Contacts of the helix formed by residues 230 - 254 (chain D) in PDB entry 4GQS
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 HIS 230 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102D LEU* 4.7 14.2 - - + +
105D ARG* 4.2 6.1 - - - -
207D ILE* 4.6 0.7 - - - -
212D TRP* 3.3 21.0 + + - -
213D ILE* 3.5 27.6 - - + -
216D CYS* 5.8 1.1 - - + +
223D ILE* 3.2 47.1 + - + +
226D PHE 3.2 14.1 + - - -
227D PRO 3.8 0.4 - - - -
228D GLY* 2.9 29.0 + - - -
229D THR* 1.3 77.4 - - - +
231D ASN* 1.3 85.4 + - - +
232D LYS 3.2 3.3 + - - -
233D LEU* 3.4 12.4 + - - +
234D LEU* 3.5 12.6 + - - +
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Residues in contact with ASN 231 (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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105D ARG* 5.7 0.2 - - - +
223D ILE 4.8 2.6 + - - -
227D PRO* 3.6 26.3 - - - +
228D GLY 3.4 12.4 + - - +
230D HIS* 1.3 106.1 + - - +
232D LYS* 1.3 60.1 + - - +
234D LEU* 3.8 7.7 + - - +
235D LYS* 3.3 21.7 + - - +
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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
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200D LYS* 5.7 4.6 - - - +
203D GLU* 3.3 34.5 - - - +
207D ILE* 5.9 6.5 - - + -
228D GLY 4.8 0.8 + - - -
229D THR* 4.6 8.7 - - - +
230D HIS* 3.2 1.0 - - - +
231D ASN* 1.3 76.5 - - - +
233D LEU* 1.3 53.6 + - - +
234D LEU 3.2 1.8 - - - -
235D LYS* 2.7 21.0 + - + +
236D ASN* 2.5 64.2 + - - +
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Residues in contact with LEU 233 (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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102D LEU* 3.4 33.4 - - + -
204D ASN* 3.0 41.3 - - + +
207D ILE* 4.1 25.8 - - + +
208D VAL* 3.4 29.8 - - + -
213D ILE* 4.6 1.6 - - + -
229D THR 4.7 1.2 + - - -
230D HIS* 3.4 11.2 + - - +
232D LYS* 1.3 76.6 - - - +
234D LEU* 1.3 58.6 + - - +
236D ASN* 3.2 4.8 + - - +
237D LEU* 2.9 42.0 + - + +
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Residues in contact with LEU 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D LEU* 5.7 4.0 - - + +
105D ARG* 3.5 27.1 - - + +
106D ALA* 3.4 37.5 - - + +
230D HIS 3.5 8.1 + - - +
231D ASN* 4.0 9.2 - - - +
232D LYS 3.2 0.4 - - - -
233D LEU* 1.3 81.4 - - - +
235D LYS* 1.3 56.8 + - - +
237D LEU* 4.6 5.2 - - + -
238D ALA* 3.1 28.5 + - + +
241D GLU* 6.1 1.3 - - - +
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Residues in contact with LYS 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 ASN 3.3 14.1 + - - +
232D LYS* 2.7 26.5 + - + +
234D LEU* 1.3 78.9 - - - +
236D ASN* 1.3 59.9 + - - +
238D ALA* 3.4 5.4 - - - +
239D PHE* 2.9 53.0 + - + +
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Residues in contact with ASN 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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200D LYS* 3.1 49.7 + - + +
203D GLU* 3.0 24.2 + - - +
204D ASN* 3.8 15.3 + - - +
232D LYS* 2.5 54.7 + - - +
233D LEU* 3.6 4.7 - - - +
235D LYS* 1.3 71.8 - - - +
237D LEU* 1.3 55.8 + - - +
238D ALA 3.0 1.6 - - - -
239D PHE* 3.7 1.6 - - - +
240D MET* 2.6 40.6 + - - +
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Residues in contact with LEU 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D LEU* 5.2 4.0 - - + -
106D ALA* 3.5 31.0 - - + -
107D ASN* 5.1 3.4 - - - +
204D ASN* 3.7 25.1 - - - +
233D LEU* 2.9 38.5 + - + +
234D LEU* 4.2 4.5 - - + +
236D ASN* 1.3 75.6 - - - +
238D ALA* 1.3 56.6 + - - +
240D MET* 3.8 14.8 - - + +
241D GLU* 2.8 42.4 + - - +
292D ALA* 5.4 12.2 - - + +
502D 0XV 5.5 6.7 - - - +
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Residues in contact with ALA 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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234D LEU* 3.1 23.1 + - + +
235D LYS* 3.4 9.0 - - - +
236D ASN 3.0 0.2 - - - -
237D LEU* 1.3 73.6 - - - +
239D PHE* 1.3 64.9 + - + +
241D GLU* 2.8 28.6 + - - +
242D SER* 2.8 15.9 + - - -
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Residues in contact with PHE 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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200D LYS* 3.2 30.1 - - - +
235D LYS* 2.9 43.7 + - + +
236D ASN 3.8 1.6 - - - +
238D ALA* 1.3 79.7 - - + +
240D MET* 1.3 62.1 + - - +
241D GLU 3.1 0.5 + - - -
242D SER* 3.2 17.2 + - - -
243D ASP* 2.9 23.0 + - - +
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Residues in contact with MET 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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197D LEU* 5.0 18.6 - - + +
200D LYS* 4.4 12.9 - - + +
201D LEU* 4.0 33.9 - - + +
204D ASN* 3.4 29.6 - - - +
236D ASN 2.6 28.0 + - - +
237D LEU* 3.8 16.8 - - + +
239D PHE* 1.3 72.9 - - - +
241D GLU* 1.3 60.3 + - - +
243D ASP* 3.8 10.0 + - - +
244D ILE* 3.1 31.3 + - + +
292D ALA* 5.0 18.6 - - - +
295D LEU* 5.1 8.3 - - + -
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Residues in contact with GLU 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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106D ALA* 4.4 8.9 - - - +
108D ARG* 3.1 28.0 + - - -
234D LEU* 6.1 0.9 - - - +
237D LEU* 2.8 34.1 + - - +
238D ALA* 2.8 18.9 + - - +
240D MET* 1.3 75.1 - - - +
242D SER* 1.3 66.0 + - - +
244D ILE* 2.7 23.8 + - - +
245D LEU* 3.2 4.0 + - - +
288D VAL* 3.6 24.4 - - + +
289D ILE* 3.3 20.4 - - + +
292D ALA* 4.5 15.5 - - + -
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Residues in contact with SER 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D ALA 2.8 13.4 + - - -
239D PHE* 3.5 13.0 - - - -
241D GLU* 1.3 72.0 - - - +
243D ASP* 1.3 59.7 + - - +
245D LEU* 2.9 32.1 + - - +
246D GLU* 3.5 10.4 + - - +
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Residues in contact with ASP 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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200D LYS* 5.1 4.2 + - - -
239D PHE* 2.9 23.5 + - - +
240D MET* 3.8 11.1 - - - +
241D GLU 3.2 0.6 - - - -
242D SER* 1.3 78.6 + - - +
244D ILE* 1.3 57.7 + - + +
246D GLU* 3.0 36.5 + - + +
247D LYS* 3.7 5.9 + - - +
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Residues in contact with ILE 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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183D PHE* 5.2 15.9 - - + -
240D MET* 3.1 22.2 - - + +
241D GLU* 2.7 17.4 + - - +
243D ASP* 1.3 73.5 - - + +
245D LEU* 1.3 59.3 + - - +
246D GLU 3.4 0.3 + - - -
247D LYS* 3.7 6.5 + - - +
248D VAL* 3.0 26.6 + - + +
264D ILE* 5.7 1.8 - - + -
287D LEU* 5.4 0.4 - - + -
288D VAL* 3.6 24.2 - - + +
291D ALA* 3.8 20.9 - - + -
292D ALA* 3.6 38.8 - - + +
295D LEU* 4.8 14.1 - - + -
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Residues in contact with LEU 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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241D GLU 3.2 5.6 + - - +
242D SER* 2.9 18.7 + - - +
244D ILE* 1.3 75.5 - - - +
246D GLU* 1.3 64.9 + - - +
248D VAL* 3.7 4.0 - - + +
249D LYS* 3.1 44.4 + - + +
284D ILE* 3.3 38.8 - - + -
288D VAL* 3.8 17.7 - - + +
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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 SER* 3.9 6.1 + - - +
243D ASP* 3.0 30.1 + - + +
245D LEU* 1.3 80.6 - - - +
247D LYS* 1.3 65.7 + - + +
249D LYS* 3.1 6.9 + - - +
250D GLU* 3.1 28.0 + - - +
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Residues in contact with LYS 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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183D PHE* 3.7 37.5 - - + +
185D LYS* 5.0 17.0 - - - +
187D PHE* 4.2 30.0 - - + -
193D GLN* 5.0 5.6 - - - +
243D ASP 3.7 4.9 + - - +
244D ILE* 3.7 5.5 + - - +
245D LEU 3.5 0.2 - - - -
246D GLU* 1.3 79.7 - - + +
248D VAL* 1.3 53.3 + - - +
250D GLU* 2.7 41.9 + - - +
251D HIS* 2.5 46.3 + - + -
264D ILE* 4.0 2.0 - - + -
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Residues in contact with VAL 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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244D ILE* 3.0 26.7 - - + +
245D LEU* 3.7 10.5 - - + +
246D GLU 3.3 0.2 - - - -
247D LYS* 1.3 76.1 - - - +
249D LYS* 1.3 64.1 + - + +
251D HIS* 3.4 3.6 + - - +
252D GLN* 3.1 22.6 + - - +
264D ILE* 3.8 21.5 - - + -
268D LEU* 3.7 16.3 - - + +
271D MET* 5.8 0.2 - - + -
284D ILE* 4.5 19.7 - - + -
287D LEU* 3.5 38.6 - - + -
288D VAL* 4.6 5.2 - - + -
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Residues in contact with LYS 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 LEU* 3.1 29.8 + - + +
246D GLU* 3.1 9.3 + - - +
248D VAL* 1.3 76.7 - - - +
250D GLU* 1.3 59.0 + - + +
252D GLN* 3.0 42.6 + - - +
253D GLU* 3.2 16.3 - - - +
284D ILE* 3.1 34.8 - - + +
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Residues in contact with GLU 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* 3.1 18.9 + - - +
247D LYS* 2.7 48.1 + - - +
249D LYS* 1.3 68.3 - - + +
251D HIS* 1.3 57.9 + - + +
252D GLN 2.8 4.3 - - - -
253D GLU* 2.8 45.4 + - - +
254D SER* 3.4 7.7 + - - -
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Residues in contact with HIS 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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183D PHE* 4.4 4.2 - + - +
184D GLN* 4.4 2.4 + - + +
247D LYS* 2.5 66.1 + - + -
248D VAL 3.9 6.5 - - - +
250D GLU* 1.3 72.9 - - + +
252D GLN* 1.3 55.9 + - - +
254D SER* 4.3 0.4 - - - -
255D MET* 2.9 30.0 + - - +
261D ARG* 2.9 22.1 + - - +
262D ASP* 2.7 43.5 + - - -
264D ILE* 3.9 18.3 - - + +
265D ASP* 3.3 19.8 - - - +
268D LEU* 3.6 6.7 - - + -
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Residues in contact with GLN 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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248D VAL* 3.1 13.6 + - - +
249D LYS* 3.0 50.1 + - - +
251D HIS* 1.3 77.7 - - - +
253D GLU* 1.3 61.7 + - + +
255D MET* 3.4 11.8 - - + +
268D LEU* 3.4 29.0 - - + +
271D MET* 4.9 11.1 - - - -
284D ILE* 5.3 3.2 - - - +
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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 LYS 3.2 17.0 - - - +
250D GLU* 2.8 24.0 + - - +
252D GLN* 1.3 80.4 - - + +
254D SER* 1.3 58.7 + - - +
255D MET 3.1 5.2 + - - +
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Residues in contact with SER 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 GLU 3.4 6.2 + - - -
251D HIS* 4.3 0.3 - - - -
253D GLU* 1.3 77.3 - - - +
255D MET* 1.3 65.0 + - - +
256D ASP* 3.2 6.6 + - - +
261D ARG* 3.0 39.9 + - - -
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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