Contacts of the helix formed by residues 219 - 242 (chain D) in PDB entry 4WLU
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 PRO 219 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185D LYS* 5.7 1.1 - - - +
217D ASP 4.5 2.7 - - - +
218D PHE* 1.3 86.4 - - + +
220D GLN* 1.3 60.6 + - - +
221D ASP* 3.2 18.2 - - - +
222D GLN* 3.2 23.8 + - + +
223D LEU* 2.9 24.1 + - - +
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Residues in contact with GLN 220 (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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218D PHE 3.7 1.8 + - - +
219D PRO* 1.3 73.1 - - - +
221D ASP* 1.3 57.7 + - - +
223D LEU* 3.2 18.4 + - - +
224D THR* 2.9 49.5 + - - +
311D PHE* 3.6 38.6 - - - +
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Residues in contact with ASP 221 (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* 3.2 21.5 - - - +
220D GLN* 1.3 75.2 - - - +
222D GLN* 1.3 72.6 + - - +
224D THR* 3.7 5.3 + - - -
225D ALA* 3.2 21.5 + - - +
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Residues in contact with GLN 222 (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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184D LEU* 4.2 26.5 - - + +
185D LYS* 5.7 0.7 + - - -
218D PHE* 3.9 21.3 - - + -
219D PRO* 3.2 28.8 + - + +
221D ASP* 1.3 87.5 + - - +
223D LEU* 1.3 54.6 + - - +
225D ALA* 3.0 8.1 + - - +
226D LEU* 2.7 36.9 + - - +
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Residues in contact with LEU 223 (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 ILE* 3.6 43.1 - - + -
218D PHE* 4.0 21.5 - - + +
219D PRO 2.9 16.7 + - - +
220D GLN* 3.2 21.7 + - - +
222D GLN* 1.3 76.2 - - - +
224D THR* 1.3 53.6 + - - +
226D LEU* 3.5 6.1 + - + +
227D THR* 2.6 40.1 + - - +
311D PHE* 3.6 33.4 - - + -
312D GLU* 6.1 0.9 - - - +
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Residues in contact with THR 224 (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 GLN* 2.9 34.2 + - - +
221D ASP* 3.9 6.9 - - - -
223D LEU* 1.3 76.2 - - - +
225D ALA* 1.3 58.1 + - - +
227D THR* 3.8 5.9 - - - -
228D GLY* 2.9 24.3 + - - -
311D PHE* 4.2 12.7 - - + -
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Residues in contact with ALA 225 (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 ASP 3.2 14.6 + - - +
222D GLN* 3.0 12.6 + - - +
224D THR* 1.3 74.1 - - - +
226D LEU* 1.3 59.6 + - - +
228D GLY* 3.2 2.1 + - - -
229D ARG* 2.8 30.5 + - - +
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Residues in contact with LEU 226 (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 PHE* 3.6 33.4 - - + -
181D VAL* 3.9 14.6 - - + +
184D LEU* 3.9 19.5 - - + -
209D ILE* 3.9 15.7 - - + -
218D PHE* 3.9 37.9 - - + -
222D GLN 2.7 18.8 + - - +
223D LEU* 3.7 6.5 - - + +
225D ALA* 1.3 71.3 - - - +
227D THR* 1.3 62.9 + - - +
229D ARG* 3.3 8.4 + - + +
230D ILE* 3.0 37.3 + - + +
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Residues in contact with THR 227 (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 PRO* 3.9 29.4 + - + +
209D ILE* 4.8 3.5 - - - +
223D LEU* 2.6 32.0 + - - +
224D THR* 3.8 7.0 - - - -
226D LEU* 1.3 76.3 - - - +
228D GLY* 1.3 63.6 + - - +
230D ILE* 3.5 2.3 + - - +
231D GLN* 3.1 33.1 + - - +
311D PHE* 3.7 15.6 - - + -
315D MET* 3.6 31.0 - - + +
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Residues in contact with GLY 228 (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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224D THR 2.9 16.2 + - - -
225D ALA* 3.6 3.4 - - - -
227D THR* 1.3 73.7 - - - +
229D ARG* 1.3 64.4 + - - +
231D GLN* 3.3 11.2 + - - +
232D GLU* 3.0 32.5 + - - +
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Residues in contact with ARG 229 (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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69C SER* 5.8 1.0 + - - -
70C HIS* 4.4 2.4 + - - -
180D PHE* 3.7 44.5 - - + +
183D GLU* 5.2 7.5 + - - -
225D ALA 2.8 16.8 + - - +
226D LEU* 3.4 13.7 - - + +
228D GLY* 1.3 73.7 - - - +
230D ILE* 1.3 57.1 + - - +
232D GLU* 3.7 2.2 - - - -
233D ALA* 3.0 31.7 + - - +
236D GLU* 2.7 39.2 + - - +
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Residues in contact with ILE 230 (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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173D ASP* 4.2 19.6 - - + +
176D ARG* 4.9 5.3 + - + -
177D ALA* 3.7 27.4 - - + +
180D PHE* 3.7 24.7 - - + -
196D VAL* 5.2 1.1 - - + -
205D ILE* 4.1 25.4 - - + +
207D PRO* 3.8 30.1 - - + -
209D ILE* 4.5 5.6 - - + -
226D LEU* 3.0 37.5 + - + +
227D THR 3.9 4.0 - - - +
228D GLY 3.3 0.4 - - - -
229D ARG* 1.3 76.4 - - - +
231D GLN* 1.3 63.1 + - - +
232D GLU 3.5 0.3 + - - -
233D ALA* 3.5 13.1 + - - +
234D GLY 5.1 0.2 + - - -
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Residues in contact with GLN 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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110D ARG* 4.8 4.7 + - - -
202D GLY* 3.3 24.4 + - - +
203D LYS* 3.7 21.9 + - - +
205D ILE* 2.9 51.0 + - + +
207D PRO* 4.8 1.6 - - + -
227D THR* 3.1 36.7 + - + +
228D GLY* 3.3 11.0 + - - +
230D ILE* 1.3 77.5 - - - +
232D GLU* 1.3 68.9 + - + +
233D ALA 3.7 0.2 + - - -
234D GLY 4.9 1.7 + - - -
315D MET* 4.0 11.9 - - - -
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Residues in contact with GLU 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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202D GLY* 4.2 14.3 - - - -
228D GLY* 3.0 20.9 + - - +
229D ARG* 3.7 2.7 - - - +
231D GLN* 1.3 85.6 - - + +
233D ALA* 1.3 58.8 + - - +
234D GLY 3.2 2.7 - - - -
235D THR* 3.0 26.9 + - + +
236D GLU* 2.9 28.1 + - + +
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Residues in contact with ALA 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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70C HIS* 3.6 10.4 - - + -
176D ARG* 3.5 31.4 - - - +
180D PHE* 4.1 9.6 - - + -
229D ARG 3.0 17.4 + - - +
230D ILE 3.5 7.6 - - - +
231D GLN 3.4 2.0 - - - -
232D GLU* 1.3 77.3 - - - +
234D GLY* 1.3 61.2 + - - +
236D GLU* 3.4 11.6 - - - +
237D VAL* 3.2 27.5 + - - +
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Residues in contact with GLY 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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104D ARG* 3.4 7.0 - - - -
110D ARG* 3.9 9.7 - - - +
176D ARG* 3.5 23.1 - - - +
230D ILE 5.1 0.2 + - - -
231D GLN 4.9 0.4 + - - -
232D GLU 3.2 1.2 - - - -
233D ALA* 1.3 76.3 - - - +
235D THR* 1.3 58.8 + - - +
237D VAL* 3.4 4.5 + - - +
238D VAL* 3.0 30.7 + - - +
246D SER* 5.4 0.2 - - - -
247D ALA 5.4 0.2 + - - -
401D LMR 3.5 18.0 - - - +
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Residues in contact with THR 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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104D ARG* 3.1 28.7 + - - +
107D GLY* 5.6 6.5 - - - +
108D MET 4.7 1.7 + - - +
110D ARG* 5.0 0.9 + - - +
232D GLU* 3.0 28.6 + - + +
234D GLY* 1.3 71.9 - - - +
236D GLU* 1.3 58.3 + - - +
238D VAL* 3.2 7.0 + - + +
239D LYS* 2.8 61.9 + - + +
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Residues in contact with GLU 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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66C ALA* 5.3 7.2 - - + +
69C SER* 5.4 0.5 + - - -
70C HIS* 3.1 22.8 + - - +
180D PHE* 4.8 0.3 - - - -
229D ARG* 2.7 48.0 + - - +
232D GLU* 2.9 12.5 + - + +
233D ALA* 3.4 14.4 - - - +
235D THR* 1.3 77.4 - - - +
237D VAL* 1.3 56.8 + - + +
239D LYS* 3.6 7.0 + - - +
240D ALA* 3.0 27.8 + - + +
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Residues in contact with VAL 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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63C GLY 4.5 1.1 - - - +
66C ALA* 4.1 17.0 - - + +
67C ASP* 4.3 17.9 - - + +
70C HIS* 3.4 35.0 - - + +
176D ARG* 4.5 5.2 - - - +
233D ALA 3.2 4.9 + - - +
234D GLY 3.8 6.5 - - - +
235D THR 3.3 0.2 - - - -
236D GLU* 1.3 74.9 - - + +
238D VAL* 1.3 66.1 + - - +
240D ALA* 3.2 6.4 + - - +
241D LYS* 2.9 30.9 + - + +
246D SER 4.2 2.7 - - - -
247D ALA* 3.7 34.3 - - + +
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Residues in contact with VAL 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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104D ARG* 4.0 30.1 - - + +
105D LYS 3.6 7.0 - - - +
106D PRO* 3.4 39.4 - - + +
107D GLY 5.2 0.2 - - - +
234D GLY 3.0 22.5 + - - +
235D THR* 3.6 9.6 - - + +
237D VAL* 1.3 76.3 - - - +
239D LYS* 1.3 62.4 + - + +
241D LYS* 3.3 4.7 + - - +
242D ALA 3.1 16.8 + - - -
243D GLY 4.2 0.5 + - - -
245D GLY 3.9 10.4 - - - +
246D SER* 3.7 27.4 - - - -
401D LMR 4.4 0.7 - - - +
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Residues in contact with LYS 239 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106D PRO* 4.4 19.3 - - + -
107D GLY* 5.4 7.4 - - - +
235D THR* 2.8 42.8 + - + +
236D GLU* 3.8 6.7 - - - +
238D VAL* 1.3 73.2 - - - +
240D ALA* 1.3 57.9 + - - +
242D ALA* 3.0 22.5 + - - +
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Residues in contact with ALA 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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62C PRO* 4.5 9.7 - - + +
63C GLY* 3.6 18.0 + - - -
66C ALA* 4.0 24.9 - - + -
236D GLU* 3.0 19.0 + - + +
237D VAL 3.2 5.1 + - - +
239D LYS* 1.3 77.5 - - - +
241D LYS* 1.3 59.2 + - - +
242D ALA* 3.6 3.3 + - - +
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Residues in contact with LYS 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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38C GLN* 4.9 4.8 + - - +
60C HIS* 4.9 3.9 + - - +
63C GLY* 3.7 33.2 - - - +
64C VAL* 4.6 6.7 - - - +
67C ASP* 3.3 12.8 + - - -
237D VAL* 2.9 15.9 + - - +
238D VAL 3.8 0.7 - - - +
239D LYS 3.2 0.2 - - - -
240D ALA* 1.3 74.3 - - - +
242D ALA* 1.3 70.1 + - - +
243D GLY 3.3 0.9 - - - -
244D ALA* 3.0 35.9 + - + +
245D GLY 3.4 30.7 - - - +
246D SER 2.9 27.1 + - - +
248D THR* 2.9 26.7 + - - +
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Residues in contact with ALA 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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58B ILE* 5.0 13.3 - - + +
106D PRO* 4.3 7.4 - - - -
238D VAL 3.1 5.1 + - - -
239D LYS 3.0 18.0 + - - +
240D ALA 4.4 3.6 - - - +
241D LYS* 1.3 80.5 - - - +
243D GLY* 1.3 57.9 + - - +
244D ALA* 3.7 0.3 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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