Contacts of the helix formed by residues 215 - 231 (chain R) in PDB entry 5GJQ
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 215 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208R PHE* 3.3 10.1 - - - -
211R TYR* 4.6 8.6 - - - +
214R MET* 1.3 87.3 - - - +
216R TYR* 1.3 63.5 + - - +
217R LYS* 3.6 6.7 - - + +
218R THR* 3.1 20.4 + - - +
219R PHE* 3.5 2.4 - - - +
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Residues in contact with TYR 216 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340J ARG* 3.0 44.9 + - - +
205R VAL* 3.0 36.4 + - + +
208R PHE* 2.8 39.9 - + + -
211R TYR* 4.2 12.6 - + + -
215R ASP* 1.3 79.7 - - - +
217R LYS* 1.3 59.7 + - + +
218R THR 3.3 0.2 - - - -
219R PHE* 3.5 8.0 - + - +
220R VAL* 2.6 58.1 + - + +
245R GLU* 4.1 8.9 - - + +
249R VAL* 4.0 19.5 - - + -
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Residues in contact with LYS 217 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215R ASP* 4.2 2.7 - - + +
216R TYR* 1.3 80.1 - - + +
218R THR* 1.3 69.9 + - - +
220R VAL* 3.2 7.8 - - - +
221R THR* 2.9 25.7 + - + +
248R GLU 5.2 2.0 + - - -
249R VAL* 3.8 25.1 - - + +
252R SER* 3.2 35.4 - - - -
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Residues in contact with THR 218 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214R MET* 2.8 31.5 - - - +
215R ASP* 3.1 13.9 + - - +
216R TYR 4.3 0.4 - - - +
217R LYS* 1.3 75.7 - - - +
219R PHE* 1.3 65.0 + - - +
221R THR* 2.3 44.1 + - - -
222R TYR* 3.0 21.4 + - - -
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Residues in contact with PHE 219 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182R VAL* 4.8 6.3 - - + -
201R PHE* 3.7 14.6 - + - -
204R THR* 2.3 51.4 - - - -
205R VAL* 4.0 10.3 - - + -
208R PHE* 3.7 32.1 - + + -
214R MET* 3.3 32.9 - - + +
215R ASP 3.5 12.6 - - - +
216R TYR* 3.5 11.7 - + - +
218R THR* 1.3 79.9 + - - +
220R VAL* 1.3 65.8 + - - +
222R TYR* 2.9 6.8 + - + +
223R THR* 2.7 48.6 + - + +
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Residues in contact with VAL 220 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205R VAL* 5.9 5.4 - - + -
216R TYR* 2.6 58.4 + - + +
217R LYS 3.2 8.3 - - - +
218R THR 2.9 0.2 + - - -
219R PHE* 1.3 77.2 - - + +
221R THR* 1.3 66.4 + - + +
223R THR* 3.0 9.6 + - - +
224R VAL* 2.9 40.9 + - + +
245R GLU 5.4 0.7 - - - +
246R ILE* 5.2 7.9 - - + -
249R VAL* 3.4 32.1 - - + -
250R LEU* 4.9 10.3 - - + +
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Residues in contact with THR 221 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217R LYS* 2.9 19.8 + - + +
218R THR* 2.3 35.2 + - - -
220R VAL* 1.3 74.5 - - + +
222R TYR* 1.3 69.0 + - - -
224R VAL* 3.8 4.1 - - - +
225R TYR* 2.8 49.6 + - + +
253R LEU* 5.6 7.4 - - + -
256R VAL* 4.5 16.8 - - + -
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Residues in contact with TYR 222 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186R LEU* 5.2 8.1 - - + -
189R VAL* 5.8 5.4 - - + -
201R PHE* 5.7 7.6 - + + -
214R MET* 4.0 19.3 - - + -
218R THR* 3.0 29.0 + - - -
219R PHE* 2.9 17.1 + - + +
221R THR* 1.3 90.0 - - - +
223R THR* 1.3 59.4 + - + +
225R TYR* 2.9 13.6 + + - +
226R VAL* 2.8 36.5 + - + +
285R ASP* 3.3 36.5 + - - -
287R LEU* 5.0 14.4 - - + +
288R PHE* 3.7 27.8 - + + -
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Residues in contact with THR 223 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198R ALA* 5.7 0.9 - - - +
201R PHE* 3.3 34.8 - - + +
202R LEU* 4.3 7.8 + - - +
205R VAL* 4.0 15.1 - - + +
219R PHE* 2.7 57.8 + - + -
220R VAL* 3.0 17.2 + - - -
222R TYR* 1.3 71.9 - - - +
224R VAL* 1.3 59.7 + - - +
226R VAL* 4.4 1.7 - - - +
227R SER* 2.8 30.5 + - - -
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Residues in contact with VAL 224 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220R VAL* 2.9 36.3 + - + +
221R THR* 3.9 5.2 - - - +
223R THR* 1.3 76.8 - - - +
225R TYR* 1.3 58.6 + - - +
227R SER* 2.4 23.0 + - - +
228R MET* 2.9 15.6 + - - +
240R VAL* 4.2 20.2 - - + -
246R ILE* 4.9 10.5 - - + -
250R LEU* 4.6 20.0 - - + -
256R VAL* 4.8 9.6 - - + -
259R TYR* 4.7 6.7 - - + -
260R LEU* 4.4 20.0 - - + -
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Residues in contact with TYR 225 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221R THR* 2.8 35.3 + - - +
222R TYR* 3.3 11.9 - + - +
224R VAL* 1.3 72.5 - - - +
226R VAL* 1.3 68.7 + - + +
228R MET* 3.1 5.2 + - - +
229R ILE 3.0 13.9 + - - -
255R ALA* 5.6 0.7 - - - +
256R VAL* 2.8 37.3 + - + +
259R TYR* 3.4 12.3 - + - -
278R VAL* 2.3 49.5 - - + +
281R GLU* 4.9 6.6 - - + +
282R MET* 5.7 5.8 - - + -
285R ASP* 6.0 1.1 - - - -
288R PHE* 4.5 23.1 - + + -
295R TYR* 2.5 32.5 + + + +
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Residues in contact with VAL 226 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189R VAL* 3.7 29.4 - - + -
194R PHE* 3.3 49.8 - - + +
197R ALA* 4.3 4.9 - - + -
198R ALA* 3.9 16.7 - - + +
201R PHE* 5.5 2.5 - - + -
222R TYR* 2.8 21.9 + - - +
223R THR* 4.4 3.4 - - - +
225R TYR* 1.3 77.3 - - + +
227R SER* 1.3 63.8 + - - +
229R ILE* 3.1 11.7 + - + +
230R ALA* 3.0 22.5 + - - +
288R PHE* 5.3 4.0 - - + -
295R TYR* 5.2 0.9 - - + -
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Residues in contact with SER 227 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198R ALA* 5.0 6.0 - - - +
202R LEU* 4.4 6.5 - - - -
223R THR 2.8 20.6 + - - -
224R VAL* 2.4 33.1 + - - -
226R VAL* 1.3 76.8 - - - +
228R MET* 1.3 63.0 + - - +
231R LEU* 3.0 58.6 + - - +
236R LEU* 4.4 0.4 - - - -
240R VAL* 3.5 20.3 - - - +
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Residues in contact with MET 228 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224R VAL 2.9 6.7 + - - +
225R TYR 3.3 0.9 - - - +
227R SER* 1.3 81.4 + - - +
229R ILE* 1.3 61.6 + - + +
231R LEU 4.4 7.8 - - - +
236R LEU* 4.1 16.9 - - + +
259R TYR* 2.7 35.0 - - + +
260R LEU* 3.5 39.7 - - + -
263R LEU* 2.9 27.0 - - + +
271R PHE* 2.3 48.5 - - + -
299R MET* 3.5 14.6 - - + +
302R HIS* 4.6 6.8 - - - -
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Residues in contact with ILE 229 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194R PHE* 4.3 19.3 - - + -
225R TYR 3.0 6.3 + - - +
226R VAL* 3.1 10.5 + - + +
228R MET* 1.3 77.1 - - + +
230R ALA* 1.3 61.4 + - + +
231R LEU 3.9 0.4 - - - -
294R TYR* 5.7 3.1 - - + -
295R TYR* 1.2 86.1 - - + +
298R GLU* 4.4 23.6 - - + +
299R MET* 4.0 14.8 - - - -
302R HIS* 3.6 22.3 + - - -
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Residues in contact with ALA 230 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194R PHE* 4.4 10.5 - - + +
195R LYS* 4.1 44.0 + - + +
198R ALA* 4.6 5.7 - - + +
226R VAL 3.0 14.3 + - - +
229R ILE* 1.3 75.6 - - + +
231R LEU* 1.4 63.0 + - - +
232R GLU* 5.7 0.9 - - - +
302R HIS* 5.6 0.9 - - - -
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Residues in contact with LEU 231 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198R ALA* 4.7 13.5 - - + -
199R GLU* 5.6 5.4 - - + +
202R LEU* 3.9 21.5 - - + -
226R VAL 4.4 0.2 + - - -
227R SER* 3.0 56.5 + - - +
228R MET 4.4 7.8 - - - +
230R ALA* 1.4 72.3 - - - +
232R GLU* 1.3 70.2 + - - +
233R ARG 4.0 0.2 + - - -
235R ASP* 4.3 3.8 - - + +
236R LEU* 4.1 18.5 - - + +
239R LYS* 4.0 19.3 - - - +
240R VAL* 3.4 19.3 - - + -
302R HIS* 4.9 10.0 + - - -
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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