Contacts of the helix formed by residues 232 - 258 (chain B) in PDB entry 3AFF
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 232 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B LYS 3.5 2.2 - - - +
231B MET* 1.3 87.9 - - + +
233B TRP* 1.3 64.9 + - - +
234B GLY* 4.1 7.2 - - - +
235B THR* 3.0 7.9 + - - +
236B MET* 2.9 24.3 + - - +
304B GLU* 3.3 28.5 - - - +
314B ILE* 3.7 19.7 - - + -
319B ARG* 3.7 37.0 - - + +
392B THR 6.2 0.2 - - - +
394B VAL 4.9 0.7 - - - +
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Residues in contact with TRP 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TRP* 3.8 22.1 - + - -
95B HIS* 3.7 32.5 - + + -
120B TYR* 3.7 30.1 - + - -
210B TYR* 3.8 27.2 - + - -
213B MET* 3.5 35.5 - - + +
214B ASN* 3.7 16.3 + - - +
231B MET 3.5 3.0 + - - -
232B PRO* 1.3 71.1 - - - +
234B GLY* 1.3 60.8 + - - +
236B MET* 4.4 1.1 - - - +
237B HIS* 2.9 65.1 + + + +
374B GLU* 2.7 30.7 + - - -
393B MET* 3.8 22.8 - - + +
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Residues in contact with GLY 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ASN* 5.3 0.6 + - - -
232B PRO* 3.2 3.4 - - - +
233B TRP* 1.3 80.9 - - - +
235B THR* 1.3 58.1 + - - +
238B PRO* 3.0 22.6 - - - +
319B ARG 5.6 0.6 - - - +
322B ALA* 5.9 0.2 - - - +
323B ARG* 3.5 20.1 + - - +
326B GLN* 5.0 0.3 - - - +
392B THR 5.4 1.6 + - - -
393B MET* 3.4 25.8 + - - +
394B VAL 3.5 15.3 + - - -
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Residues in contact with THR 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B MET* 4.9 2.7 - - + -
232B PRO* 3.0 14.2 + - - +
234B GLY* 1.3 77.7 - - - +
236B MET* 1.4 66.0 + - - +
237B HIS 3.3 1.6 - - - -
238B PRO* 3.6 2.5 - - - +
239B THR* 2.7 40.9 + - - +
300B ASN* 5.3 0.9 - - + -
301B VAL* 4.4 18.6 - - + +
304B GLU* 2.7 43.2 + - - +
319B ARG* 4.5 5.0 + - - +
322B ALA* 3.9 20.1 - - + +
326B GLN* 4.8 2.0 - - - +
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Residues in contact with MET 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 5.6 2.5 - - + -
65B PRO* 4.2 9.4 - - - -
69B PHE* 4.0 25.0 - - + -
91B VAL* 4.0 22.7 - - + -
94B TRP* 3.9 36.8 - - + -
228B VAL* 5.3 0.4 - - - -
231B MET* 3.0 52.3 - - + -
232B PRO 2.9 18.8 + - - +
233B TRP 4.3 0.9 - - - +
235B THR* 1.4 75.0 - - - +
237B HIS* 1.3 57.9 + - - +
239B THR* 4.0 0.7 - - - -
240B THR* 2.7 33.9 + - - -
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Residues in contact with HIS 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B VAL* 6.3 0.2 - - - -
120B TYR* 3.6 37.1 - + + +
233B TRP* 2.9 43.8 + + + +
236B MET* 1.3 77.9 - - - +
238B PRO* 1.4 66.4 - - + +
240B THR* 3.2 22.5 + - - +
241B ILE* 4.0 7.0 + - + +
372B ASP* 4.2 16.8 + - - -
374B GLU* 3.2 37.8 + - + +
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Residues in contact with PRO 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B TRP 3.8 0.2 - - - +
234B GLY* 3.0 30.5 - - - +
235B THR 3.6 2.7 - - - +
237B HIS* 1.4 98.1 - - + +
239B THR* 1.3 56.1 + - - +
241B ILE* 3.0 24.1 + - + +
242B SER* 3.0 13.7 + - - +
323B ARG* 3.6 22.9 - - - +
326B GLN* 3.6 32.5 - - + +
372B ASP* 5.4 4.7 - - - +
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Residues in contact with THR 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PHE* 3.6 39.4 - - + -
235B THR* 2.7 34.1 + - - +
238B PRO* 1.3 77.7 - - - +
240B THR* 1.4 57.3 + - - +
242B SER* 4.1 1.1 - - - -
243B ALA* 3.0 33.1 + - + +
297B LEU* 4.2 21.1 + - + +
298B ILE* 5.5 0.9 - - + -
301B VAL* 4.0 11.3 - - + +
326B GLN* 3.0 20.7 + - - +
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Residues in contact with THR 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PHE* 3.8 5.6 - - - -
87B SER* 2.8 48.3 + - - +
88B ILE* 3.6 24.9 - - + +
91B VAL* 3.6 26.6 - - + +
236B MET 2.7 21.3 + - - -
237B HIS* 3.2 16.3 + - - +
239B THR* 1.4 75.9 - - - +
241B ILE* 1.3 59.3 + - + +
244B PRO* 3.1 14.6 - - - +
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Residues in contact with ILE 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B TRP* 3.6 31.5 - - + -
88B ILE* 3.6 34.5 - - + -
237B HIS* 4.8 5.8 - - + +
238B PRO* 3.0 11.0 + - + +
240B THR* 1.3 85.8 - - + +
242B SER* 1.3 68.9 + - - +
243B ALA 3.3 0.8 + - - -
244B PRO* 3.4 5.6 - - - +
245B ILE* 3.2 37.4 + - + +
368B HIS* 4.0 14.4 - - + +
369B ALA* 4.0 24.0 - - + -
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Residues in contact with SER 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B PRO* 3.0 7.8 + - - +
239B THR 4.1 1.3 - - - -
241B ILE* 1.3 79.5 - - - +
243B ALA* 1.3 57.2 + - - +
245B ILE* 3.2 3.4 + - - +
246B VAL* 2.9 34.0 + - - +
297B LEU* 3.6 15.9 - - - -
326B GLN* 2.6 39.5 + - - +
330B THR* 3.6 26.4 - - - +
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Residues in contact with ALA 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PHE* 4.1 15.9 - - + -
72B THR* 3.6 16.8 - - - +
73B ARG* 4.3 2.9 - - - -
239B THR* 3.0 20.1 + - + +
242B SER* 1.3 78.1 - - - +
244B PRO* 1.3 70.7 - - + +
245B ILE 3.2 0.2 + - - -
246B VAL* 3.3 2.6 + - - +
247B GLY* 3.0 17.8 + - - -
294B TRP* 3.9 21.8 - - + -
297B LEU* 3.7 12.7 - - + +
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Residues in contact with PRO 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B THR* 3.9 11.2 - - - +
76B ALA* 3.1 20.9 - - + +
83B GLY 3.8 27.4 - - - +
84B TRP* 4.0 14.8 - - + +
87B SER* 4.0 2.7 - - - +
240B THR 3.1 27.8 - - - +
241B ILE* 3.4 10.1 - - - +
243B ALA* 1.3 90.7 - - + +
245B ILE* 1.3 55.1 + - - +
248B MET* 2.8 39.4 + - + +
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Residues in contact with ILE 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B TRP* 4.1 11.4 - - + -
241B ILE* 3.2 31.8 + - + +
242B SER 3.2 7.0 + - - +
244B PRO* 1.3 72.5 - - - +
246B VAL* 1.3 67.2 + - - +
248B MET* 3.1 22.8 + - + +
249B ALA* 3.4 9.0 + - - +
330B THR* 4.0 24.2 - - + +
333B SER* 4.7 2.4 - - - -
334B ILE* 3.7 31.2 - - + -
337B ILE* 4.8 0.2 - - - +
362B ALA* 4.3 9.1 - - + +
365B GLY* 3.7 33.2 - - - +
366B ARG* 3.9 5.6 - - - +
369B ALA* 4.9 2.2 - - + -
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Residues in contact with VAL 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B SER 2.9 17.1 + - - +
243B ALA 3.8 4.0 - - - +
245B ILE* 1.3 73.7 - - - +
247B GLY* 1.3 56.8 + - - +
249B ALA* 2.9 27.4 + - - +
250B TYR* 3.4 20.5 + - + -
290B ILE* 4.2 4.9 - - + +
293B ALA* 4.8 1.8 - - + -
294B TRP* 3.9 37.2 - - + +
297B LEU* 4.2 13.7 - - + -
329B ALA* 4.3 16.8 - - + +
330B THR* 4.6 3.8 - - + -
333B SER* 3.5 26.0 - - - +
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Residues in contact with GLY 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ARG* 3.6 32.4 - - - +
76B ALA* 3.9 1.1 - - - -
77B SER* 3.1 17.2 - - - -
243B ALA 3.0 12.6 + - - -
244B PRO 3.2 4.7 + - - -
246B VAL* 1.3 75.1 - - - +
248B MET* 1.3 61.7 + - - +
250B TYR* 3.1 15.0 + - - +
251B GLY 3.1 8.8 + - - -
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Residues in contact with MET 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ALA* 3.9 5.4 - - + +
80B GLY* 3.5 38.6 - - - +
84B TRP* 4.1 15.0 - - + -
187B LEU* 3.7 16.6 - - + -
244B PRO* 2.8 33.3 + - + +
245B ILE* 3.1 12.1 + - + +
247B GLY* 1.3 72.7 - - - +
249B ALA* 1.3 56.7 + - - +
251B GLY 3.1 0.9 + - - -
252B ALA* 2.9 26.9 + - - +
337B ILE* 4.0 2.4 - - - +
358B PHE* 3.3 23.4 - - + +
361B ASP* 3.6 11.9 - - - +
362B ALA* 3.5 39.0 - - + -
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Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ILE 3.4 2.6 + - - +
246B VAL 2.9 14.5 + - - +
248B MET* 1.3 74.1 - - - +
250B TYR* 1.3 58.0 + - - +
251B GLY 3.1 1.8 - - - -
252B ALA* 3.4 2.3 + - - +
253B TYR* 3.0 22.5 + - - +
290B ILE* 3.4 31.1 - - + +
333B SER* 3.7 22.2 - - - +
337B ILE* 3.5 26.8 - - + +
340B LEU* 4.6 0.3 - - - +
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Residues in contact with TYR 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ARG* 3.3 40.3 - - - +
77B SER* 3.9 14.5 - - - -
246B VAL* 3.4 24.7 + - + -
247B GLY* 3.1 14.4 + - - +
249B ALA* 1.3 76.2 - - - +
251B GLY* 1.3 60.0 + - - +
253B TYR* 3.9 7.8 - + + +
254B ALA* 3.2 23.2 + - - +
287B ALA 5.7 1.3 - - - -
290B ILE* 3.5 24.0 - - + +
291B ASP* 3.7 22.7 + - - -
294B TRP* 3.4 23.9 - - + +
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Residues in contact with GLY 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B SER* 3.1 26.5 - - - -
247B GLY 3.1 6.3 + - - -
248B MET 3.1 7.0 + - - -
249B ALA 3.1 0.6 - - - -
250B TYR* 1.3 75.8 - - - +
252B ALA* 1.3 60.4 - - - +
254B ALA* 3.3 3.4 + - - +
255B ALA* 2.9 30.7 + - - +
358B PHE* 3.6 16.9 - - - -
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Residues in contact with ALA 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B MET 2.9 14.8 + - - +
249B ALA 3.7 5.2 - - - +
251B GLY* 1.3 74.9 - - - +
253B TYR* 1.3 63.5 + - - +
255B ALA* 3.5 2.1 + - - -
256B HIS* 3.1 10.6 + - - +
337B ILE* 3.9 31.2 - - + -
340B LEU* 4.2 7.2 - - + -
355B ILE* 3.0 36.7 - - + +
358B PHE* 3.8 14.2 - - + -
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Residues in contact with TYR 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ALA 3.0 17.2 + - - +
250B TYR* 3.9 8.1 - + - +
251B GLY 3.2 0.2 - - - -
252B ALA* 1.3 78.9 - - - +
254B ALA* 1.3 60.1 + - + +
256B HIS* 3.1 9.3 + + - +
257B VAL* 3.1 45.7 + - + +
284B ALA 5.8 2.5 - - - -
286B ALA* 4.4 2.9 - - + -
287B ALA* 3.4 45.0 - - + +
290B ILE* 4.3 5.4 - - + -
340B LEU* 3.7 32.9 - - + +
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Residues in contact with ALA 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B SER 5.7 1.3 - - - +
250B TYR 3.2 17.9 + - - +
251B GLY* 3.3 4.9 + - - +
253B TYR* 1.3 76.4 - - + +
255B ALA* 1.3 60.5 + - - +
256B HIS 3.1 1.1 - - - -
257B VAL* 3.8 6.5 - - - +
258B GLU* 2.9 33.6 + - - +
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Residues in contact with ALA 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B GLY 2.9 17.3 + - - +
252B ALA* 3.5 7.0 - - - +
254B ALA* 1.3 77.8 - - - +
256B HIS* 1.3 56.1 + - - +
258B GLU* 3.2 23.1 - - - +
259B HIS* 3.8 7.4 - - - +
344B SER* 5.9 0.7 - - - -
354B PRO* 4.1 16.2 - - + -
355B ILE* 4.0 32.4 - - + +
358B PHE* 4.7 2.5 - - + -
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Residues in contact with HIS 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ALA 3.1 13.2 + - - +
253B TYR* 3.5 14.1 - + - +
254B ALA 3.1 0.6 - - - -
255B ALA* 1.3 77.8 - - - +
257B VAL* 1.3 74.0 + - + +
259B HIS* 4.0 14.4 - - - +
340B LEU* 3.7 30.2 + - + +
343B ALA* 3.1 27.3 + - + -
344B SER* 3.2 29.8 + - - +
355B ILE* 4.3 3.8 - - + -
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Residues in contact with VAL 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B TYR* 3.1 42.1 + - + +
254B ALA* 3.8 8.1 - - - +
256B HIS* 1.3 82.2 - - + +
258B GLU* 1.3 53.2 + - - +
259B HIS 2.8 22.0 + - - +
----------------------------------------------------------
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Residues in contact with GLU 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ALA 2.9 19.8 + - - +
255B ALA* 3.2 11.9 - - - +
257B VAL* 1.3 69.4 - - - +
259B HIS* 1.3 65.6 + - - +
----------------------------------------------------------
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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