Contacts of the helix formed by residues 226 - 249 (chain B) in PDB entry 3V3E
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 GLY 226 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B SER 3.1 17.9 + - - -
223B ARG* 3.6 8.7 - - - -
224B LEU 3.2 0.4 - - - -
225B LEU* 1.3 76.9 - - - +
227B LYS* 1.3 59.0 + - - +
228B LEU 3.2 0.4 + - - -
229B PRO* 3.6 15.2 - - - +
230B GLU* 3.4 20.7 - - - +
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Residues in contact with LYS 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 5.8 0.4 - - + -
158B PHE* 3.6 29.4 - - + -
161B SER* 2.6 38.1 + - - -
162B LEU* 3.8 21.3 - - + +
165B LEU* 4.0 24.5 - - + -
175B LEU* 5.0 12.1 - - + -
223B ARG 3.5 8.6 + - - +
224B LEU* 2.9 20.3 + - + +
226B GLY* 1.3 76.5 - - - +
228B LEU* 1.3 64.9 + - - +
230B GLU* 2.8 31.5 + - - +
231B LEU* 3.1 24.1 + - - +
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Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B GLU* 5.0 1.0 - - - +
175B LEU* 3.6 36.8 - - + +
178B LEU* 4.9 17.3 - - + +
179B VAL* 3.7 28.3 - - + -
225B LEU* 3.0 30.5 + - + +
227B LYS* 1.3 80.0 - - + +
229B PRO* 1.4 68.9 - - + +
231B LEU* 3.0 19.5 + - + +
232B ARG* 3.1 16.8 + - - +
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Residues in contact with PRO 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B LEU 3.5 9.0 - - - +
226B GLY* 3.6 14.8 - - - +
228B LEU* 1.4 91.0 - - + +
230B GLU* 1.3 62.6 + - + +
232B ARG* 3.1 13.0 + - + +
233B THR* 3.1 23.8 + - - -
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Residues in contact with GLU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B PHE* 3.7 12.8 - - + -
226B GLY 3.4 20.7 - - - +
227B LYS* 2.8 40.8 + - - +
228B LEU 3.4 0.4 - - - -
229B PRO* 1.3 77.1 - - + +
231B LEU* 1.3 62.7 + - - +
233B THR* 3.3 10.3 + - - +
234B LEU* 3.1 24.3 + - - +
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Residues in contact with LEU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B GLU* 3.7 38.3 - - + +
117B ILE* 3.7 32.5 - - + -
118B LEU* 3.8 19.3 - - + +
158B PHE* 4.1 13.9 - - + -
179B VAL* 3.7 29.8 - - + -
227B LYS 3.1 13.9 + - - +
228B LEU* 3.0 16.4 + - + +
230B GLU* 1.3 74.6 - - - +
232B ARG* 1.3 60.0 + - - +
234B LEU* 3.2 8.4 + - + +
235B CYS* 2.9 27.2 + - - +
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Residues in contact with ARG 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B GLU* 2.9 29.4 + - - +
179B VAL 5.2 0.4 + - - -
182B THR* 3.8 20.0 + - - +
183B ASP 4.5 5.1 + - - -
184B ARG* 3.3 32.8 - - - +
228B LEU 3.1 16.3 + - - +
229B PRO* 3.4 13.0 - - + +
231B LEU* 1.3 76.0 - - - +
233B THR* 1.3 63.0 + - - +
235B CYS* 3.2 11.7 + - - +
236B THR* 3.1 25.0 + - - -
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Residues in contact with THR 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B PRO 3.1 10.3 + - - -
230B GLU* 3.4 13.5 - - - +
231B LEU 3.2 0.2 - - - -
232B ARG* 1.3 79.4 - - - +
234B LEU* 1.3 61.3 + - + +
236B THR* 3.3 22.2 + - - -
237B GLN* 3.4 21.3 + - + +
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Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ILE* 3.9 21.8 - - + -
151B TRP* 2.8 37.8 + - - +
154B SER* 3.4 41.1 - - - +
155B ILE* 3.9 7.4 - - + +
158B PHE* 3.5 43.1 - - + -
230B GLU 3.1 15.9 + - - +
231B LEU* 3.2 7.6 + - - +
233B THR* 1.3 72.0 - - + +
235B CYS* 1.3 65.3 + - - +
236B THR 3.1 1.6 - - - -
237B GLN* 3.1 16.6 + - - +
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Residues in contact with CYS 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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110B SER 5.2 6.1 - - - -
113B LEU* 3.8 28.0 - - + +
114B GLU* 3.9 25.4 - - + -
117B ILE* 3.5 13.6 - - + +
151B TRP* 5.0 0.2 - - - -
231B LEU 2.9 15.5 + - - +
232B ARG* 3.3 12.3 - - - +
234B LEU* 1.3 71.3 - - - +
236B THR* 1.3 64.5 + - - +
238B GLY* 2.8 13.4 + - - +
239B LEU* 3.0 24.8 + - - +
264B THR* 6.5 0.9 - - - -
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Residues in contact with THR 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A TYR* 4.5 16.4 - - + -
247A LEU* 3.8 24.2 - - + -
232B ARG 3.1 12.8 + - - -
233B THR* 3.3 13.0 + - - -
234B LEU 3.1 0.6 - - - -
235B CYS* 1.3 77.7 - - - +
237B GLN* 1.3 58.2 + - - +
239B LEU* 3.1 14.8 + - - +
240B GLN* 2.9 36.0 + - - +
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Residues in contact with GLN 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B ASP* 5.2 1.4 - - - +
151B TRP* 3.4 22.6 + - + +
154B SER* 2.8 37.6 + - - -
233B THR* 3.4 21.5 + - + +
234B LEU* 3.1 22.8 + - - +
235B CYS 3.1 0.6 - - - -
236B THR* 1.3 75.4 - - - +
238B GLY* 1.3 58.2 + - - +
240B GLN* 3.5 19.2 + - - +
241B ARG* 3.1 26.0 + - - +
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Residues in contact with GLY 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B LEU* 4.3 7.2 - - - -
151B TRP* 3.4 36.1 - - - +
234B LEU 3.1 6.3 + - - -
235B CYS 2.8 8.4 + - - -
237B GLN* 1.3 75.2 - - - +
239B LEU* 1.3 58.4 + - - +
241B ARG* 3.1 4.0 + - - +
242B ILE* 2.9 33.2 + - - +
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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
----------------------------------------------------------
243A PHE* 3.9 14.1 - - + -
247A LEU* 4.3 24.0 - - + -
113B LEU* 3.6 21.3 - - + +
235B CYS* 3.0 28.3 + - - +
236B THR* 3.5 10.1 - - - +
238B GLY* 1.3 74.3 - - - +
240B GLN* 1.3 53.1 + - - +
242B ILE* 3.2 3.7 + - + +
243B PHE* 2.7 34.7 + - - +
260B ILE* 5.7 0.7 - - + -
261B PHE* 3.4 31.4 - - + -
264B THR* 4.0 31.9 - - - +
265B LEU* 4.7 5.2 - - + -
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Residues in contact with GLN 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A GLN* 4.8 8.6 + - - +
243A PHE* 3.9 23.6 - - + -
244A TYR* 3.4 43.1 - - + +
247A LEU* 4.8 0.4 - - + -
236B THR* 2.9 19.0 + - + +
237B GLN* 3.5 31.0 + - - +
239B LEU* 1.3 74.9 - - - +
241B ARG* 1.3 64.4 + - - +
243B PHE* 3.4 4.2 + - - +
244B TYR* 2.9 23.7 + - - +
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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
----------------------------------------------------------
67B GLU* 3.6 17.2 + - - +
75B PHE* 4.1 14.1 - - + -
146B ARG 3.1 25.7 + - - -
147B GLY 3.0 15.5 + - - -
148B PHE 3.4 20.9 - - - +
149B GLY* 3.8 16.1 - - - +
151B TRP* 4.6 4.7 - - + -
237B GLN 3.1 14.6 + - - +
238B GLY* 3.1 9.8 + - - +
240B GLN* 1.3 74.8 - - - +
242B ILE* 1.3 59.8 + - - +
244B TYR* 3.1 27.1 + - - +
245B LEU* 2.9 57.3 + - + +
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Residues in contact with ILE 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B PHE* 4.1 20.6 - - + -
76B TYR* 4.3 11.0 - - + +
79B LEU* 4.4 9.6 - - + -
113B LEU* 4.5 20.2 - - + -
151B TRP* 6.2 0.4 - - + -
238B GLY 2.9 18.4 + - - +
239B LEU* 3.7 5.2 - - + +
241B ARG* 1.3 72.9 - - - +
243B PHE* 1.3 66.7 + - - +
245B LEU* 3.1 6.5 + - - +
246B LYS* 2.9 37.1 + - + +
253B PRO* 4.7 6.1 - - + -
257B ILE* 4.1 21.8 - - + -
261B PHE* 3.4 32.5 - - + -
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Residues in contact with PHE 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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239A LEU* 3.8 13.2 - - + -
240A GLN* 4.0 17.9 - - + -
243A PHE* 3.6 46.9 - + + -
261A PHE* 3.7 34.1 - + - -
265A LEU* 4.1 14.6 - - + -
267A PHE* 3.8 27.6 - + - -
239B LEU 2.7 21.0 + - - +
240B GLN 3.6 4.9 - - - +
242B ILE* 1.3 73.8 - - - +
244B TYR* 1.3 65.7 + - - +
246B LYS* 3.3 3.5 + - - +
247B LEU* 3.0 37.8 + - + +
261B PHE* 3.5 12.4 - + + -
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Residues in contact with TYR 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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236A THR* 4.1 21.3 - - + -
240A GLN* 3.6 35.2 - - + +
67B GLU* 3.1 29.2 + - - -
240B GLN 2.9 13.9 + - - +
241B ARG* 3.1 37.4 + - - +
243B PHE* 1.3 83.4 - - - +
245B LEU* 1.3 65.1 + - + +
247B LEU* 3.3 7.1 + - + +
248B GLU* 3.1 41.3 + - + +
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Residues in contact with LEU 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLU* 4.5 0.2 - - + -
72B VAL* 4.0 23.3 - - + +
75B PHE* 3.5 38.8 - - + -
76B TYR* 3.5 20.9 - - + +
147B GLY 4.1 3.4 - - - +
241B ARG* 2.9 57.8 + - + +
242B ILE* 4.0 0.9 - - - +
244B TYR* 1.3 77.2 - - + +
246B LYS* 1.3 61.4 + - - +
248B GLU* 3.5 23.3 - - - +
249B ASP* 2.7 27.9 + - - -
250B LEU 4.3 1.0 + - - -
251B VAL 4.8 4.1 - - - +
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Residues in contact with LYS 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A PRO* 4.0 9.5 - - - +
267A PHE* 3.5 38.0 - - + +
76B TYR* 4.3 1.1 - - - +
242B ILE* 2.9 32.9 + - + +
243B PHE* 3.7 3.4 - - - +
245B LEU* 1.3 77.4 - - - +
247B LEU* 1.3 63.1 + - - +
249B ASP* 3.4 18.2 - - - +
251B VAL 5.9 0.2 - - - -
252B PRO* 6.3 0.4 - - - -
253B PRO* 3.9 21.2 - - + +
258B ASP* 2.6 30.0 + - - +
261B PHE* 3.5 25.4 - - + -
262B MET* 3.0 27.2 - - - +
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Residues in contact with LEU 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A THR* 3.6 33.0 - - + +
239A LEU* 4.1 28.7 - - + -
240A GLN* 5.0 2.2 - - + -
264A THR* 4.5 4.0 - - + +
265A LEU* 4.5 10.1 - - + -
266A PRO* 4.0 27.6 - - + +
267A PHE* 4.3 4.0 - - + -
243B PHE* 3.0 36.2 + - + +
244B TYR* 3.4 11.2 - - - +
245B LEU 3.1 0.2 - - - -
246B LYS* 1.3 78.1 - - - +
248B GLU* 1.3 65.6 + - - +
249B ASP* 3.9 3.5 - - - +
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Residues in contact with GLU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLU* 2.0 37.6 - - - +
72B VAL* 4.3 2.9 - - - +
244B TYR* 3.1 26.6 + - + +
245B LEU* 3.5 26.6 - - - +
247B LEU* 1.3 80.0 - - - +
249B ASP* 1.3 68.1 + - - +
250B LEU* 3.4 40.6 - - + +
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Residues in contact with ASP 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A PRO* 5.0 12.4 - - + +
245B LEU 2.7 21.1 + - - -
246B LYS* 3.4 15.0 - - - +
247B LEU 3.2 3.6 - - - +
248B GLU* 1.3 77.1 - - - +
250B LEU* 1.3 63.3 + - - +
251B VAL 4.6 2.5 - - - +
252B PRO* 4.3 22.3 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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