0 + - - +
232B THR 4.1 1.6 - - - +
234B ASN* 1.3 75.8 + - - +
236B ALA* 1.3 67.1 + - - +
238B ALA* 3.2 7.2 + - + +
239B TRP* 3.0 25.4 + - + +
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Residues in contact with ALA 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU* 4.3 7.3 - - + +
218B ALA* 4.2 11.9 - - + +
219B LEU* 3.6 29.2 - - + +
222B LEU* 3.8 18.3 - - + +
232B THR 2.9 20.2 + - - +
233B VAL 3.8 1.6 - - - +
235B GLU* 1.3 77.1 - - - +
237B LYS* 1.3 57.6 + - - +
239B TRP* 3.5 6.6 + - - +
240B LEU* 3.0 28.4 + - - +
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Residues in contact with LYS 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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174B LEU* 5.1 5.2 - - + -
187B ASP* 2.8 42.4 + - - -
198B PHE* 3.9 26.3 - - + +
202B ARG* 5.7 5.7 - - - +
215B LEU* 4.4 18.4 - - + +
233B VAL* 3.1 33.3 + - + +
234B ASN* 4.0 3.6 - - - +
236B ALA* 1.3 74.6 - - - +
238B ALA* 1.3 67.1 + - - +
240B LEU* 3.3 8.4 + - + +
241B SER* 2.9 28.2 + - - +
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Residues in contact with ALA 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* 3.2 14.8 + - - +
235B GLU* 3.2 12.9 + - + +
237B LYS* 1.3 78.3 - - - +
239B TRP* 1.3 64.6 + - - +
241B SER* 3.4 7.2 + - - -
242B ALA* 3.2 20.6 + - - +
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Residues in contact with TRP 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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26B THR* 3.9 24.2 - - + -
29B ALA* 3.8 17.4 + - + +
30B LEU* 3.6 31.5 - - + +
214B THR* 3.5 30.1 - - + -
218B ALA* 4.2 14.4 - - + -
222B LEU* 5.2 2.2 - - + -
235B GLU* 3.0 19.3 + - + +
236B ALA* 3.7 4.5 - - - +
238B ALA* 1.3 77.4 - - - +
240B LEU* 1.3 71.5 + - + +
242B ALA* 3.1 9.4 + - - +
243B ALA* 3.0 22.1 + - + -
261B HIS* 3.2 36.0 + - - -
263B HIS* 3.3 29.1 + + - -
264B ALA* 5.3 4.7 - - + +
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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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211B THR* 4.3 19.3 - - + +
214B THR* 4.1 28.7 - - + -
215B LEU* 4.7 20.0 - - + +
218B ALA* 6.0 0.2 - - + -
236B ALA 3.0 17.7 + - - +
237B LYS* 3.7 9.2 - - + +
239B TRP* 1.3 82.7 - - + +
241B SER* 1.3 69.1 + - - +
243B ALA* 2.9 9.1 + - + -
244B LEU* 2.9 50.7 + - + +
259B VAL* 4.5 7.4 - - + -
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Residues in contact with SER 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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202B ARG* 5.9 3.3 - - - -
237B LYS* 2.9 18.6 + - - +
238B ALA* 3.7 7.6 - - - -
240B LEU* 1.3 81.0 - - - +
242B ALA* 1.3 57.5 + - - +
244B LEU* 3.3 8.7 + - - +
245B ALA* 2.9 30.2 + - - +
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Residues in contact with ALA 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 ALA 3.2 9.6 + - - +
239B TRP* 3.1 11.5 + - - +
241B SER* 1.3 80.9 - - - +
243B ALA* 1.3 60.2 + - - +
245B ALA* 3.4 14.8 + - - +
246B GLN* 3.5 21.1 + - - +
263B HIS* 3.6 24.3 - - + +
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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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239B TRP* 3.0 17.0 + - + +
240B LEU* 2.9 15.3 + - + +
242B ALA* 1.3 75.8 - - - +
244B LEU* 1.3 64.1 + - - +
246B GLN* 3.3 2.9 + - - -
247B ALA 3.2 9.5 + - - -
259B VAL* 3.8 20.0 - - + -
260B HIS* 3.1 36.1 + - - +
263B HIS* 3.3 17.0 - - + +
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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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203B VAL* 4.2 26.2 - - + -
204B ASN* 5.8 1.3 - - - +
205B THR* 3.6 35.1 - - + +
207B ASN 3.8 9.0 - - - +
208B THR* 3.8 14.8 - - + -
211B THR* 4.0 9.2 - - + +
240B LEU* 2.9 39.2 + - + +
241B SER* 3.7 10.3 - - - +
243B ALA* 1.3 71.2 - - - +
245B ALA* 1.3 59.0 + - - +
246B GLN 3.0 9.9 + - - -
247B ALA* 3.1 19.3 + - - +
248B ASP* 4.7 0.5 + - - -
259B VAL* 3.5 26.2 - - + -
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Residues in contact with ALA 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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204B ASN* 5.2 15.2 + - - +
205B THR* 5.7 0.2 - - - -
241B SER 2.9 17.3 + - - +
242B ALA* 3.7 9.2 - - - +
243B ALA 3.2 0.6 - - - -
244B LEU* 1.3 76.8 - - - +
246B GLN* 1.3 62.1 + - + +
248B ASP* 5.2 2.1 + - - +
249B THR* 5.5 1.2 - - - +
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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
------------------------------------------------------------
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