Contacts of the helix formed by residues 239 - 261 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237D GLY 3.7 2.2 + - - +
238D ALA* 1.3 79.2 - - - +
240D LEU* 1.3 65.7 + - - +
241D GLN* 3.5 7.4 + - - +
242D GLU* 2.8 47.1 + - - +
243D ALA* 2.9 18.9 + - - +
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Residues in contact with LEU 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D ILE* 4.0 27.4 - - + -
198D LEU* 3.6 27.8 - - + +
200D THR* 3.8 26.7 - - + -
203D GLU* 3.9 28.9 - - - +
205D TRP* 4.3 17.5 - - + +
234D LEU* 4.1 11.2 - - + -
239D THR* 1.3 75.0 - - - +
241D GLN* 1.4 62.5 + - - +
243D ALA* 4.7 2.7 - - - -
244D LEU* 2.9 27.5 + - - +
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Residues in contact with GLN 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D TRP* 3.2 47.9 - - + -
239D THR* 3.2 7.4 + - - +
240D LEU* 1.4 80.1 - - - +
242D GLU* 1.3 58.6 + - + +
244D LEU* 3.8 3.8 - - - +
245D GLU* 2.8 67.1 + - + +
281D TYR* 4.6 3.6 + - - -
283D SER* 4.8 2.2 + - - -
284D ALA* 4.1 11.0 + - + -
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Residues in contact with GLU 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233D LYS* 4.8 3.4 - - - +
237D GLY 4.5 1.0 - - - +
238D ALA* 3.4 14.4 - - + +
239D THR* 2.8 48.8 + - - +
241D GLN* 1.3 77.0 - - + +
243D ALA* 1.4 59.4 + - - +
245D GLU* 3.4 6.9 + - - +
246D HIS* 2.8 32.7 + - - +
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Residues in contact with ALA 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D LEU* 3.9 18.2 - - + -
233D LYS* 3.5 31.4 - - + -
234D LEU* 4.1 14.6 - - + -
238D ALA* 3.9 4.4 - - + +
239D THR 2.9 17.6 + - - +
240D LEU* 4.0 2.5 - - - +
242D GLU* 1.4 76.3 - - - +
244D LEU* 1.3 63.5 + - - +
246D HIS* 3.9 0.5 - - - +
247D VAL* 2.9 30.3 + - - +
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Residues in contact with LEU 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D LEU* 4.1 19.5 - - + -
196D MSE 3.7 32.3 - - + +
198D LEU* 4.1 14.4 - - + +
205D TRP* 4.0 30.3 - - + +
207D ILE* 3.8 28.9 - - + -
230D LEU* 4.2 7.5 - - + +
240D LEU 2.9 18.8 + - - +
241D GLN 3.8 2.2 - - - +
243D ALA* 1.3 78.3 - - - +
245D GLU* 1.3 57.3 + - - +
247D VAL* 3.9 1.5 - - + +
248D THR* 2.8 34.8 + - - -
284D ALA* 4.0 14.4 - - + -
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Residues in contact with GLU 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D ILE* 4.1 7.2 - - + -
241D GLN* 2.8 51.1 + - - +
242D GLU* 3.9 6.0 - - - +
244D LEU* 1.3 73.0 - - - +
246D HIS* 1.3 65.8 + - - +
248D THR* 3.5 1.2 + - - -
249D ALA* 3.2 24.3 + - - +
281D TYR* 2.8 36.9 + - + -
282D PHE 3.5 17.6 + - - +
283D SER* 3.5 1.0 + - - -
284D ALA* 2.7 33.3 + - + -
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Residues in contact with HIS 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D LEU* 3.8 24.4 - - + +
229D LEU* 6.0 0.2 - - + -
233D LYS* 2.8 38.4 + - + +
242D GLU 2.8 21.5 + - - +
243D ALA 4.1 0.7 - - - +
245D GLU* 1.3 73.1 - - - +
247D VAL* 1.3 65.1 + - - +
249D ALA* 3.9 2.9 - - - +
250D ALA* 3.0 24.7 + - + +
275D ILE 2.8 26.0 + - - -
276D ALA 3.5 16.8 + - - -
278D PRO* 4.0 13.9 - - + +
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Residues in contact with VAL 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D MSE 4.8 4.3 - - + -
226D THR* 3.5 43.3 - - + +
229D LEU* 3.5 17.7 - - + +
230D LEU* 3.4 37.2 - - + +
233D LYS* 4.3 5.2 - - + -
243D ALA 2.9 22.4 + - - +
244D LEU* 3.9 4.0 - - - +
246D HIS* 1.3 75.9 - - + +
248D THR* 1.3 64.5 + - - +
250D ALA* 3.3 4.2 + - - +
251D VAL* 3.1 27.4 + - + +
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Residues in contact with THR 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D MSE 3.3 19.8 - - + +
207D ILE* 3.4 34.4 - - + +
208D SER 5.0 0.7 - - - -
209D ARG* 3.3 46.1 + - + +
244D LEU 2.8 21.0 + - - -
245D GLU 3.9 1.6 - - - -
247D VAL* 1.3 78.6 - - - +
249D ALA* 1.3 57.4 + - - +
252D TYR* 3.1 23.4 + - - +
282D PHE* 4.1 7.9 - - + -
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Residues in contact with ALA 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D GLU 3.2 15.5 + - - +
246D HIS* 3.9 1.1 - - - +
248D THR* 1.3 75.6 - - - +
250D ALA* 1.3 67.2 + - - +
252D TYR* 3.2 8.6 + - - +
253D GLU* 2.9 26.9 + - - +
278D PRO* 3.5 17.0 - - + -
280D HIS 3.1 28.5 - - - +
281D TYR* 4.6 5.2 - - + -
282D PHE* 4.2 9.4 - - + +
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Residues in contact with ALA 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D LEU* 3.9 24.2 - - + -
246D HIS* 3.0 19.9 + - + +
247D VAL 3.9 0.4 - - - +
249D ALA* 1.3 76.5 - - - +
251D VAL* 1.3 64.7 + - - +
253D GLU* 3.2 4.3 + - - +
254D ILE* 3.1 26.9 + - - +
274D ARG 4.1 11.4 - - - -
275D ILE* 3.7 29.9 - - + +
278D PRO* 3.8 1.3 - - - +
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Residues in contact with VAL 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D ARG* 3.7 29.2 - - - +
222D VAL* 3.9 22.2 - - + +
225D VAL* 3.8 28.7 - - + -
226D THR* 3.8 22.9 - - - +
229D LEU* 4.5 2.5 - - + -
247D VAL* 3.1 20.0 + - + +
250D ALA* 1.3 75.5 - - - +
252D TYR* 1.3 64.1 + - - +
254D ILE* 3.2 11.2 + - + +
255D MSE 2.9 33.4 + - + +
266D LEU* 6.5 0.4 - - + -
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Residues in contact with TYR 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D ARG* 3.6 24.0 - - - +
210D PRO* 3.8 42.4 - - + +
212D VAL* 3.9 18.8 - - + +
248D THR 3.1 15.5 + - - +
249D ALA 3.3 8.5 - - - +
251D VAL* 1.3 78.2 - - - +
253D GLU* 1.3 58.3 + - - +
255D MSE 3.0 8.3 + - + +
256D VAL* 2.8 54.6 + - + +
280D HIS* 4.0 31.5 - + + -
282D PHE* 3.7 26.5 - + + -
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Residues in contact with GLU 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D ALA 2.9 19.5 + - - +
250D ALA 3.2 8.0 + - - +
252D TYR* 1.3 77.0 - - + +
254D ILE* 1.3 62.5 + - - +
256D VAL* 3.3 13.9 - - - +
257D THR* 3.1 29.5 + - - -
271D ALA* 4.3 3.4 - - + -
274D ARG* 3.5 53.5 + - + +
278D PRO* 4.0 4.5 - - + -
279D GLU* 2.5 32.1 + - - +
280D HIS* 3.1 29.0 + - + +
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Residues in contact with ILE 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D PRO* 5.0 0.2 - - + -
225D VAL* 4.0 27.8 - - + -
250D ALA* 3.1 14.1 + - + +
251D VAL* 3.2 11.0 + - + +
253D GLU* 1.3 74.7 - - - +
255D MSE 1.3 53.1 + - - +
257D THR* 3.9 1.9 - - - -
258D THR* 2.6 38.7 + - - +
266D LEU* 3.8 35.2 - - + -
267D GLN* 4.1 8.5 + - - +
268D VAL* 4.1 15.3 - - + -
271D ALA* 3.8 11.9 - - + -
275D ILE* 3.6 36.8 - - + -
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Residues in contact with MSE 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D ARG* 4.7 9.0 - - - +
212D VAL* 3.7 23.8 - - + -
214D PHE* 3.2 44.8 - - + -
219D PRO* 3.6 12.8 - - + -
222D VAL* 3.7 17.7 - - + -
251D VAL* 2.9 33.3 + - + +
252D TYR* 3.0 8.9 + - - +
254D ILE* 1.3 77.0 - - - +
256D VAL* 1.3 58.8 + - - +
258D THR* 3.2 4.0 + - - -
259D LYS* 3.0 26.7 + - - +
266D LEU* 3.3 34.3 - - + -
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Residues in contact with VAL 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D VAL* 4.4 6.3 - - + -
252D TYR* 2.8 60.3 + - + +
253D GLU* 3.3 26.5 - - - +
255D MSE 1.3 71.6 - - - +
257D THR* 1.3 70.4 + - - +
259D LYS* 3.4 6.0 + - - +
260D ALA* 3.0 24.6 + - - +
274D ARG* 5.7 0.7 - - - +
280D HIS* 5.3 7.6 - - + +
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Residues in contact with THR 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253D GLU 3.1 17.4 + - - -
254D ILE 3.9 3.6 - - - -
256D VAL* 1.3 79.8 - - - +
258D THR* 1.3 58.9 + - - +
260D ALA* 3.3 6.3 + - + +
261D MSE 3.0 51.3 + - + +
267D GLN* 4.1 4.3 - - + -
270D ALA* 3.9 18.8 - - + -
271D ALA* 3.9 7.0 - - - +
274D ARG* 2.9 30.3 + - - +
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Residues in contact with THR 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D PHE* 3.5 17.0 - - + -
219D PRO* 5.6 0.9 - - + -
254D ILE* 2.6 24.4 + - - +
255D MSE 3.2 7.2 + - + -
257D THR* 1.3 78.0 - - - +
259D LYS* 1.3 60.2 + - - +
261D MSE 3.5 0.9 + - - -
262D GLN 3.2 2.8 + - - -
263D GLU* 3.1 50.4 + - + +
264D TYR 4.7 2.2 - - - +
265D GLU 3.5 20.4 - - - +
266D LEU* 3.7 9.4 - - + +
267D GLN* 3.0 27.7 + - - -
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Residues in contact with LYS 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D VAL* 3.9 19.7 - - + -
213D ASP* 3.4 37.5 - - - +
214D PHE* 3.8 11.4 - - + -
255D MSE 3.0 15.7 + - - +
256D VAL* 4.0 4.7 - - - +
258D THR* 1.3 74.5 - - - +
260D ALA* 1.3 60.1 - - - +
262D GLN* 2.9 26.9 + - - +
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Residues in contact with ALA 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256D VAL 3.0 17.5 + - - +
257D THR* 3.6 9.0 - - + +
259D LYS* 1.3 76.7 - - - +
261D MSE 1.3 62.7 + - + +
262D GLN* 3.4 6.6 + - - +
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Residues in contact with MSE 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C LEU* 4.6 23.9 - - + +
2C MSE 4.9 14.1 - - + +
257D THR* 3.0 36.1 + - + +
258D THR 4.1 3.4 - - - +
260D ALA* 1.3 77.6 - - + +
262D GLN* 1.3 70.3 + - - +
263D GLU* 3.2 18.7 + - + +
267D GLN* 3.0 31.6 - - - +
270D ALA* 3.8 14.1 - - + -
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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
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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