Contacts of the helix formed by residues 225 - 241 (chain B) in PDB entry 2JDQ
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 ARG 225 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B GLU* 3.6 20.4 + - - +
184B ASP* 5.9 0.8 + - - -
187B GLU* 4.4 6.1 - - - -
224B ASN* 1.3 79.1 - - - +
226B LEU* 1.3 66.8 + - + +
227B THR* 2.7 40.5 + - - +
228B MET* 3.3 8.1 + - + +
229B THR* 3.1 19.4 + - - -
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Residues in contact with LEU 226 (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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224B ASN 3.7 1.0 + - - -
225B ARG* 1.3 71.6 - - + +
227B THR* 1.3 66.6 + - + +
228B MET 3.1 1.8 - - - -
229B THR* 3.2 10.9 + - + +
230B ARG* 3.1 42.9 + - - +
265B VAL* 5.5 4.3 - - + -
267B ASP* 3.8 38.8 - - + +
270B VAL* 4.6 6.1 - - + -
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Residues in contact with THR 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B GLU* 2.7 21.8 + - - -
225B ARG* 2.7 45.2 + - - +
226B LEU* 1.3 77.7 - - + +
228B MET* 1.3 56.4 + - - +
230B ARG* 3.8 28.7 - - - +
231B ASN* 2.9 36.4 + - - -
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Residues in contact with MET 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B GLU* 3.0 35.7 - - - +
186B GLN* 3.8 14.1 - - + -
187B GLU* 3.5 51.8 + - + +
190B VAL* 4.7 4.9 - - - -
219B LEU* 4.1 30.5 - - + +
224B ASN* 4.0 15.3 - - + +
225B ARG* 3.3 14.7 + - + +
226B LEU 3.1 0.6 - - - -
227B THR* 1.3 80.0 + - - +
229B THR* 1.3 61.0 + - - +
230B ARG 3.2 0.2 - - - -
231B ASN* 3.3 1.0 + - - +
232B ALA* 2.9 29.9 + - + +
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Residues in contact with THR 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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220B PHE* 3.9 17.0 - - + -
224B ASN* 4.2 10.7 + - - +
225B ARG 3.1 14.2 + - - -
226B LEU* 3.6 13.4 - - + +
228B MET* 1.3 79.3 - - - +
230B ARG* 1.3 59.0 + - - +
232B ALA* 4.6 0.4 - - - -
233B VAL* 2.9 33.5 + - - +
262B LEU* 4.1 24.5 - - + -
265B VAL* 5.8 3.4 - - + -
270B VAL* 3.9 20.6 - - + -
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Residues in contact with ARG 230 (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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226B LEU* 3.1 36.1 + - - +
227B THR* 3.8 27.6 - - - +
228B MET 3.2 0.2 - - - -
229B THR* 1.3 78.2 - - - +
231B ASN* 1.3 61.8 + - - +
233B VAL* 4.0 1.4 - - - +
234B TRP* 3.1 24.8 + - - +
267B ASP* 3.1 41.5 + - - +
269B ASP* 3.2 34.1 + - + -
270B VAL* 3.8 10.5 - - + +
273B ASP* 4.0 7.0 - - - +
753D ARG* 5.8 1.6 - - - +
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Residues in contact with ASN 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B GLU* 3.1 29.6 + - + +
190B VAL* 4.0 18.1 - - + +
191B TRP* 3.8 28.2 - - - +
227B THR* 2.9 22.4 + - - +
228B MET 3.7 4.7 - - - +
230B ARG* 1.3 80.9 - - - +
232B ALA* 1.3 55.4 + - - +
234B TRP* 3.4 9.5 + - - +
235B ALA* 3.0 30.0 + - - +
753D ARG* 2.8 31.3 + - - +
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Residues in contact with ALA 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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190B VAL* 4.2 11.2 - - + +
216B LEU* 4.1 16.4 - - + +
219B LEU* 4.3 17.3 - - + -
220B PHE* 3.4 29.4 - - + -
228B MET* 2.9 18.6 + - + +
230B ARG 3.3 0.2 - - - -
231B ASN* 1.3 77.8 - - - +
233B VAL* 1.3 55.9 + - - +
235B ALA* 3.6 2.4 + - - +
236B LEU* 3.0 27.0 + - - +
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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
----------------------------------------------------------
220B PHE* 3.6 17.7 - - + -
229B THR* 2.9 27.2 + - + +
230B ARG* 4.2 2.7 - - - +
232B ALA* 1.3 72.9 - - - +
234B TRP* 1.3 61.2 + - - +
236B LEU* 3.2 7.0 + - + +
237B SER* 2.8 28.6 + - - -
259B LEU* 4.3 10.5 - - + -
262B LEU* 3.6 20.0 - - + -
270B VAL* 4.1 14.6 - - + +
273B ASP* 3.9 10.3 - - + +
274B ALA* 3.7 34.3 - - + +
277B ALA* 5.2 0.9 - - + -
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Residues in contact with TRP 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B TRP* 3.5 33.2 - + - -
194B GLY* 3.6 16.6 - - - -
195B ASN* 3.2 24.2 - - - -
230B ARG 3.1 18.6 + - - +
231B ASN* 3.6 11.7 - - - +
233B VAL* 1.3 75.5 - - - +
235B ALA* 1.3 74.5 + - + +
237B SER* 2.6 27.0 + - - -
238B ASN* 3.2 29.4 + - - +
273B ASP* 3.7 23.9 + - - +
750D ALA 3.8 16.3 + - - -
751D THR 3.9 10.1 - - - -
752D LYS* 4.2 2.5 - - - -
753D ARG* 3.6 44.4 - - + +
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Residues in contact with ALA 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B VAL* 3.6 36.3 - - + +
193B LEU* 5.3 1.3 - - + -
194B GLY* 4.3 12.5 - - - +
197B ALA* 5.1 0.9 - - - +
212B ILE* 6.0 1.6 - - + -
216B LEU* 4.6 5.4 - - + -
231B ASN 3.0 16.6 + - - +
232B ALA 3.7 4.7 - - - +
233B VAL 3.2 0.2 - - - -
234B TRP* 1.3 83.6 - - + +
236B LEU* 1.3 63.2 + - - +
238B ASN* 3.2 15.1 + - - +
239B LEU* 3.2 16.5 + - - +
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Residues in contact with LEU 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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213B LEU* 3.8 20.9 - - + -
216B LEU* 4.4 5.1 - - + +
217B LEU* 4.3 4.5 - - + -
220B PHE* 4.2 24.2 - - + -
232B ALA 3.0 16.4 + - - +
233B VAL* 3.2 8.0 + - + +
235B ALA* 1.3 76.1 - - - +
237B SER* 1.3 61.9 + - - +
239B LEU* 3.2 24.9 + - + +
240B CYS* 3.3 21.6 + - - -
252B VAL* 5.5 1.3 - - + -
255B CYS* 3.7 35.2 - - + -
258B VAL* 4.9 2.2 - - + -
259B LEU* 3.7 29.8 - - + -
277B ALA* 5.3 0.9 - - + -
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Residues in contact with SER 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 VAL 2.8 13.4 + - - -
234B TRP* 2.6 30.2 + - - -
236B LEU* 1.3 75.4 - - - +
238B ASN* 1.3 61.7 + - - +
240B CYS* 3.2 2.5 + - - +
241B ARG* 3.0 22.7 + - - +
273B ASP* 4.0 21.6 + - - -
276B TRP* 4.7 4.3 - - - +
277B ALA* 4.0 19.5 - - - -
280B TYR* 3.3 19.4 - - - -
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Residues in contact with ASN 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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194B GLY* 3.0 25.2 + - - +
197B ALA* 4.3 9.3 - - + +
198B GLY* 3.8 18.8 - - - +
204B ARG* 3.6 14.7 - - - +
234B TRP* 3.5 27.1 + - - +
235B ALA* 3.2 10.8 + - - +
237B SER* 1.3 85.6 + - - +
239B LEU* 1.3 60.7 + - - +
240B CYS 3.3 0.2 - - - -
241B ARG* 3.6 41.2 + - - +
751D THR 3.2 18.3 + - - +
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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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197B ALA* 4.2 10.3 - - + -
204B ARG* 3.6 23.5 - - + +
207B VAL* 4.1 14.8 - - + -
208B LEU* 3.6 30.2 - - + +
212B ILE* 3.8 24.9 - - + -
213B LEU* 4.4 5.8 - - + -
216B LEU* 3.6 31.2 - - + -
235B ALA 3.2 12.2 + - - +
236B LEU* 3.2 21.1 + - + +
238B ASN* 1.3 76.1 - - - +
240B CYS* 1.3 59.8 + - - +
247B PRO* 3.7 7.6 - - - +
252B VAL* 3.5 20.8 - - + +
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Residues in contact with CYS 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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236B LEU* 3.3 16.6 - - - -
237B SER 3.2 8.1 + - - +
239B LEU* 1.3 76.0 - - - +
241B ARG* 1.3 65.3 + - - +
242B GLY 4.0 2.1 + - - +
247B PRO* 4.0 14.4 - - - +
252B VAL* 3.7 21.8 - - - -
255B CYS* 4.4 9.9 - - - -
277B ALA* 4.0 12.8 - - - +
280B TYR* 3.3 30.0 - - + +
281B LEU* 3.8 29.7 - - + +
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Residues in contact with ARG 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B GLY* 6.1 1.3 - - - -
204B ARG* 2.7 35.3 + - - -
237B SER 3.0 13.9 + - - +
238B ASN* 3.7 27.3 + - - +
239B LEU 3.4 1.2 - - - -
240B CYS* 1.3 81.9 - - - +
242B GLY* 1.3 58.5 + - - +
247B PRO* 4.0 0.3 - - - +
280B TYR* 3.4 39.9 + - + -
748D GLN* 4.0 16.2 + - - +
749D THR* 3.4 38.5 + - - +
750D ALA 4.2 2.0 + - - -
751D THR* 3.4 39.1 - - - +
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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
------------------------------------------------------------
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