Contacts of the helix formed by residues 218 - 240 (chain B) in PDB entry 5M8N
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B GLY* 1.3 82.5 - - - +
219B ALA* 1.3 60.6 + - - +
220B PHE 3.2 0.5 + - - -
221B LEU 3.7 7.3 + - - -
222B THR* 4.1 1.4 + - - -
342B PHE* 3.7 17.5 - - + -
343B ASP* 3.3 24.7 - - - +
347B PHE* 3.8 16.6 - - + +
356B ARG* 3.9 5.9 - - + +
425B PHE* 3.6 32.2 - - + -
426B PRO* 3.7 25.8 - - + -
430B ALA* 4.5 0.2 - - + -
434B HIS* 3.7 27.4 - - + +
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Residues in contact with ALA 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B PHE 4.1 9.0 - - - +
214B SER 4.6 0.2 - - - -
218B PRO* 1.3 76.7 - - - +
220B PHE* 1.3 58.7 + - - +
221B LEU 3.2 0.2 - - - -
222B THR* 2.8 11.8 + - - -
223B TRP* 2.7 37.7 + - + +
425B PHE* 3.8 3.2 - - - -
433B GLY 3.9 11.7 - - - +
434B HIS* 3.0 29.9 + - + +
440B MET* 5.5 0.7 - - + -
449B ASN* 3.1 20.2 - - - +
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Residues in contact with PHE 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B SER 3.2 27.9 + - - +
215B HIS* 3.9 7.2 - + - -
217B GLY 3.1 19.0 + - - +
219B ALA* 1.3 76.3 - - - +
221B LEU* 1.3 87.9 + - + +
224B HIS* 2.8 47.2 + + + +
356B ARG* 4.1 5.2 - - - -
360B GLU* 3.5 48.9 - - + +
377B HIS* 3.3 50.3 - + + -
404B HIS* 4.2 5.2 - + - -
407B THR* 4.4 5.2 - - + -
434B HIS* 4.0 1.6 + - - -
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Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B PRO 3.7 2.2 + - - -
219B ALA 2.9 1.4 + - - -
220B PHE* 1.3 104.3 - - + +
222B THR* 1.3 61.2 + - - +
224B HIS* 4.0 2.6 - - + +
225B ARG* 3.0 28.8 + - - +
342B PHE* 3.5 25.6 - - + -
355B PHE* 3.7 16.4 - - + -
356B ARG* 4.4 7.9 - - + -
359B VAL* 4.1 12.8 - - + -
407B THR* 4.0 17.7 - - + +
408B ASP* 4.8 1.0 - - - +
411B PHE* 3.5 54.6 - - + -
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Residues in contact with THR 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B PRO 4.4 0.9 + - - +
219B ALA* 2.8 17.5 + - - -
221B LEU* 1.3 71.8 - - + +
223B TRP* 1.3 62.6 + - - -
225B ARG* 3.2 3.6 + - - +
226B TYR 3.1 19.4 + - - -
342B PHE* 5.6 0.4 - - + -
411B PHE* 4.3 15.9 - - + -
425B PHE* 4.1 16.6 - - + -
440B MET* 3.6 5.9 - - - +
449B ASN* 2.7 50.6 + - - +
452B MET* 3.5 29.3 - - + +
453B PHE* 4.4 4.3 - - + +
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Residues in contact with TRP 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B THR 3.6 10.8 - - - -
192B HIS* 3.3 42.0 - + - -
195B SER* 3.5 19.2 - - - -
213B PHE 3.8 11.0 - - - +
214B SER* 3.3 30.7 - - - -
219B ALA* 2.7 22.6 + - + +
220B PHE 4.2 1.6 - - - +
222B THR* 1.3 74.5 + - - +
224B HIS* 1.3 68.9 + + - +
226B TYR 3.5 0.3 + - - -
227B HIS* 2.9 53.3 + + + -
440B MET* 3.6 29.1 - - + -
441B VAL 2.5 30.3 + - - -
442B PRO* 4.5 0.4 - - + -
443B PHE* 3.6 17.8 - + - -
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Residues in contact with HIS 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B HIS* 3.3 2.6 + - - -
214B SER 3.2 16.2 + - - -
215B HIS* 3.1 16.4 - + - -
220B PHE* 2.8 34.3 + + + +
221B LEU* 4.3 2.7 - - + +
223B TRP* 1.3 94.5 - + - +
225B ARG* 1.3 65.0 + - - +
227B HIS* 3.3 4.8 - - - +
228B LEU* 3.1 30.1 + - + +
400B PHE* 3.9 11.7 - + - -
404B HIS* 3.1 37.1 - + - +
407B THR* 6.5 0.2 - - + -
408B ASP* 6.1 0.2 - - - -
513B ZN 1.9 37.5 - - - -
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Residues in contact with ARG 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ARG* 5.3 0.3 + - - -
221B LEU 3.0 19.5 + - - +
222B THR* 3.4 6.5 - - - +
224B HIS* 1.3 77.4 - - - +
226B TYR* 1.3 56.4 + - - +
228B LEU* 3.4 6.6 + - - +
229B LEU* 3.0 24.8 + - + +
408B ASP* 2.7 37.6 + - - +
411B PHE* 3.5 15.1 - - - -
412B ASP* 2.9 45.7 + - - +
415B LEU* 3.8 1.8 - - - +
452B MET* 3.2 40.7 + - + -
454B VAL 2.8 27.3 + - - -
456B ALA* 3.8 2.4 - - - +
460B LEU* 3.5 12.7 - - - +
462B TYR* 3.2 17.8 + - + +
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Residues in contact with TYR 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B PRO* 6.2 2.2 - - + -
222B THR 3.1 7.5 + - - +
225B ARG* 1.3 73.8 - - - +
227B HIS* 1.3 66.3 + - - +
229B LEU* 3.9 16.4 - - + -
230B ARG* 2.9 45.4 + - + +
440B MET* 3.7 15.5 - - + -
443B PHE* 3.5 44.6 - + + -
444B TRP 4.0 16.0 + - - -
445B PRO* 4.7 5.0 + - - +
447B VAL* 3.9 25.0 - - + +
452B MET* 3.5 30.7 - - + -
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Residues in contact with HIS 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B PHE* 2.5 72.3 + + - -
191B THR* 3.1 18.1 + - - -
192B HIS* 3.9 14.5 - + + +
223B TRP* 2.9 39.5 + + + +
224B HIS* 3.3 12.4 - - - +
226B TYR* 1.3 78.5 - - - +
228B LEU* 1.3 61.9 + - - +
230B ARG* 3.6 4.0 + - + +
231B LEU* 3.2 19.6 + - - +
395B PRO* 4.4 0.7 - - + -
400B PHE* 3.7 17.4 - + - -
443B PHE* 3.6 12.4 - + - -
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Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ARG* 4.2 10.5 - - - +
188B PHE* 4.2 20.4 - - + -
224B HIS 3.1 17.7 + - - +
225B ARG 3.7 5.8 - - - +
227B HIS* 1.3 76.1 - - + +
229B LEU* 1.3 61.2 + - - +
231B LEU* 3.2 2.5 + - - +
232B GLU* 2.8 31.2 + - - +
246B LEU* 3.6 23.9 - - + +
401B VAL* 3.9 22.7 - - + +
404B HIS* 3.3 42.2 - - + +
405B THR* 3.6 8.3 - - + +
408B ASP* 4.2 10.8 - - + -
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Residues in contact with LEU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B PRO* 4.2 26.2 - - + -
130B ARG* 3.7 11.2 - - - +
225B ARG 3.0 13.6 + - - +
226B TYR* 3.1 18.8 + - + +
228B LEU* 1.3 75.4 - - - +
230B ARG* 1.3 58.7 + - - +
232B GLU* 3.3 9.0 + - - +
233B LYS* 2.9 30.9 + - - +
452B MET* 3.6 28.9 - - + -
460B LEU* 4.3 14.1 - - + +
462B TYR* 3.6 33.0 - - + -
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Residues in contact with ARG 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B LEU* 4.6 7.6 - - - +
159B PHE* 3.7 35.5 - - - -
187B TYR* 3.9 18.6 - - + +
188B PHE* 6.4 0.7 - - + -
226B TYR* 2.9 42.4 + - + +
227B HIS* 3.9 4.7 - - + +
229B LEU* 1.3 78.2 - - - +
231B LEU* 1.3 60.2 + - - +
233B LYS* 3.1 35.3 - - - +
234B ASP* 2.9 62.3 + - - +
237B GLU* 4.4 3.2 + - - -
443B PHE* 5.1 6.5 - - + -
444B TRP 4.4 7.3 + - - -
445B PRO* 5.7 2.0 - - - +
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Residues in contact with LEU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 5.0 0.9 - - + -
151B ALA* 5.2 0.2 - - + -
184B ILE* 4.2 16.6 - - + +
185B TYR* 4.3 17.9 - - + -
188B PHE* 3.6 39.7 - - + -
227B HIS 3.2 7.3 + - - +
228B LEU 3.2 6.2 + - - +
230B ARG* 1.3 75.6 - - - +
232B GLU* 1.3 59.5 + - - +
234B ASP* 3.2 7.3 + - - +
235B MET* 2.9 56.5 + - + +
246B LEU* 4.3 10.8 - - + -
401B VAL* 3.8 38.8 - - + -
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Residues in contact with GLU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ILE* 3.5 19.7 - - - +
130B ARG* 2.7 43.7 + - - -
228B LEU 2.8 16.1 + - - +
229B LEU* 3.5 12.4 - - - +
231B LEU* 1.3 76.7 - - - +
233B LYS* 1.3 58.2 + - - +
235B MET* 3.1 3.3 + - - +
236B GLN* 2.8 48.9 + - - +
244B PHE* 3.9 8.4 - - + +
245B SER* 3.3 5.4 - - - -
246B LEU* 2.9 38.1 + - + +
462B TYR* 4.8 1.4 - - - -
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Residues in contact with LYS 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B THR* 2.5 46.4 + - - +
113B CYS* 4.2 7.4 + - - +
118B ARG* 5.6 5.9 - - - +
229B LEU 2.9 17.5 + - - +
230B ARG* 3.1 29.2 - - - +
232B GLU* 1.3 72.0 - - - +
234B ASP* 1.3 66.8 + - - +
236B GLN* 3.2 21.4 + - + +
237B GLU* 3.1 51.2 + - + +
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Residues in contact with ASP 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B HIS* 2.9 34.2 + - - +
157B PRO* 6.0 0.6 - - + +
184B ILE* 3.8 26.6 - - + +
187B TYR* 4.2 4.0 - - - -
230B ARG* 2.9 55.0 + - - +
231B LEU* 3.6 5.6 - - - +
233B LYS* 1.3 76.0 - - - +
235B MET* 1.3 59.7 + - - +
237B GLU* 3.4 11.5 + - - +
238B MET* 3.0 27.9 + - - +
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Residues in contact with MET 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B PHE* 4.9 1.6 - - + -
147B ALA* 3.6 37.2 - - + +
148B LEU* 3.7 22.0 - - + +
151B ALA* 4.4 12.8 - - + -
184B ILE* 4.5 2.5 - - + -
231B LEU* 2.9 46.3 + - + +
232B GLU 3.8 0.7 - - - +
233B LYS 3.1 0.2 - - - -
234B ASP* 1.3 74.8 - - - +
236B GLN* 1.3 67.7 + - - +
238B MET* 4.2 8.5 - - + -
239B LEU* 3.0 31.6 + - + +
244B PHE* 3.3 40.8 - - + -
246B LEU* 4.2 5.4 - - - -
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Residues in contact with GLN 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ARG* 4.0 17.9 + - - +
128B ILE* 3.9 11.3 - - - +
232B GLU* 2.8 31.2 + - - +
233B LYS* 3.2 26.0 + - - +
235B MET* 1.3 77.9 - - - +
237B GLU* 1.3 58.6 + - + +
240B GLN* 2.8 24.9 + - - -
241B GLU 3.0 24.5 + - - +
242B PRO* 3.1 24.8 + - - +
244B PHE* 2.9 28.5 + - + +
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Residues in contact with GLU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B THR* 5.0 2.9 + - - -
118B ARG* 5.9 2.9 - - - +
156B HIS* 6.1 0.3 - - - -
157B PRO* 5.5 8.4 - - + +
230B ARG* 4.4 2.4 + - - -
233B LYS* 3.1 47.2 + - + +
234B ASP* 3.9 17.5 - - - +
236B GLN* 1.3 76.7 - - + +
238B MET* 1.3 64.4 + - - +
240B GLN* 3.2 22.5 + - - +
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Residues in contact with MET 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ALA* 3.5 23.8 - - - +
150B MET* 3.9 29.9 - - + +
151B ALA* 3.7 30.7 - - + -
154B THR* 4.3 11.2 - - + -
184B ILE* 3.9 21.3 - - + -
234B ASP 3.0 17.9 + - - +
235B MET* 3.9 11.4 - - + +
237B GLU* 1.3 78.1 - - - +
239B LEU* 1.3 84.0 + - + +
240B GLN* 3.4 5.7 + - - +
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Residues in contact with LEU 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B HIS* 4.1 18.2 - - + +
147B ALA* 3.9 13.2 - - + -
150B MET* 4.2 20.9 - - + -
235B MET* 3.0 19.5 + - + +
238B MET* 1.3 89.6 - - + +
240B GLN* 1.3 69.9 + - - +
241B GLU* 3.1 20.9 + - + +
244B PHE* 3.6 40.8 - - + -
203C VAL* 3.8 13.9 - - - +
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Residues in contact with GLN 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B GLN 2.8 8.6 + - - -
237B GLU* 3.2 17.0 + - - +
238B MET 4.2 4.5 - - - +
239B LEU* 1.3 78.7 - - - +
241B GLU* 1.3 51.4 + - - +
242B PRO* 3.8 4.0 - - - -
84C ARG* 6.0 1.0 - - - +
165C ARG* 2.9 28.6 + - - -
167C GLU* 2.9 29.8 + - - +
168C GLU* 4.8 11.8 - - - +
200C PHE* 4.9 5.6 - - + -
202C GLY* 3.2 8.1 - - - -
203C VAL* 2.7 37.6 + - + +
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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