Contacts of the helix formed by residues 239 - 261 (chain B) in PDB entry 5A86
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 LEU 239 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B PRO* 3.9 26.7 - - + -
209B LEU* 5.9 4.7 - - + -
210B LYS* 6.3 0.2 - - - -
211B VAL* 3.5 27.8 - - + +
213B LEU* 4.1 22.7 - - + -
225B TYR* 3.9 24.2 - - + -
227B PRO* 4.4 9.4 - - + -
236B ILE 5.0 1.8 + - - +
237B PHE 3.2 0.8 - - - -
238B SER* 1.3 79.5 + - - +
240B LEU* 1.3 60.5 + - + +
241B PRO* 3.5 1.8 - - - -
242B HIS* 3.3 14.6 + - + +
243B MET* 2.9 28.7 + - - +
1432B D7E 3.8 21.9 - - - -
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Residues in contact with LEU 240 (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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206B LEU* 4.9 13.7 - - + -
209B LEU* 5.0 7.0 - - + -
236B ILE 4.9 2.7 - - - +
237B PHE* 3.2 45.3 + - + +
239B LEU* 1.3 77.0 - - + +
241B PRO* 1.3 64.9 - - + +
243B MET* 3.1 19.3 + - - +
244B ALA* 2.8 30.5 + - - +
414B ILE* 3.6 23.8 - - + -
418B HIS* 4.2 6.7 - - + -
420B PHE* 3.7 38.9 - - + -
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Residues in contact with PRO 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ARG* 3.5 42.6 + - + +
174B LEU 6.1 1.8 - - - +
237B PHE 3.5 10.1 - - - +
238B SER 3.8 8.3 - - - +
239B LEU 3.6 2.9 - - - -
240B LEU* 1.3 93.4 - - + +
242B HIS* 1.3 61.0 + - - +
244B ALA* 3.2 5.9 + - + +
245B ASP* 3.1 27.4 + - - -
418B HIS* 5.8 4.0 - - - +
420B PHE* 5.1 7.9 - - + +
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Residues in contact with HIS 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B PHE* 4.2 9.2 - + - -
172B PHE* 3.6 31.3 - + - +
173B ARG* 2.8 31.7 + - - +
174B LEU* 3.7 12.7 - - + +
175B PRO* 4.8 1.1 - - + -
213B LEU* 3.6 18.4 - - + +
238B SER 5.3 0.4 + - - +
239B LEU* 3.3 16.9 + - + +
241B PRO* 1.3 77.8 - - - +
243B MET* 1.3 56.9 - - - +
245B ASP* 3.1 7.3 + - - +
246B MET* 2.9 26.4 + - + +
304B LEU* 4.4 2.9 - - + -
306B TYR* 2.7 33.6 + + - -
1432B D7E 3.4 24.5 - - - -
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Residues in contact with MET 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LEU* 5.1 2.9 - - - -
239B LEU 2.9 11.4 + - - +
240B LEU* 3.4 23.3 - - + +
242B HIS* 1.3 74.1 - - - +
244B ALA* 1.3 58.7 + - - +
246B MET* 3.3 2.2 + - - +
247B SER* 2.9 46.1 + - - +
407B HIS* 5.1 13.5 - - + +
411B LEU* 5.3 2.5 - - + -
420B PHE* 3.8 29.4 - - + -
425B MET* 4.7 8.7 - - + -
1432B D7E 3.2 76.9 - - + -
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Residues in contact with ALA 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ARG* 4.0 8.1 - - - +
240B LEU 2.8 12.7 + - - +
241B PRO 3.4 9.6 - - - +
243B MET* 1.3 77.5 - - - +
245B ASP* 1.3 54.1 + - - +
248B THR* 2.7 38.0 + - - -
420B PHE* 3.6 28.9 - - + +
422B THR* 4.0 4.3 - - + -
425B MET* 3.7 23.8 - - - +
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Residues in contact with ASP 245 (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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169B PHE* 3.5 5.9 - - + -
171B ASN 4.8 1.0 - - - +
172B PHE* 3.6 21.1 - - + -
173B ARG* 2.8 62.1 + - - +
241B PRO 3.1 7.2 + - - +
242B HIS 3.1 7.3 + - - +
244B ALA* 1.3 75.3 - - - +
246B MET* 1.3 59.7 + - - +
248B THR* 3.5 5.3 + - - -
249B TYR* 3.0 29.3 + - - +
422B THR* 4.1 6.1 - - - +
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Residues in contact with MET 246 (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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166B PHE* 3.6 39.9 - - + -
169B PHE* 3.6 27.3 - - + -
242B HIS* 2.9 16.8 + - - +
243B MET 3.8 4.9 - - - +
245B ASP* 1.3 75.3 - - - +
247B SER* 1.3 57.6 + - - +
249B TYR* 3.2 6.0 + - - +
250B MET* 3.0 32.5 + - - +
288B PHE* 4.0 17.7 - - + -
301B CYS* 4.1 8.1 - - + -
304B LEU* 4.5 1.3 - - + -
306B TYR* 3.4 39.9 - - + +
1432B D7E 4.4 15.9 - - + -
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Residues in contact with SER 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B MET* 2.9 32.9 + - - +
244B ALA 3.9 3.6 - - - -
246B MET* 1.3 76.6 - - - +
248B THR* 1.3 57.5 + - - +
250B MET* 3.2 7.4 + - - +
251B PHE* 2.8 56.8 + - - -
288B PHE* 5.8 4.0 - - - -
425B MET* 4.5 11.0 - - - -
1432B D7E 4.8 10.4 + - - +
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Residues in contact with THR 248 (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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244B ALA 2.7 23.0 + - - -
245B ASP* 3.8 5.8 - - - -
247B SER* 1.3 72.3 - - - +
249B TYR* 1.3 65.8 + - - +
251B PHE* 3.3 10.2 + - - +
252B LYS* 3.0 32.8 + - + +
422B THR* 2.7 32.9 + - + +
424B LEU* 4.1 21.8 - - + -
425B MET* 3.7 5.5 - - - +
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Residues in contact with TYR 249 (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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163B ASP* 2.6 38.8 + - + +
166B PHE* 4.2 20.4 - + - -
168B HIS* 3.4 28.3 - - + +
169B PHE* 3.6 39.3 - + + -
245B ASP 3.0 14.1 + - - +
246B MET* 3.4 9.4 - - - +
248B THR* 1.3 78.2 - - - +
250B MET* 1.3 70.8 + - - +
252B LYS* 3.4 13.7 + - + +
253B GLY* 3.3 16.5 + - - -
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Residues in contact with MET 250 (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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162B PHE* 4.6 7.0 - - + -
166B PHE* 3.6 31.9 - - + -
246B MET* 3.0 20.3 + - - +
247B SER* 3.5 9.4 - - - +
249B TYR* 1.3 81.1 - - - +
251B PHE* 1.3 57.2 + - - +
253B GLY* 3.1 4.8 + - - -
254B ILE* 3.0 30.8 + - - +
284B CYS* 3.6 26.0 - - + +
287B ARG* 3.7 39.8 + - + +
288B PHE* 3.4 35.0 - - + -
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Residues in contact with PHE 251 (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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247B SER* 2.8 42.8 + - - +
248B THR* 3.3 8.9 + - - +
250B MET* 1.3 73.0 - - - +
252B LYS* 1.3 58.6 + - - +
254B ILE* 3.1 5.8 + - - +
255B ILE* 2.9 35.4 + - + +
280B ALA* 3.5 26.2 - - + -
281B PHE* 4.0 7.4 - + + -
284B CYS* 2.9 33.2 - - + -
424B LEU* 4.3 7.0 - - + -
425B MET* 4.0 11.2 - - + -
428B LEU* 3.5 26.9 - - + -
429B PHE* 3.4 39.3 - + - -
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Residues in contact with LYS 252 (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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248B THR* 3.0 27.0 + - + +
249B TYR* 3.7 15.3 - - + +
250B MET 3.3 0.2 - - - -
251B PHE* 1.3 75.2 - - - +
253B GLY* 1.3 57.2 + - - +
255B ILE* 3.3 10.5 + - - +
256B SER* 3.0 32.6 + - - -
424B LEU* 3.9 16.8 - - + -
693D LEU* 4.7 24.8 - - + +
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Residues in contact with GLY 253 (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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161B THR* 3.7 17.0 - - - -
249B TYR 3.3 6.3 + - - -
250B MET* 3.1 8.0 + - - -
252B LYS* 1.3 79.5 - - - +
254B ILE* 1.3 55.6 + - - +
256B SER* 3.4 6.9 + - - -
257B PHE* 3.0 23.4 + - - +
287B ARG* 3.4 17.5 + - - -
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Residues in contact with ILE 254 (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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250B MET* 3.0 17.1 + - + +
251B PHE* 3.4 9.4 - - - +
253B GLY* 1.3 75.0 - - - +
255B ILE* 1.3 64.9 + - + +
257B PHE* 3.3 6.7 + - + +
258B ALA* 3.1 21.8 + - - +
276B LEU* 4.4 12.6 - - + -
280B ALA* 4.4 15.7 - - + +
283B LEU* 3.6 48.0 - - + -
284B CYS* 3.6 20.4 - - - +
287B ARG* 3.3 39.3 - - + +
348B LEU* 5.9 0.7 - - + -
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Residues in contact with ILE 255 (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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251B PHE* 2.9 21.9 + - + +
252B LYS* 3.6 8.1 - - - +
254B ILE* 1.3 75.0 - - + +
256B SER* 1.3 58.3 + - - +
258B ALA* 3.2 4.0 + - - +
259B LYS* 3.0 44.0 + - + +
276B LEU* 4.0 33.7 - - + -
280B ALA* 6.4 1.3 - - + -
424B LEU* 4.1 15.3 - - + -
428B LEU* 5.1 4.3 - - + -
690D LEU* 3.6 25.4 - - + -
693D LEU* 3.7 34.8 - - + -
694D LEU* 4.4 4.7 - - + -
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Residues in contact with SER 256 (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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161B THR* 3.5 21.6 - - - +
252B LYS 3.0 17.3 + - - -
253B GLY* 3.6 6.4 - - - -
254B ILE 3.3 0.2 - - - -
255B ILE* 1.3 72.2 - - - +
257B PHE* 1.3 66.1 + - - +
259B LYS* 3.3 17.1 + - - +
260B VAL* 3.2 26.3 + - - +
698D SER 4.7 4.9 - - - +
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Residues in contact with PHE 257 (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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154B LEU* 3.9 5.2 - - + -
157B ALA* 3.8 23.6 - - + -
158B GLN* 3.8 4.9 - - - -
161B THR* 3.4 18.8 - - - +
253B GLY 3.0 11.6 + - - +
254B ILE* 3.4 11.0 - - - +
255B ILE 3.2 0.2 - - - -
256B SER* 1.3 75.2 - - - +
258B ALA* 1.3 65.4 + - - +
260B VAL* 3.1 19.2 - - - +
261B ILE* 3.3 33.9 - - + +
283B LEU* 3.9 23.8 - - + -
287B ARG* 3.6 18.6 - - - +
341B VAL* 3.7 26.7 - - + -
344B GLN* 3.4 32.5 - - + -
345B ALA 4.8 1.1 - - - -
348B LEU* 4.6 7.2 - - + -
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Residues in contact with ALA 258 (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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254B ILE 3.1 9.7 + - - +
255B ILE 3.5 7.9 - - - +
257B PHE* 1.3 79.3 - - + +
259B LYS* 1.3 61.0 + - - +
261B ILE* 3.1 14.5 + - - +
264B PHE* 3.2 46.9 - - + +
276B LEU* 3.9 11.9 - - + -
348B LEU* 3.8 25.1 - - + -
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Residues in contact with LYS 259 (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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255B ILE* 3.0 31.0 + - + +
256B SER* 3.3 16.4 + - - +
258B ALA* 1.3 77.8 - - - +
260B VAL* 1.3 57.7 + - - +
264B PHE* 4.3 5.4 - - - -
265B ARG* 3.1 34.3 + - + +
693D LEU* 2.8 30.9 + - + +
694D LEU* 3.9 24.2 - - + +
696D GLU* 4.0 5.7 + - - +
697D GLY* 3.0 46.2 + - - +
698D SER 4.2 8.8 + - - +
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Residues in contact with VAL 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B GLU* 3.9 9.7 - - - +
157B ALA* 3.2 34.7 - - + +
160B LYS* 5.2 12.8 - - + -
161B THR* 4.4 8.7 - - + -
256B SER 3.2 10.1 + - - +
257B PHE* 3.1 18.8 - - - +
259B LYS* 1.3 75.0 - - - +
261B ILE* 1.3 60.7 + - - +
262B SER 3.5 3.1 + - - -
265B ARG* 4.1 10.3 + - - +
698D SER* 3.4 27.4 - - - +
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Residues in contact with ILE 261 (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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153B GLU* 3.8 11.7 - - - +
154B LEU* 3.9 18.8 - - + -
157B ALA* 4.2 11.4 - - + -
257B PHE* 3.3 48.9 - - + +
258B ALA* 3.1 7.5 + - - +
259B LYS 4.5 0.2 - - - -
260B VAL* 1.3 76.7 - - - +
262B SER* 1.3 57.9 + - - +
263B TYR* 3.7 28.3 - - + +
264B PHE* 2.9 26.9 + - + +
265B ARG* 3.0 13.8 + - - +
345B ALA* 5.5 1.3 - - + -
348B LEU* 4.3 15.0 - - + -
349B PHE* 4.3 10.8 - - + -
369B PHE* 5.0 0.2 - - + -
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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) + - + + + + + -
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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