Contacts of the helix formed by residues 216 - 238 (chain P) 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 GLU 216 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213P PHE* 3.7 10.4 + - + +
214P PHE 3.2 0.6 - - - -
215P GLN* 1.3 85.7 - - + +
217P GLU* 1.3 68.8 + - + +
218P ASN* 3.7 22.7 - - + +
219P THR* 3.0 10.5 + - - +
220P GLU* 2.8 20.2 + - - +
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Residues in contact with GLU 217 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215P GLN 4.5 3.8 - - - +
216P GLU* 1.3 73.0 - - + +
218P ASN* 1.3 65.0 + - - +
220P GLU* 3.0 24.6 + - - +
221P LYS* 2.9 22.2 + - - +
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Residues in contact with ASN 218 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180P LYS* 6.1 5.2 - - - -
216P GLU* 3.0 15.6 + - + +
217P GLU* 1.3 77.1 - - - +
219P THR* 1.3 61.2 + - - +
221P LYS* 2.3 41.9 - - - +
222P LEU* 4.0 6.0 - - - +
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Residues in contact with THR 219 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179P LYS* 5.4 4.2 - - - +
180P LYS* 5.4 5.0 + - - +
213P PHE* 3.2 42.6 + - - -
214P PHE* 4.0 8.0 - - - -
216P GLU* 3.0 11.4 + - - +
218P ASN* 1.3 79.5 - - - +
220P GLU* 1.3 56.4 + - - +
222P LEU* 3.0 18.8 + - - +
223P LYS* 2.9 28.8 + - - +
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Residues in contact with GLU 220 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214P PHE* 2.6 31.9 - - - +
215P GLN* 2.7 18.2 - - - +
216P GLU 2.8 16.8 + - - +
217P GLU* 3.1 33.0 - - - +
219P THR* 1.3 74.2 - - - +
221P LYS* 1.3 64.2 + - - +
223P LYS* 3.2 38.4 + - - +
224P LEU* 4.1 6.6 + - - +
253P THR* 5.1 10.5 - - + +
254P PRO* 6.0 2.9 - - - +
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Residues in contact with LYS 221 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217P GLU 2.9 10.6 + - - +
218P ASN* 2.3 37.5 - - - +
220P GLU* 1.3 77.5 - - - +
222P LEU* 1.3 78.8 + - + +
224P LEU* 3.5 24.5 - - - +
225P LYS* 5.6 0.3 - - - +
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Residues in contact with LEU 222 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179P LYS 5.6 0.7 - - - +
180P LYS* 4.5 30.5 - - + +
183P VAL* 6.1 2.9 - - + -
184P GLU* 5.7 4.3 - - + +
187P LEU* 5.3 12.1 - - + -
214P PHE* 6.1 0.4 - - + -
218P ASN* 4.0 13.7 - - - +
219P THR* 3.0 18.0 + - - +
221P LYS* 1.3 89.3 - - + +
223P LYS* 1.3 53.8 + - - +
224P LEU 2.7 17.3 + - - -
225P LYS* 2.8 30.7 + - + +
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Residues in contact with LYS 223 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187P LEU* 6.0 1.1 - - - -
214P PHE* 3.3 63.5 - - + -
219P THR 2.9 5.9 + - - -
220P GLU* 3.2 32.5 - - - +
222P LEU* 1.3 73.0 - - - +
224P LEU* 1.3 66.5 + - + +
225P LYS 3.0 0.7 - - - -
226P TYR* 2.8 20.8 + - - +
227P TYR* 2.9 37.1 + - + -
249P ALA 4.4 9.5 + - - -
250P ILE* 4.6 2.0 - - - +
252P ASP 5.9 0.2 - - - -
253P THR* 3.3 25.5 + - - +
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Residues in contact with LEU 224 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220P GLU 4.3 4.7 - - - +
221P LYS* 3.5 22.2 - - - +
222P LEU 2.7 4.8 + - - +
223P LYS* 1.3 77.7 - - + +
225P LYS* 1.3 59.3 + - + +
227P TYR* 3.5 3.9 + - - +
228P ASN* 2.8 42.2 + - - +
250P ILE* 3.6 33.8 - - + +
253P THR* 4.1 18.8 - - + +
255P CYS* 6.1 3.4 - - + -
256P ILE* 4.3 19.7 - - + -
262P LYS* 6.5 0.4 - - - -
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Residues in contact with LYS 225 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187P LEU* 3.7 23.8 - - + -
221P LYS 5.6 0.2 - - - +
222P LEU* 2.8 25.2 + - + +
224P LEU* 1.3 72.5 - - + +
226P TYR* 1.3 64.2 + - - +
228P ASN* 3.0 12.9 + - - +
229P LEU* 3.0 31.3 + - + +
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Residues in contact with TYR 226 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187P LEU* 4.7 15.8 - - + +
190P MET* 5.7 9.9 - - + -
206P SER* 4.0 12.7 + - - -
207P LYS* 5.1 1.0 - - - -
209P ILE* 2.1 63.7 - - + +
211P THR* 5.9 2.9 - - - -
214P PHE* 4.0 23.1 - + + -
223P LYS* 2.8 22.3 + - + +
225P LYS* 1.3 75.4 - - - +
227P TYR* 1.3 85.6 + + - +
229P LEU* 3.2 8.1 + - + +
230P MET* 3.0 41.9 + - + +
246P HIS* 6.3 0.7 - + - -
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Residues in contact with TYR 227 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211P THR* 4.7 6.9 - - - -
214P PHE* 3.8 16.6 - + - -
223P LYS* 2.9 66.3 + - + +
224P LEU 4.1 3.4 - - - +
226P TYR* 1.3 97.5 - + - +
228P ASN* 1.3 65.2 + - - +
230P MET* 2.8 7.0 + - + +
231P ILE* 2.8 23.8 + - - +
246P HIS* 3.9 32.2 - + + +
249P ALA* 3.9 26.5 - - + +
250P ILE* 4.4 24.9 - - + -
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Residues in contact with ASN 228 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224P LEU* 2.8 36.6 + - - +
225P LYS* 3.0 11.1 + - - +
227P TYR* 1.3 76.5 - - - +
229P LEU* 1.3 67.0 + - + +
231P ILE* 3.2 9.5 - - - +
232P GLN* 3.1 25.0 + - + +
247P TYR* 6.1 1.2 - - - -
250P ILE* 3.8 18.1 - - - +
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Residues in contact with LEU 229 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187P LEU* 4.2 14.8 - - + +
190P MET* 3.5 37.7 - - + -
191P ARG* 4.4 23.1 - - + +
225P LYS* 3.0 20.0 + - + +
226P TYR* 3.5 8.3 - - - +
228P ASN* 1.3 77.5 - - + +
230P MET* 1.3 58.9 + - + +
232P GLN* 2.5 37.7 + - + +
233P LEU* 2.9 18.5 + - + +
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Residues in contact with MET 230 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190P MET* 6.6 0.2 - - - -
206P SER* 5.7 7.2 - - - -
226P TYR* 3.0 44.3 + - + +
227P TYR* 2.8 12.7 + - - +
229P LEU* 1.3 72.3 - - + +
231P ILE* 1.3 58.3 + - - +
233P LEU* 3.6 9.3 - - - +
234P ASP* 2.7 37.8 + - - -
246P HIS* 3.9 29.8 - - + +
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Residues in contact with ILE 231 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227P TYR 2.8 11.3 + - - +
228P ASN* 3.2 13.7 - - - +
229P LEU 2.9 0.2 + - - -
230P MET* 1.3 75.0 - - - +
232P GLN* 1.3 67.6 + - + +
234P ASP* 2.8 8.1 + - - +
235P GLN* 2.8 32.4 + - + +
243P ILE* 4.1 5.4 - - + -
246P HIS* 4.7 7.2 - - + -
247P TYR* 1.9 53.2 - - + +
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Residues in contact with GLN 232 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194P LEU* 5.5 11.4 - - + -
228P ASN* 3.4 14.8 - - + +
229P LEU* 2.5 24.6 + - + +
231P ILE* 1.3 76.7 - - + +
233P LEU* 1.3 66.0 + - + +
235P GLN* 3.4 9.3 + - - +
236P HIS* 3.0 17.2 + - - +
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Residues in contact with LEU 233 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190P MET* 6.0 4.3 - - - -
194P LEU* 5.8 12.0 - - + +
202P THR* 4.7 22.9 - - - +
206P SER* 6.0 3.4 - - - -
229P LEU* 2.9 21.6 + - + +
230P MET* 3.6 12.1 - - - +
232P GLN* 1.3 71.9 - - + +
234P ASP* 1.3 58.5 + - - +
236P HIS* 2.6 32.2 + - - +
237P GLU* 2.9 17.1 + - + +
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Residues in contact with ASP 234 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230P MET* 2.7 25.8 - - - +
231P ILE* 2.8 11.0 + - - +
233P LEU* 1.3 74.3 - - - +
235P GLN* 1.3 61.9 + - - +
237P GLU* 3.0 14.2 + - - -
238P GLY 3.0 17.5 + - - -
239P SER* 3.1 26.0 + - - -
242P SER* 4.2 11.0 - - - -
243P ILE* 4.6 14.1 - - + +
246P HIS* 4.1 19.1 - - - -
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Residues in contact with GLN 235 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231P ILE* 2.8 35.3 + - + +
232P GLN* 3.4 11.9 - - - +
234P ASP* 1.3 70.6 - - - +
236P HIS* 1.3 63.0 + - - +
238P GLY* 2.9 14.3 + - - -
239P SER 4.6 5.8 + - - -
243P ILE* 5.2 3.7 - - + +
247P TYR* 4.7 0.2 - - - +
273P TYR* 4.3 20.9 - - + +
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Residues in contact with HIS 236 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194P LEU* 6.3 2.9 - - + -
198P ASP 5.6 3.1 + - - -
199P TYR* 5.4 13.2 - - + +
232P GLN 3.0 11.0 + - - +
233P LEU* 2.6 21.0 + - - +
235P GLN* 1.3 71.7 - - - +
237P GLU* 1.3 62.5 + - + -
238P GLY* 3.0 5.4 + - - -
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Residues in contact with GLU 237 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203P GLN* 6.6 0.4 - - + -
233P LEU* 2.9 19.2 + - + +
234P ASP* 3.0 15.2 + - - +
236P HIS* 1.3 81.1 - - + +
238P GLY* 1.3 59.8 + - - +
239P SER* 3.3 14.8 + - - +
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Residues in contact with GLY 238 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234P ASP 3.0 0.4 + - - -
235P GLN* 2.9 17.3 + - - -
236P HIS 3.0 2.6 + - - -
237P GLU* 1.3 76.9 - - - +
239P SER* 1.3 61.9 + - - +
240P TYR* 3.2 29.1 - - - -
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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
------------------------------------------------------------
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