Contacts of the helix formed by residues 239 - 261 (chain C) in PDB entry 1VI9
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 THR 239 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C LEU* 5.4 0.2 - - - -
237C GLY 5.1 2.0 - - - +
238C ALA* 1.3 77.1 - - - +
240C LEU* 1.3 55.7 + - - +
241C GLN* 3.5 7.4 + - - +
242C GLU* 2.7 48.1 + - - +
243C ALA* 2.7 32.2 + - - +
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Residues in contact with LEU 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C ILE* 4.6 9.9 - - + -
198C LEU* 3.5 30.9 - - + +
200C THR* 3.7 33.4 - - + +
203C GLU* 3.6 31.2 - - + +
205C TRP* 3.9 23.6 - - + +
234C LEU* 4.4 15.3 - - + -
239C THR* 1.3 73.9 - - - +
241C GLN* 1.3 57.7 + - - +
243C ALA* 4.6 2.0 - - - -
244C LEU* 3.0 31.4 + - - +
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Residues in contact with GLN 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C TRP* 3.7 46.6 - - + -
239C THR* 3.2 7.2 + - - +
240C LEU* 1.3 77.0 - - - +
242C GLU* 1.3 61.0 - - + +
244C LEU* 3.9 3.4 - - - +
245C GLU* 2.9 63.4 + - - +
281C TYR* 5.3 2.0 + - - -
283C SER* 5.4 1.0 + - - -
284C ALA* 4.0 10.1 + - + -
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Residues in contact with GLU 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C LYS* 4.4 4.2 - - - +
237C GLY 4.7 0.7 - - - +
238C ALA* 3.4 14.2 - - + +
239C THR* 2.7 48.3 + - - +
241C GLN* 1.3 76.2 - - + +
243C ALA* 1.3 66.1 + - - +
245C GLU* 3.5 6.5 + - - +
246C HIS* 3.1 26.0 + - - +
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Residues in contact with ALA 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C LEU* 4.8 0.7 - - + -
230C LEU* 4.0 20.2 - - + -
233C LYS* 3.7 28.4 - - + +
234C LEU* 4.1 14.1 - - + -
238C ALA* 3.9 4.4 - - + +
239C THR 2.7 21.1 + - - +
240C LEU* 4.0 3.6 - - - +
242C GLU* 1.3 74.4 - - - +
244C LEU* 1.3 60.9 + - - +
246C HIS* 4.0 0.9 - - - +
247C VAL* 3.0 28.9 + - - +
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Residues in contact with LEU 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C LEU* 4.2 18.8 - - + -
196C MSE 3.9 19.3 - - + +
198C LEU* 4.2 16.5 - - + +
205C TRP* 3.8 37.7 - - + +
206C HIS 4.3 0.2 - - - -
207C ILE* 3.6 40.2 - - + -
230C LEU* 5.5 1.3 - - - -
240C LEU 3.0 17.9 + - - +
241C GLN* 3.9 2.5 - - - +
243C ALA* 1.3 75.4 - - - +
245C GLU* 1.3 58.5 + - - +
247C VAL* 4.2 4.0 - - + +
248C THR* 2.3 34.7 + - - -
284C ALA* 4.2 8.5 - - + -
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Residues in contact with GLU 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C ILE* 4.0 6.3 - - + -
241C GLN* 2.9 50.5 + - - +
242C GLU* 4.1 5.0 - - - +
244C LEU* 1.3 76.8 - - - +
246C HIS* 1.3 62.9 + - - +
248C THR* 3.7 1.2 - - - -
249C ALA* 3.1 26.2 + - - +
281C TYR* 4.0 18.2 + - + -
282C PHE* 3.4 21.1 + - - +
283C SER* 3.8 2.9 - - - -
284C ALA* 2.8 33.6 + - + +
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Residues in contact with HIS 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LEU* 3.5 27.6 - - + +
229C LEU* 6.2 0.2 - - + -
233C LYS* 3.1 37.9 + - + +
242C GLU 3.1 18.7 + - - +
243C ALA 4.1 0.2 - - - +
245C GLU* 1.3 75.4 - - - +
247C VAL* 1.3 67.8 + - - +
248C THR 3.2 0.2 + - - -
249C ALA* 3.3 2.8 + - - -
250C ALA* 2.8 25.2 + - + +
275C ILE 2.7 23.8 + - - -
276C ALA 3.5 15.3 + - - -
278C PRO* 3.5 20.7 - - + +
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Residues in contact with VAL 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C LEU* 6.0 1.1 - - + -
196C MSE 4.9 6.1 - - + -
226C THR* 3.7 41.1 - - + +
229C LEU* 3.7 15.5 - - + +
230C LEU* 3.4 37.5 - - + +
233C LYS* 4.1 6.7 - - + -
243C ALA 3.0 19.3 + - - +
244C LEU* 4.2 4.5 - - + +
246C HIS* 1.3 75.5 - - - +
248C THR* 1.3 64.4 + - - +
250C ALA* 3.9 4.0 - - - +
251C VAL* 3.0 28.7 + - + +
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Residues in contact with THR 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C MSE 3.4 20.8 - - + +
207C ILE* 3.6 32.9 - - + +
208C SER* 4.3 0.7 - - - +
209C ARG* 3.4 40.8 + - + +
244C LEU 2.3 26.8 + - - -
245C GLU 3.7 3.4 - - - -
247C VAL* 1.3 77.8 - - - +
249C ALA* 1.3 62.3 + - - +
252C TYR* 3.1 23.6 + - - +
282C PHE* 4.2 7.4 - - + -
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Residues in contact with ALA 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C GLU 3.1 14.9 + - - +
246C HIS* 4.8 0.4 - - - -
248C THR* 1.3 79.2 - - - +
250C ALA* 1.3 53.6 + - - +
252C TYR* 3.2 2.3 + - - +
253C GLU* 2.7 40.4 + - - +
278C PRO* 3.5 16.4 - - + -
280C HIS* 3.3 27.3 - - - +
281C TYR* 5.3 0.2 - - - -
282C PHE* 4.0 19.0 - - + +
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Residues in contact with ALA 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C LEU* 3.8 23.1 - - + -
246C HIS* 2.8 27.4 + - + +
247C VAL 3.9 0.7 - - - +
249C ALA* 1.3 71.7 - - - +
251C VAL* 1.3 60.5 + - - +
253C GLU* 3.2 3.8 + - - +
254C ILE* 3.1 29.1 + - - +
274C ARG 4.0 11.7 - - - -
275C ILE* 3.7 27.3 - - + +
278C PRO* 3.9 1.4 - - - +
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Residues in contact with VAL 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C ARG* 3.6 30.1 - - - +
222C VAL* 4.1 15.0 - - + +
225C VAL* 4.2 17.5 - - + -
226C THR* 3.7 35.2 - - + +
229C LEU* 4.3 5.4 - - + -
247C VAL* 3.0 20.3 + - + +
250C ALA* 1.3 72.4 - - - +
252C TYR* 1.3 66.9 + - - +
254C ILE* 3.1 10.4 + - + +
255C MSE 3.0 32.4 + - + +
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Residues in contact with TYR 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C ARG* 3.7 24.0 - - - +
210C PRO* 3.5 40.1 - - + +
212C VAL* 3.5 22.4 - - + +
248C THR 3.1 20.1 + - - +
249C ALA 3.5 3.1 - - - +
251C VAL* 1.3 76.9 - - - +
253C GLU* 1.3 64.7 + - - +
255C MSE 3.0 8.2 + - + +
256C VAL* 2.9 44.5 + - + +
280C HIS* 3.6 32.3 + + - -
282C PHE* 3.4 26.7 - + + -
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Residues in contact with GLU 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C ALA 2.7 20.9 + - - +
250C ALA 3.4 8.3 - - - +
251C VAL 3.2 0.2 - - - -
252C TYR* 1.3 78.1 - - - +
254C ILE* 1.3 63.4 + - + +
256C VAL* 3.4 10.4 + - - +
257C THR* 3.1 27.0 + - - -
271C ALA* 4.4 3.1 - - + -
274C ARG* 3.4 53.6 + - + +
278C PRO* 4.1 3.6 - - + -
279C GLU* 2.7 30.9 + - - +
280C HIS* 3.0 33.5 + - + +
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Residues in contact with ILE 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C PRO* 4.9 0.2 - - + -
225C VAL* 4.0 26.9 - - + -
229C LEU* 5.0 0.2 - - + -
250C ALA 3.1 13.9 + - - +
251C VAL* 3.1 10.4 + - + +
253C GLU* 1.3 74.6 - - - +
255C MSE 1.3 55.0 + - - +
257C THR* 3.4 2.6 + - - -
258C THR* 2.6 36.9 + - - -
266C LEU* 3.9 23.8 - - + -
267C GLN 4.1 13.6 + - - +
268C VAL* 4.0 22.2 - - + -
271C ALA* 4.0 13.2 - - + -
275C ILE* 3.4 40.8 - - + -
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Residues in contact with MSE 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C ARG* 5.2 7.0 - - - +
212C VAL* 4.1 20.4 - - + -
214C PHE* 3.2 45.8 - - + -
218C GLN* 4.8 3.8 - - - +
219C PRO* 4.0 8.1 - - + -
222C VAL* 3.5 26.2 - - + -
251C VAL* 3.0 29.8 + - + +
252C TYR* 3.0 11.4 + - + +
254C ILE* 1.3 78.1 - - - +
256C VAL* 1.3 57.7 + - - +
258C THR* 3.3 3.1 + - - -
259C LYS* 3.0 25.5 + - - +
266C LEU* 3.2 33.2 - - + -
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Residues in contact with VAL 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C VAL* 4.6 5.4 - - + -
252C TYR* 2.9 60.9 + - + +
253C GLU* 3.4 24.7 - - - +
255C MSE 1.3 70.3 - - - +
257C THR* 1.4 69.1 + - - +
259C LYS* 3.3 6.8 + - - +
260C ALA* 2.8 31.9 + - - +
274C ARG* 5.9 0.2 - - - +
280C HIS* 4.7 10.1 - - + -
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Residues in contact with THR 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C GLU 3.1 16.7 + - - -
254C ILE 3.8 3.4 - - - -
256C VAL* 1.4 81.0 - - - +
258C THR* 1.3 63.0 + - - +
260C ALA* 3.4 6.5 + - + +
261C MSE 3.1 34.2 + - + +
267C GLN* 4.1 4.9 - - + -
270C ALA* 3.7 29.6 - - + -
271C ALA* 3.6 7.5 - - + +
274C ARG* 2.6 33.1 + - - +
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Residues in contact with THR 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C PHE* 3.9 13.7 - - + -
219C PRO* 4.4 5.8 - - + -
254C ILE 2.6 24.3 + - - -
255C MSE 3.5 5.6 - - - -
257C THR* 1.3 77.3 - - - +
259C LYS* 1.3 64.9 + - - +
261C MSE 3.4 1.0 + - - -
262C GLN 3.3 2.8 + - - -
263C GLU* 3.2 43.9 + - + +
265C GLU 3.2 27.1 - - - +
266C LEU* 3.7 7.6 - - + +
267C GLN* 3.0 26.7 + - - -
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Residues in contact with LYS 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C VAL* 3.4 26.2 - - + -
213C ASP* 3.0 31.1 + - - +
214C PHE* 3.8 15.5 - - + +
255C MSE 3.0 13.2 + - - +
256C VAL* 3.5 8.7 - - - +
258C THR* 1.3 74.1 - - - +
260C ALA* 1.3 55.2 + - - +
262C GLN* 2.6 33.9 + - - +
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Residues in contact with ALA 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C VAL 2.8 21.9 + - - +
257C THR* 3.7 8.1 - - + +
259C LYS* 1.3 73.6 - - - +
261C MSE 1.3 60.5 + - + +
262C GLN* 3.5 6.8 + - - +
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Residues in contact with MSE 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C THR* 3.1 25.1 + - + +
258C THR 4.0 4.0 - - - +
259C LYS 2.9 1.6 + - - -
260C ALA* 1.3 75.7 - - + +
262C GLN* 1.3 75.8 + - - +
263C GLU* 3.3 17.2 + - + +
267C GLN* 3.4 26.9 - - + +
270C ALA* 3.7 28.3 - - + -
2D MSE 4.6 14.8 - - + +
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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
------------------------------------------------------------
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