Contacts of the helix formed by residues 230 - 255 (chain D) in PDB entry 1OHV
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 PHE 230 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224D LYS* 3.6 49.6 - - + +
225D TYR 3.4 21.5 - - - -
226D PRO* 3.4 21.8 - - + +
227D LEU 3.3 6.0 + - - -
229D GLU* 1.3 95.7 - - + +
231D VAL* 1.3 59.3 + - - +
232D LYS 3.4 2.5 - - - -
233D GLU* 3.4 28.3 - - + +
234D ASN* 2.8 34.3 + - - +
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Residues in contact with VAL 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D LEU 3.5 13.6 + - - +
228D GLU* 4.0 17.7 - - + +
229D GLU 3.8 0.8 - - - -
230D PHE* 1.3 77.2 - - - +
232D LYS* 1.3 62.8 + - + +
233D GLU* 4.2 0.2 + - - -
234D ASN* 3.9 3.8 - - - +
235D GLN* 3.0 56.6 + - + +
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Residues in contact with LYS 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230D PHE 3.4 0.2 - - - -
231D VAL* 1.3 81.1 - - + +
233D GLU* 1.3 68.3 + - + +
235D GLN* 3.3 16.0 + - - +
236D GLN* 3.0 29.6 + - - +
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Residues in contact with GLU 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D LYS* 4.3 21.5 + - + +
229D GLU 4.1 3.8 - - - +
230D PHE* 3.4 47.3 - - + +
232D LYS* 1.3 85.4 + - - +
234D ASN* 1.3 59.0 + - - +
236D GLN* 3.4 6.7 + - - +
237D GLU* 3.0 28.3 + - - +
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Residues in contact with ASN 234 (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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222D ARG 4.6 1.2 - - - +
223D LEU* 3.5 18.7 - - + +
224D LYS* 2.8 53.0 + - - +
227D LEU* 3.7 24.5 + - - +
230D PHE* 2.8 23.8 + - - +
231D VAL* 4.0 3.3 - - - +
233D GLU* 1.3 75.3 - - - +
235D GLN* 1.3 63.8 + - - +
237D GLU* 3.7 5.0 - - - +
238D GLU* 3.1 31.3 + - - +
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Residues in contact with GLN 235 (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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231D VAL* 3.0 45.1 + - + +
232D LYS* 3.5 16.4 - - - +
234D ASN* 1.3 77.4 - - - +
236D GLN* 1.3 57.1 + - - +
238D GLU* 3.4 8.8 + - - +
239D ALA* 3.0 27.6 + - - +
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Residues in contact with GLN 236 (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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232D LYS 3.0 17.0 + - - +
233D GLU* 3.7 6.5 - - - +
235D GLN* 1.3 73.4 - - - +
237D GLU* 1.3 61.5 + - - +
239D ALA* 3.7 6.3 - - - +
240D ARG* 2.9 30.5 + - - +
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Residues in contact with GLU 237 (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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220D PHE 4.3 0.5 - - - +
221D PRO* 3.5 10.6 - - + +
222D ARG* 2.7 51.4 + - - +
223D LEU* 4.9 1.6 - - + -
224D LYS* 4.9 10.3 + - - +
233D GLU 3.0 18.3 + - - +
234D ASN* 3.7 8.1 - - - +
235D GLN 3.4 0.2 - - - -
236D GLN* 1.3 76.5 - - - +
238D GLU* 1.3 64.1 + - - +
240D ARG* 3.4 36.8 + - - +
241D CYS* 3.0 25.1 + - - -
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Residues in contact with GLU 238 (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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221D PRO* 3.9 27.4 - - + -
223D LEU* 3.6 16.3 - - + +
234D ASN* 3.1 21.3 + - - +
235D GLN* 3.7 7.7 - - - +
237D GLU* 1.3 78.3 - - - +
239D ALA* 1.3 56.3 + - - +
241D CYS* 3.3 3.5 + - - +
242D LEU* 3.0 35.7 + - + +
276D ALA* 3.8 1.2 - - - -
277D SER* 2.5 48.8 + - - -
279D ASP* 4.7 4.5 - - - +
280D PHE* 3.6 19.5 + - + +
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Residues in contact with ALA 239 (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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235D GLN 3.0 18.0 + - - +
236D GLN* 3.7 7.6 - - - +
237D GLU 3.3 0.2 - - - -
238D GLU* 1.3 72.5 - - - +
240D ARG* 1.3 66.2 - - - +
242D LEU* 3.4 11.7 + - - +
243D GLU* 3.0 25.7 + - - +
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Residues in contact with ARG 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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219D PRO* 4.0 14.5 - - - +
220D PHE 5.2 0.8 + - - -
236D GLN 2.9 18.1 + - - +
237D GLU* 3.4 38.2 + - - +
239D ALA* 1.3 77.4 - - - +
241D CYS* 1.3 74.1 + - - +
243D GLU* 3.4 6.2 + - - +
244D GLU* 2.9 60.2 + - + +
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Residues in contact with CYS 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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219D PRO* 3.3 34.6 - - - +
220D PHE 3.8 1.1 - - - -
221D PRO* 3.5 35.7 - - + -
237D GLU 3.0 19.7 + - - +
238D GLU 3.3 4.2 + - - +
240D ARG* 1.3 100.3 - - - +
242D LEU* 1.3 57.1 + - - +
244D GLU* 3.3 3.1 + - - +
245D VAL* 3.0 33.6 + - - +
280D PHE* 4.2 4.0 - - + -
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Residues in contact with LEU 242 (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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238D GLU* 3.0 26.0 + - + +
239D ALA* 3.7 8.7 - - - +
241D CYS* 1.3 72.2 - - - +
243D GLU* 1.3 64.9 + - - +
245D VAL* 3.3 7.3 + - - +
246D GLU* 3.2 18.6 + - - +
280D PHE* 3.6 42.0 - - + +
283D LYS* 3.7 33.7 - - + +
284D LEU* 3.8 25.6 - - + +
287D ILE* 3.7 23.8 - - + +
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Residues in contact with GLU 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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239D ALA 3.0 17.4 + - - +
240D ARG* 3.6 7.6 - - - +
242D LEU* 1.3 78.0 - - - +
244D GLU* 1.3 56.2 + - + +
246D GLU* 3.2 9.7 + - - +
247D ASP* 3.0 37.2 + - - +
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Residues in contact with GLU 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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219D PRO* 3.4 32.6 - - + +
240D ARG* 2.9 50.2 + - + +
241D CYS 3.3 5.4 + - - +
243D GLU* 1.3 73.9 - - + +
245D VAL* 1.3 63.9 + - - +
247D ASP* 3.4 10.9 + - - +
248D LEU* 3.0 32.9 + - + +
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Residues in contact with VAL 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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183D LEU* 3.8 11.5 - - + +
185D PHE* 3.7 23.3 - - + -
218D ALA* 3.6 26.7 - - + +
241D CYS 3.0 19.8 + - - +
242D LEU* 3.5 10.3 - - + +
243D GLU 3.3 0.2 - - - -
244D GLU* 1.3 75.6 - - - +
246D GLU* 1.3 65.9 + - - +
248D LEU* 3.2 5.9 + - - +
249D ILE* 3.0 37.8 + - + +
262D ILE* 4.4 4.7 - - + -
280D PHE* 5.8 0.4 - - + -
284D LEU* 3.9 22.2 - - + -
287D ILE* 4.2 7.2 - - + -
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Residues in contact with GLU 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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242D LEU 3.2 8.5 + - - +
243D GLU* 3.5 10.9 - - - +
245D VAL* 1.3 83.2 - - - +
247D ASP* 1.3 65.1 + - - +
249D ILE* 3.2 11.1 + - - +
250D VAL* 3.0 26.2 + - + +
287D ILE* 4.0 20.7 - - + +
290D LYS* 2.7 31.8 + - - +
291D HIS* 2.6 36.6 + - + +
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Residues in contact with ASP 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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243D GLU* 3.0 27.6 + - - +
244D GLU* 3.7 10.8 - - + +
246D GLU* 1.3 77.8 - - - +
248D LEU* 1.3 58.6 + - + +
250D VAL* 3.4 8.5 + - - +
251D LYS* 2.8 31.1 + - - +
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Residues in contact with LEU 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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183D LEU* 4.0 4.9 - - + -
216D PRO* 4.0 20.6 - - + -
217D ILE 3.5 31.6 - - - +
218D ALA* 3.5 23.1 - - + -
219D PRO* 4.8 2.2 - - + -
244D GLU* 3.0 23.2 + - + +
245D VAL* 3.2 6.9 + - - +
247D ASP* 1.3 73.2 - - + +
249D ILE* 1.3 62.1 + - - +
251D LYS* 3.2 17.9 + - + +
252D TYR* 2.8 48.3 + - + +
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Residues in contact with ILE 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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183D LEU* 3.8 13.7 - - + -
245D VAL* 3.0 17.9 + - + +
246D GLU* 3.2 7.6 + - - +
248D LEU* 1.3 77.5 - - - +
250D VAL* 1.3 62.6 + - - +
252D TYR* 3.4 1.2 + - - +
253D ARG* 3.0 24.1 + - + +
259D VAL* 4.0 19.4 + - + +
262D ILE* 3.9 26.0 - - + -
287D ILE* 3.9 23.1 - - + +
291D HIS* 3.7 33.9 - - + +
293D CYS* 3.9 17.3 - - - -
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Residues in contact with VAL 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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246D GLU* 3.0 20.8 + - + +
247D ASP* 3.7 10.8 - - - +
249D ILE* 1.3 75.0 - - - +
251D LYS* 1.3 63.7 + - - +
253D ARG* 3.2 8.7 + - - +
254D LYS* 3.1 50.1 + - + +
291D HIS* 4.1 20.9 - - + +
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Residues in contact with LYS 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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247D ASP 2.8 20.0 + - - +
248D LEU* 3.5 24.1 - - + +
250D VAL* 1.3 79.3 - - - +
252D TYR* 1.3 64.7 + - + +
254D LYS* 3.4 10.0 + - - +
255D LYS* 3.1 54.9 + - + +
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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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181D SER* 4.4 0.2 - - - -
214D ASP* 2.8 41.4 + - - -
215D TRP 4.1 5.2 + - - -
216D PRO* 3.6 39.2 - - + +
248D LEU* 2.8 35.2 + - + +
251D LYS* 1.3 85.7 + - + +
253D ARG* 1.3 62.6 + - - +
255D LYS* 3.5 28.1 + - + +
256D LYS 3.4 2.6 + - - -
257D LYS* 2.9 59.8 + - + +
258D THR* 4.4 0.7 - - - -
259D VAL* 3.9 13.7 - - + -
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Residues in contact with ARG 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 ILE* 3.0 15.6 + - + +
250D VAL* 3.2 12.3 + - - +
252D TYR* 1.3 75.9 - - - +
254D LYS* 1.3 60.0 + - + +
256D LYS* 2.9 22.9 + - - +
258D THR* 4.5 26.3 + - + +
259D VAL 5.9 0.2 - - - +
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Residues in contact with LYS 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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250D VAL* 3.1 35.2 + - + +
251D LYS* 3.7 10.1 - - - +
252D TYR 3.3 0.2 - - - -
253D ARG* 1.3 73.7 - - + +
255D LYS* 1.3 57.6 + - + +
256D LYS* 3.1 16.5 + - - +
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Residues in contact with LYS 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D ASP* 4.6 11.4 + - - -
251D LYS* 3.1 39.4 + - + +
252D TYR* 3.9 45.0 + - + +
253D ARG 3.3 0.6 - - - -
254D LYS* 1.3 75.3 - - + +
256D LYS* 1.3 70.1 + - - +
257D LYS* 3.3 21.6 + - + +
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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