Contacts of the helix formed by residues 225 - 244 (chain X) in PDB entry 3J7Y
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 PRO 225 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1199 PHE* 4.0 19.7 - - + -
1219 PRO 5.8 2.5 - - - +
223X PRO 3.7 6.7 - - - +
224X VAL* 1.4 95.4 - - + +
226X LEU* 1.3 64.6 + - - +
227X PHE 4.3 0.7 - - - +
228X LYS* 3.4 31.9 + - + +
229X ILE* 3.7 5.9 + - - +
155Y LEU 4.3 0.2 - - - +
156Y LEU 3.9 7.6 - - - +
157Y GLN 3.3 26.0 - - - +
158Y THR* 3.8 15.3 - - - +
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Residues in contact with LEU 226 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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889 ALA* 4.4 9.2 - - + -
224X VAL 3.3 4.2 + - - +
225X PRO* 1.3 70.5 - - - +
227X PHE* 1.3 60.7 + - - +
229X ILE* 3.2 23.4 + - + -
230X TYR* 2.9 71.7 + - + +
155Y LEU* 3.4 42.5 + - + +
156Y LEU* 5.0 0.7 - - + -
159Y GLY* 4.3 1.9 - - - -
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Residues in contact with PHE 227 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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929 PHE* 3.8 28.7 - + - -
1189 GLY* 3.8 17.3 - - - -
1199 PHE* 3.3 44.4 - + + -
191V LEU* 5.1 6.5 - - + -
226X LEU* 1.3 78.0 - - - +
228X LYS* 1.3 63.4 + - + +
230X TYR* 3.2 6.3 + - - +
231X VAL* 2.9 46.4 + - + +
156Y LEU* 2.8 50.7 + - + +
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Residues in contact with LYS 228 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199 PHE* 3.8 32.3 - - + -
1219 PRO* 6.3 0.6 - - - +
224X VAL* 4.8 8.7 - - + -
225X PRO* 3.4 33.2 + - + +
226X LEU 3.2 0.2 - - - -
227X PHE* 1.3 85.5 - - + +
229X ILE* 1.3 58.5 + - + +
231X VAL* 3.2 7.3 + - - +
232X ALA* 2.9 29.6 + - - +
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Residues in contact with ILE 229 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224X VAL* 4.7 18.8 - - + +
225X PRO 3.7 15.7 + - - +
226X LEU* 3.2 26.6 + - + +
228X LYS* 1.3 77.8 - - + +
230X TYR* 1.3 61.5 - - + +
232X ALA* 3.2 9.0 + - + +
233X GLU* 2.9 34.3 + - + +
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Residues in contact with TYR 230 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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879 THR* 4.7 3.1 + - - -
889 ALA* 3.6 18.0 + - + +
899 ALA* 3.0 47.6 + - + +
929 PHE* 3.3 39.7 - + + -
226X LEU* 2.9 44.3 + - + +
227X PHE* 3.4 6.7 - - - +
229X ILE* 1.3 80.0 - - + +
231X VAL* 1.3 56.1 + - - +
233X GLU* 3.2 11.1 + - + +
234X LEU* 2.9 28.8 + - - +
156Y LEU* 3.9 11.9 - - + -
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Residues in contact with VAL 231 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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929 PHE* 3.6 20.4 - - + -
999 ALA* 6.4 1.8 - - + -
227X PHE* 2.9 47.6 + - + +
228X LYS* 3.4 9.9 - - - +
230X TYR* 1.3 76.3 - - - +
232X ALA* 1.3 56.9 + - - +
234X LEU* 3.2 6.4 + - + +
235X ILE* 2.9 47.0 + - + +
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Residues in contact with ALA 232 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228X LYS 2.9 12.6 + - - +
229X ILE* 3.3 12.1 - - + +
231X VAL* 1.3 76.1 - - - +
233X GLU* 1.3 58.4 + - - +
235X ILE* 3.2 14.2 + - - +
236X GLN* 2.9 28.4 + - - +
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Residues in contact with GLU 233 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229X ILE* 2.9 18.9 + - + +
230X TYR* 3.2 15.5 + - + +
232X ALA* 1.3 76.5 - - - +
234X LEU* 1.3 56.9 + - - +
236X GLN* 3.2 13.1 + - - +
237X GLN* 2.9 30.8 + - + +
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Residues in contact with LEU 234 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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929 PHE* 4.1 8.1 - - + -
969 VAL* 3.8 29.8 - - + +
999 ALA* 3.4 33.9 - - + -
1009 ILE* 4.5 11.0 - - + +
230X TYR 2.9 13.0 + - - +
231X VAL* 3.3 11.7 - - + +
233X GLU* 1.3 76.9 - - - +
235X ILE* 1.3 58.3 + - + +
237X GLN* 3.2 10.9 + - + +
238X LEU* 2.9 49.5 + - + +
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Residues in contact with ILE 235 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231X VAL* 2.9 41.0 + - + +
232X ALA* 3.2 11.9 + - - +
234X LEU* 1.3 77.0 - - + +
236X GLN* 1.3 58.2 + - - +
238X LEU* 3.2 14.6 + - + +
239X GLN* 2.9 45.4 + - + +
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Residues in contact with GLN 236 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232X ALA 2.9 12.4 + - - +
233X GLU* 3.3 17.3 - - - +
235X ILE* 1.3 78.2 - - - +
237X GLN* 1.3 59.3 + - - +
239X GLN* 3.2 19.4 + - - +
240X GLN* 2.9 50.2 + - + +
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Residues in contact with GLN 237 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233X GLU* 2.9 14.1 + - + +
234X LEU* 3.2 17.0 + - + +
236X GLN* 1.3 77.1 - - - +
238X LEU* 1.3 58.7 + - + +
240X GLN* 3.2 11.4 + - - +
241X GLN* 2.9 43.6 + - + +
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Residues in contact with LEU 238 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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999 ALA 4.9 6.3 - - - +
1009 ILE* 4.9 17.3 - - + -
1039 ASP* 3.5 45.4 - - + +
234X LEU* 2.9 40.6 + - + +
235X ILE* 3.2 14.1 + - + +
237X GLN* 1.3 74.9 - - + +
239X GLN* 1.3 59.2 + - + +
241X GLN* 3.2 12.9 + - + +
242X ALA* 2.9 28.8 + - - +
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Residues in contact with GLN 239 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235X ILE* 2.9 30.0 + - + +
236X GLN* 3.4 23.2 + - - +
238X LEU* 1.3 77.6 - - + +
240X GLN* 1.3 56.5 + - - +
242X ALA* 3.2 10.1 + - - +
243X LEU* 2.9 38.8 + - + +
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Residues in contact with GLN 240 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236X GLN* 2.9 29.8 + - + +
237X GLN* 3.3 16.2 - - - +
239X GLN* 1.3 77.6 - - - +
241X GLN* 1.3 57.2 + - + +
243X LEU* 3.2 21.1 + - - +
244X SER* 2.9 31.3 + - - +
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Residues in contact with GLN 241 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237X GLN* 2.9 31.2 + - + +
238X LEU* 3.2 17.5 + - + +
240X GLN* 1.3 78.1 - - + +
242X ALA* 1.3 62.9 + - - +
244X SER* 3.0 33.2 + - - -
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Residues in contact with ALA 242 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238X LEU 2.9 12.6 + - - +
239X GLN* 3.2 12.8 + - - +
241X GLN* 1.3 79.3 - - - +
243X LEU* 1.3 63.5 + - - +
244X SER 4.0 3.5 - - - -
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Residues in contact with LEU 243 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239X GLN* 2.9 22.6 + - + +
240X GLN* 3.4 26.0 - - + +
242X ALA* 1.3 78.7 - - + +
244X SER* 1.3 58.6 + - - +
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Residues in contact with SER 244 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240X GLN* 2.9 14.2 + - - +
241X GLN* 3.0 34.5 + - - -
242X ALA 4.0 3.4 - - - -
243X LEU* 1.3 79.8 - - - +
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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