Contacts of the helix formed by residues 219 - 247 (chain D) in PDB entry 2QW4
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 SER 219 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ALA* 5.9 4.4 - - - +
220D CYS* 1.3 64.8 + - - +
221D LEU* 3.3 19.1 - - - -
222D SER* 3.3 35.1 + - - -
223D ARG* 3.5 12.6 + - - +
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Residues in contact with CYS 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D VAL* 5.6 11.2 - - + -
219D SER* 1.3 71.4 - - - +
221D LEU* 1.3 51.7 + - - +
223D ARG* 2.7 39.1 + - - +
224D LEU* 2.6 38.7 + - + +
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Residues in contact with LEU 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 3.7 24.7 - - + -
62B PRO* 5.9 1.8 - - + -
204D LEU* 3.6 33.2 - - + -
205D LYS* 4.4 15.5 - - + -
208D VAL* 3.7 37.6 - - + +
219D SER* 3.7 11.4 - - - -
220D CYS* 1.3 76.0 - - - +
222D SER* 1.3 59.1 + - - +
224D LEU* 4.0 12.1 - - + -
225D LEU* 2.8 51.5 + - + +
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Residues in contact with SER 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PRO* 5.8 4.9 - - - +
219D SER* 3.3 30.8 + - - -
220D CYS 3.1 0.4 - - - -
221D LEU* 1.3 77.9 - - - +
223D ARG* 1.3 55.5 + - - +
225D LEU* 3.7 2.8 - - - +
226D GLY* 2.7 36.2 + - - -
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Residues in contact with ARG 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ALA 5.8 3.9 + - - -
165D LEU* 3.7 44.4 + - + +
219D SER 3.8 9.5 + - - +
220D CYS* 2.7 42.9 + - - +
222D SER* 1.3 76.6 - - - +
224D LEU* 1.3 58.3 + - - +
226D GLY* 4.1 1.6 - - - -
227D LYS* 3.7 20.4 + - - +
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Residues in contact with LEU 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D LEU* 5.0 3.8 - - + -
165D LEU* 4.0 9.4 - - + -
167D VAL* 3.8 32.5 - - + -
171D ALA* 4.3 23.1 - - + +
175D LEU* 3.7 38.1 - - + +
204D LEU* 4.8 5.8 - - + -
208D VAL* 5.1 4.3 - - + -
220D CYS* 2.6 19.9 + - + +
221D LEU* 3.9 22.9 - - + +
223D ARG* 1.3 73.0 - - - +
225D LEU* 1.3 65.3 + - + +
226D GLY 3.5 0.2 + - - -
227D LYS* 3.5 15.5 + - + +
228D LEU* 4.4 1.0 + - - +
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Residues in contact with LEU 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 3.8 35.7 - - + -
62B PRO* 4.1 25.1 - - + +
64B PHE* 3.6 27.1 - - + -
175D LEU* 4.4 18.4 - - + -
178D LEU* 4.7 5.6 - - + -
204D LEU* 4.5 9.6 - - + -
221D LEU* 2.8 38.6 + - + +
222D SER* 4.1 2.7 - - - +
224D LEU* 1.3 69.1 - - + +
226D GLY* 1.3 54.8 + - - +
227D LYS 3.0 2.7 - - - -
228D LEU* 2.8 41.6 + - + +
229D PRO* 3.6 3.5 - - - +
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Residues in contact with GLY 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PHE* 4.2 12.1 - - - +
222D SER 2.7 22.5 + - - -
223D ARG* 4.1 4.3 - - - -
224D LEU 3.3 0.4 - - - -
225D LEU* 1.3 71.5 - - - +
227D LYS* 1.3 57.8 + - - +
228D LEU 3.2 0.2 - - - -
229D PRO* 3.0 18.2 - - - +
230D GLU* 4.4 4.2 + - - +
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Residues in contact with LYS 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D LEU* 6.5 0.2 - - + -
158D PHE* 3.7 23.3 - - + -
161D SER* 2.4 44.6 + - - -
162D LEU* 4.1 13.9 - - + +
165D LEU* 3.8 31.3 - - + +
175D LEU* 5.9 3.1 - - + -
223D ARG* 3.7 15.0 + - - +
224D LEU* 3.5 11.4 + - + +
225D LEU 3.0 0.8 + - - -
226D GLY* 1.3 78.2 - - - +
228D LEU* 1.3 56.3 + - + +
230D GLU* 3.0 38.5 + - + +
231D LEU* 3.1 11.0 + - - +
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Residues in contact with LEU 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PHE* 3.7 30.7 - - + -
114D GLU* 5.7 3.1 - - - +
118D LEU* 5.3 0.9 - - + -
175D LEU* 4.0 27.8 - - + -
178D LEU* 5.5 8.1 - - + -
179D VAL* 3.5 32.8 - - + +
225D LEU* 2.8 23.3 + - + +
227D LYS* 1.3 77.2 - - + +
229D PRO* 1.3 59.3 - - + +
231D LEU* 3.3 20.1 - - + +
232D ARG* 3.1 25.5 + - - +
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Residues in contact with PRO 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PHE* 3.5 30.3 - - + +
65B GLY* 3.8 19.5 - - - +
225D LEU 3.6 5.4 - - - +
226D GLY 3.0 27.4 - - - +
228D LEU* 1.3 82.7 - - + +
230D GLU* 1.3 62.8 + - - +
232D ARG* 3.2 11.3 - - + +
233D THR* 3.0 23.6 + - - -
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Residues in contact with GLU 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D SER 5.1 1.4 - - - +
157D ALA* 5.1 2.3 - - - +
158D PHE* 3.6 34.0 + - + +
161D SER* 4.3 8.8 + - - -
226D GLY 4.4 2.6 + - - +
227D LYS* 3.0 28.1 + - - +
229D PRO* 1.3 74.9 - - - +
231D LEU* 1.3 65.0 + - - +
233D THR* 3.1 13.5 + - - +
234D LEU* 3.0 31.8 + - + +
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Residues in contact with LEU 231 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D GLU* 3.8 25.6 - - + +
117D ILE* 3.4 40.6 - - + -
118D LEU* 3.8 33.2 - - + +
158D PHE* 3.6 21.1 - - + -
179D VAL* 4.5 1.8 - - + -
227D LYS 3.1 9.9 + - - +
228D LEU* 3.3 31.6 - - + +
230D GLU* 1.3 75.4 - - - +
232D ARG* 1.3 62.6 + - - +
234D LEU* 2.9 22.1 + - - +
235D CYS* 3.3 10.8 - - - -
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Residues in contact with ARG 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D GLU* 3.1 42.5 + - - +
182D THR* 5.2 5.3 + - - +
184D ARG* 3.6 24.4 - - - +
228D LEU 3.1 11.3 + - - +
229D PRO* 3.2 17.0 - - + +
231D LEU* 1.3 80.2 - - - +
233D THR* 1.3 57.1 + - - -
235D CYS* 3.6 20.3 + - - +
236D THR* 4.0 7.8 + - - -
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Residues in contact with THR 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D PRO 3.0 15.1 + - - -
230D GLU* 3.1 12.6 + - - -
232D ARG* 1.3 72.7 - - - +
234D LEU* 1.3 66.5 + - - +
235D CYS 3.2 0.2 - - - -
236D THR* 3.4 19.9 + - + +
237D GLN* 3.8 11.7 + - + +
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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
----------------------------------------------------------
117D ILE* 3.9 26.7 - - + -
151D TRP* 3.1 22.2 + - - +
154D SER* 3.5 39.0 - - - +
155D ILE* 4.1 8.1 - - + +
158D PHE* 3.5 37.9 - - + -
230D GLU* 3.0 32.0 + - + +
231D LEU* 2.9 11.4 + - - +
233D THR* 1.3 76.5 - - - +
235D CYS* 1.3 63.5 + - - +
236D THR 3.2 0.7 + - - -
237D GLN* 3.2 14.4 + - - +
238D GLY 3.2 4.9 + - - -
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Residues in contact with CYS 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D LEU* 4.2 16.5 - - + +
114D GLU* 3.5 36.6 - - - -
117D ILE* 3.6 21.5 - - + -
231D LEU 3.3 17.5 - - - -
232D ARG* 3.7 13.2 - - - +
233D THR 3.2 0.8 - - - -
234D LEU* 1.3 75.0 - - - +
236D THR* 1.3 58.5 + - - +
238D GLY* 3.0 4.2 + - - +
239D LEU* 2.9 34.6 + - + +
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Residues in contact with THR 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D ARG 4.0 7.1 + - - -
233D THR* 3.4 15.1 + - + -
234D LEU 3.1 0.4 - - - -
235D CYS* 1.3 74.5 - - - +
237D GLN* 1.3 66.5 + - - +
238D GLY 3.0 1.1 - - - -
239D LEU* 3.0 19.0 + - + +
240D GLN* 2.9 40.0 + - + +
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Residues in contact with GLN 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D ASP* 4.4 3.5 - - - +
151D TRP* 3.3 35.1 + - + +
154D SER* 2.6 40.4 + - - -
233D THR* 3.8 11.1 + - + +
234D LEU* 3.4 13.8 - - - +
236D THR* 1.3 77.7 - - - +
238D GLY* 1.3 63.7 + - - +
240D GLN* 3.2 16.0 + - - +
241D ARG* 2.9 21.7 + - - +
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Residues in contact with GLY 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D LEU* 5.1 2.0 - - - -
151D TRP* 3.4 35.5 - - - -
234D LEU 3.2 3.6 + - - -
235D CYS 3.0 8.6 + - - -
236D THR 3.0 1.0 - - - -
237D GLN* 1.3 77.7 - - - +
239D LEU* 1.3 52.8 + - - +
241D ARG* 2.7 24.4 + - - +
242D ILE* 2.9 21.8 + - - +
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Residues in contact with LEU 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D LEU* 4.2 18.3 - - + +
235D CYS* 2.9 23.0 + - + +
236D THR* 3.0 20.8 + - + +
238D GLY* 1.3 69.6 - - - +
240D GLN* 1.3 58.6 + - + +
242D ILE* 3.1 10.0 + - + +
243D PHE* 2.8 31.4 + - - +
260D ILE 5.1 1.8 - - - +
261D PHE* 3.9 29.2 - - + +
264D THR* 3.6 33.9 - - + -
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Residues in contact with GLN 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236D THR* 2.9 39.5 + - + +
237D GLN* 3.3 17.4 - - - +
239D LEU* 1.3 72.4 - - + +
241D ARG* 1.3 57.0 + - - +
243D PHE* 3.9 7.7 - - - +
244D TYR* 3.4 23.0 + - - +
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Residues in contact with ARG 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D GLU* 3.8 16.2 + - - +
75D PHE* 4.5 7.9 - - + -
145D ALA 4.4 0.6 + - - -
146D ARG 3.3 19.2 + - - -
147D GLY 3.0 26.9 + - - +
148D PHE* 3.0 27.8 + - - +
149D GLY* 3.7 15.0 - - - +
151D TRP* 4.2 15.5 - - + -
237D GLN 2.9 9.8 + - - +
238D GLY 2.7 17.2 + - - +
240D GLN* 1.3 71.5 - - - +
242D ILE* 1.3 64.9 + - - +
243D PHE 3.3 0.2 - - - -
244D TYR* 3.6 27.8 + - - +
245D LEU* 3.1 40.3 + - + +
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Residues in contact with ILE 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D PHE* 4.3 22.4 - - + -
76D TYR* 4.7 12.6 - - + +
79D LEU* 5.9 3.8 - - + -
113D LEU* 4.5 20.2 - - + -
151D TRP* 5.4 1.3 - - + -
238D GLY* 2.9 34.0 + - - +
239D LEU* 3.1 8.0 + - + +
241D ARG* 1.3 76.6 - - - +
243D PHE* 1.3 63.2 + - - +
245D LEU* 3.1 9.0 + - - +
246D LYS* 3.0 35.4 + - + +
253D PRO* 5.6 2.5 - - + -
257D ILE* 5.0 17.9 - - + -
258D ASP* 5.8 0.4 - - - +
261D PHE* 3.7 32.3 - - + -
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Residues in contact with PHE 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239D LEU 2.8 20.7 + - - +
240D GLN* 4.0 7.6 - - - +
242D ILE* 1.3 72.4 - - - +
244D TYR* 1.3 66.1 + - + +
246D LYS* 3.0 24.3 + - + +
247D LEU* 3.0 47.0 + - + +
261D PHE* 3.9 26.2 - + + -
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Residues in contact with TYR 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D LYS* 4.2 7.1 - - - +
67D GLU* 2.9 24.9 + - - -
240D GLN 3.4 16.9 + - - +
241D ARG* 3.6 37.5 - - - +
243D PHE* 1.3 79.5 - - + +
245D LEU* 1.3 76.9 + - + +
247D LEU* 3.2 24.3 + - + +
248D GLU* 3.2 45.3 + - + +
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Residues in contact with LEU 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D GLU* 4.8 5.4 - - + +
72D VAL* 4.4 30.1 - - + +
75D PHE* 3.6 36.8 - - + -
76D TYR* 3.5 21.3 - - + +
147D GLY 4.3 9.4 - - - +
241D ARG* 3.1 36.5 + - - +
242D ILE* 3.1 7.1 + - - +
244D TYR* 1.3 95.6 - - + +
246D LYS* 1.3 57.6 + - - +
248D GLU* 2.9 24.2 + - + +
249D ASP* 3.2 10.9 + - - -
250D LEU* 4.8 1.1 + - + +
251D VAL 5.7 0.9 - - - +
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Residues in contact with LYS 246 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D TYR* 4.2 8.7 + - - +
242D ILE* 3.0 32.2 + - + +
243D PHE* 3.4 13.4 - - + +
245D LEU* 1.3 75.5 - - - +
247D LEU* 1.3 61.3 + - - +
249D ASP* 3.3 16.0 + - - +
253D PRO* 4.6 17.0 - - + -
258D ASP* 3.7 23.1 - - - +
261D PHE* 3.8 32.8 - - + -
262D MET* 5.1 5.6 - - - -
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Residues in contact with LEU 247 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D PHE* 3.0 50.6 + - + +
244D TYR* 3.3 19.3 - - + +
245D LEU 3.1 0.4 - - - -
246D LYS* 1.3 76.9 - - + +
248D GLU* 1.3 68.0 + - - +
249D ASP* 3.5 0.6 - - - +
----------------------------------------------------------
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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