Contacts of the helix formed by residues 218 - 239 (chain D) in PDB entry 5M8L
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 218 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217D GLY* 1.3 85.0 - - - +
219D ALA* 1.3 58.9 + - - +
220D PHE 3.1 2.7 + - - -
221D LEU 4.1 1.9 + - - -
222D THR* 4.2 1.2 - - - +
342D PHE* 3.6 20.7 - - + -
343D ASP* 3.3 23.8 - - + +
347D PHE* 3.8 16.8 - - + +
356D ARG* 4.0 7.1 - - + +
425D PHE* 3.5 30.2 - - + -
426D PRO* 3.8 25.1 - - + -
430D ALA* 4.4 0.9 - - + -
434D HIS* 3.6 27.8 - - + +
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Residues in contact with ALA 219 (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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213D PHE 4.5 5.2 - - - +
214D SER 4.4 0.4 - - - -
218D PRO* 1.3 78.9 - - - +
220D PHE* 1.3 58.0 + - - +
221D LEU 3.4 0.7 - - - -
222D THR* 3.5 9.6 - - - -
223D TRP* 2.8 34.7 + - + +
425D PHE* 3.9 1.5 - - - -
433D GLY 3.9 5.2 - - - +
434D HIS* 3.0 30.6 + - + +
440D MET* 5.5 0.4 - - + -
449D ASN* 3.3 28.9 - - - +
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Residues in contact with PHE 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D SER 3.1 25.3 + - - +
215D HIS* 3.9 9.2 - + - -
217D GLY 3.2 9.9 + - - +
218D PRO 3.1 2.0 - - - -
219D ALA* 1.3 77.5 - - - +
221D LEU* 1.3 93.8 + - + +
224D HIS* 3.0 50.2 + + + +
356D ARG* 4.0 3.6 - - - -
360D GLU* 3.5 52.9 - - + +
377D HIS* 3.6 45.8 - + - -
404D HIS* 3.9 6.3 - + - -
407D THR* 4.3 4.7 - - + -
434D HIS* 4.1 1.0 + - - -
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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
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218D PRO 4.1 2.2 + - - -
220D PHE* 1.3 106.4 - - + +
222D THR* 1.3 58.3 + - - +
224D HIS* 3.7 3.0 + - + +
225D ARG* 3.0 27.5 + - - +
342D PHE* 3.8 16.8 - - + -
355D PHE* 3.8 21.3 - - + -
356D ARG* 4.3 7.8 - - + +
359D VAL* 3.8 15.3 - - + -
407D THR* 3.8 21.8 - - + +
408D ASP* 4.4 2.1 - - - +
411D PHE* 3.6 50.6 - - + -
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Residues in contact with THR 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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218D PRO 4.2 0.4 + - - +
219D ALA* 3.3 16.2 - - - +
221D LEU* 1.3 78.0 - - - +
223D TRP* 1.3 65.7 + - - +
225D ARG* 3.5 7.6 + - - +
226D TYR 3.2 15.9 + - - -
342D PHE* 6.1 0.7 - - - -
411D PHE* 4.5 10.8 - - - -
425D PHE* 4.1 11.7 - - + -
440D MET* 3.4 9.0 - - - +
449D ASN* 2.9 61.3 + - + +
452D MET* 3.0 21.7 - - - +
453D PHE* 4.2 1.1 + - - -
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Residues in contact with TRP 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D THR 3.7 7.0 - - - -
192D HIS* 3.7 33.7 - + - -
195D SER* 3.5 17.3 - - - -
213D PHE 3.8 10.9 + - - -
214D SER* 3.4 26.1 - - - -
219D ALA* 2.8 23.2 + - + +
220D PHE 3.9 3.1 - - - +
222D THR* 1.3 77.1 - - - +
224D HIS* 1.3 72.2 + + - +
226D TYR* 3.3 3.3 + - - -
227D HIS* 3.0 55.6 + + - -
440D MET* 3.7 29.2 - - + -
441D VAL 2.8 28.8 + - - -
443D PHE* 3.5 24.9 - + - -
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Residues in contact with HIS 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192D HIS* 3.3 3.1 + + - -
214D SER 3.6 11.1 + - - -
215D HIS* 3.2 20.9 - + - -
220D PHE* 3.0 31.5 + + + +
221D LEU* 4.3 3.1 - - - +
223D TRP* 1.3 93.7 - + - +
225D ARG* 1.3 64.2 + - - +
227D HIS* 3.4 4.6 + - - +
228D LEU* 3.2 30.4 + - + +
400D PHE* 3.8 13.7 - + - -
404D HIS* 3.0 38.1 - + + +
408D ASP* 5.9 0.4 - - - -
518D ZN 1.8 37.9 - - - -
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Residues in contact with ARG 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D ARG* 5.5 0.7 + - - -
221D LEU 3.0 17.1 + - - +
222D THR* 3.6 6.1 - - - +
223D TRP 3.2 0.2 - - - -
224D HIS* 1.3 74.3 - - - +
226D TYR* 1.3 65.9 + - - +
228D LEU* 3.2 6.7 + - - +
229D LEU* 3.1 20.5 + - + +
408D ASP* 2.7 40.4 + - - +
411D PHE* 3.6 18.5 - - - -
412D ASP* 3.0 37.6 + - - +
415D LEU* 3.6 5.1 - - - +
452D MET* 3.0 41.1 + - - -
454D VAL 2.7 27.7 + - - -
456D ALA* 4.0 1.5 - - - +
460D LEU* 4.0 10.7 - - + +
462D TYR* 3.2 20.1 + - + +
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Residues in contact with TYR 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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115D PRO* 6.4 1.3 - - + -
222D THR 3.2 4.0 + - - -
223D TRP 3.3 4.2 + - - +
225D ARG* 1.3 79.6 - - - +
227D HIS* 1.3 62.3 + - - +
229D LEU* 3.1 13.3 + - + +
230D ARG* 2.9 48.1 + - + +
440D MET* 3.6 24.2 - - + -
443D PHE* 3.4 46.2 - + + -
444D TRP 4.0 15.8 + - - -
445D PRO* 4.9 3.6 + - - +
447D VAL* 3.9 23.8 - - + +
452D MET* 4.0 26.9 - - + -
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Residues in contact with HIS 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D PHE* 2.7 75.1 + + - -
191D THR* 3.4 18.0 + - - -
192D HIS* 4.0 10.5 - + + -
223D TRP* 3.0 42.0 + + + +
224D HIS* 3.4 13.8 + - - +
226D TYR* 1.3 76.3 - - - +
228D LEU* 1.3 61.6 + - - +
230D ARG* 3.5 4.5 + - + +
231D LEU 3.2 15.9 + - - -
395D PRO* 4.6 0.4 - - + -
400D PHE* 3.8 19.1 - + - -
443D PHE* 3.9 12.0 - + + -
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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
----------------------------------------------------------
130D ARG* 4.4 11.7 - - - +
188D PHE* 4.7 11.4 - - + -
224D HIS 3.2 17.1 + - - +
225D ARG* 3.6 6.1 - - - +
226D TYR 3.2 0.8 - - - -
227D HIS* 1.3 75.2 - - + +
229D LEU* 1.3 60.3 + - - +
231D LEU* 3.2 2.9 + - - -
232D GLU* 2.8 31.5 + - - +
246D LEU* 3.6 18.5 - - + +
400D PHE* 5.7 0.4 - - + -
401D VAL* 3.7 20.0 - - + +
404D HIS* 3.5 38.4 - - + +
405D THR* 3.7 25.8 - - + +
408D ASP* 4.1 12.6 - - + -
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Residues in contact with LEU 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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115D PRO* 3.9 30.5 - - + -
130D ARG* 4.0 2.8 - - - +
225D ARG* 3.1 13.6 + - + +
226D TYR* 3.6 17.5 - - + +
228D LEU* 1.3 75.7 - - - +
230D ARG* 1.3 56.2 + - - +
232D GLU* 3.8 16.6 - - - +
233D LYS* 3.0 29.6 + - - +
452D MET* 4.3 25.1 - - + -
460D LEU* 4.4 15.9 - - + +
462D TYR* 3.9 29.4 - - + -
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Residues in contact with ARG 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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156D HIS* 4.9 0.6 - - - -
158D LEU* 4.5 10.9 - - - +
159D PHE* 3.6 35.2 - - - -
187D TYR* 4.1 18.4 - - + +
226D TYR* 2.9 45.4 + - + +
227D HIS* 3.7 7.2 - - + +
229D LEU* 1.3 73.9 - - - +
231D LEU* 1.3 60.4 + - - +
233D LYS* 3.2 21.3 + - - +
234D ASP* 2.9 66.6 + - - +
237D GLU* 5.4 3.4 + - - -
443D PHE* 5.2 4.9 - - + -
444D TRP 3.8 10.6 + - - -
445D PRO* 5.0 4.4 - - - +
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Residues in contact with LEU 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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148D LEU* 5.1 0.9 - - + -
151D ALA* 5.1 0.2 - - + -
184D ILE* 4.3 16.2 - - + +
185D TYR* 4.3 20.4 - - + -
188D PHE* 3.5 45.5 - - + -
227D HIS 3.2 5.1 + - - +
228D LEU 3.7 5.8 - - - +
230D ARG* 1.3 79.4 - - - +
232D GLU* 1.3 62.5 + - - +
234D ASP* 3.3 6.4 + - - +
235D MET* 2.9 49.4 + - + +
246D LEU* 4.2 7.0 - - + -
401D VAL* 3.9 32.3 - - + -
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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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128D ILE* 3.6 21.1 - - - +
130D ARG* 2.8 36.0 + - - -
228D LEU 2.8 21.4 + - - +
229D LEU* 3.8 14.3 - - + +
231D LEU* 1.3 73.4 - - - +
233D LYS* 1.3 56.7 + - - +
235D MET* 3.3 4.4 + - - +
236D GLN* 2.9 46.3 + - - +
244D PHE* 3.9 8.0 - - + +
245D SER* 3.2 5.2 - - - -
246D LEU* 2.7 43.8 + - + +
462D TYR* 4.8 1.6 - - - +
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Residues in contact with LYS 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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112D THR* 2.9 34.9 + - - +
113D CYS* 4.5 10.1 + - - +
117D TRP 6.0 0.4 + - - -
229D LEU 3.0 17.9 + - - +
230D ARG* 3.2 24.4 + - - +
232D GLU* 1.3 73.1 - - - +
234D ASP* 1.3 67.4 + - - +
236D GLN* 3.3 20.8 + - + +
237D GLU* 3.1 49.3 + - + +
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Residues in contact with ASP 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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156D HIS* 2.8 33.9 + - - +
157D PRO* 6.4 0.2 - - + -
184D ILE* 3.9 24.9 - - + +
187D TYR* 4.4 4.0 - - - -
230D ARG* 2.9 56.9 + - - +
231D LEU* 3.7 6.6 - - - +
233D LYS* 1.3 75.5 - - - +
235D MET* 1.3 58.5 + - - +
237D GLU* 3.4 9.3 + - - +
238D MET* 2.9 29.7 + - - +
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Residues in contact with MET 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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144D PHE* 5.3 0.7 - - + -
147D ALA* 3.7 33.9 - - + +
148D LEU* 3.8 19.1 - - + +
151D ALA* 4.2 13.5 - - + -
184D ILE* 4.7 1.6 - - + -
231D LEU* 2.9 47.7 + - + +
232D GLU 3.9 1.3 - - - +
234D ASP* 1.3 76.2 - - - +
236D GLN* 1.3 65.4 - - - +
238D MET* 4.2 8.7 - - + -
239D LEU* 2.9 33.9 + - + +
244D PHE* 3.6 38.6 - - + -
246D LEU* 4.1 9.6 - - + -
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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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128D ILE* 3.5 20.2 - - - +
232D GLU* 2.9 28.6 + - - +
233D LYS* 3.3 22.4 + - + +
235D MET* 1.3 75.9 - - - +
237D GLU* 1.3 59.1 + - + +
240D GLN* 3.1 7.3 + - - -
241D GLU 2.9 48.0 + - - +
242D PRO* 3.5 19.4 + - + +
244D PHE* 2.9 33.4 + - + +
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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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112D THR* 4.4 5.0 + - - +
157D PRO* 5.7 6.4 - - + +
230D ARG* 5.4 3.0 + - - -
233D LYS* 3.1 53.6 + - + +
234D ASP* 3.9 8.5 - - - +
236D GLN* 1.3 76.3 - - + +
238D MET* 1.3 67.3 + - - +
240D GLN* 3.2 17.0 + - - +
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Residues in contact with MET 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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147D ALA 3.7 21.5 - - - +
150D MET* 3.7 36.8 - - + +
151D ALA* 3.5 33.0 - - + +
154D THR* 4.0 8.7 - - + +
184D ILE* 3.7 21.5 - - + -
234D ASP 2.9 18.3 + - - +
235D MET* 3.8 12.1 - - + +
237D GLU* 1.3 78.2 - - - +
239D LEU* 1.3 83.4 + - + +
240D GLN* 3.5 2.6 + - - +
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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
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203B VAL* 4.4 9.7 - - - +
143D HIS* 4.3 14.6 - - + +
147D ALA* 3.9 26.0 - - + -
150D MET* 4.4 11.7 - - - -
235D MET* 2.9 22.6 + - + +
238D MET* 1.3 89.9 - - + +
240D GLN* 1.3 68.5 + - - +
241D GLU* 3.1 21.4 + - + +
244D PHE* 3.5 42.2 - - + -
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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