Contacts of the helix formed by residues 233 - 256 (chain B) in PDB entry 3A0B
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 ASN 233 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ILE* 6.1 1.8 - - - +
135B LEU* 4.5 0.9 - - - -
230B ARG* 3.2 28.6 - - + +
231B MET 2.9 2.6 - - - -
232B GLY 1.3 80.1 - - - +
234B ILE* 1.3 63.8 + - - +
235B GLU* 2.5 45.2 + - + +
236B THR* 2.7 28.0 + - - +
472B ARG 4.6 4.7 - - - +
473B THR* 4.7 3.2 - - + +
476B ARG* 5.0 7.9 - - - +
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Residues in contact with ILE 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ILE* 2.9 36.3 - - + +
19B LEU* 6.2 3.4 - - + -
133B LEU* 5.7 5.4 - - + -
135B LEU* 4.6 6.2 - - + +
138B MET* 5.1 11.7 - - + -
232B GLY 3.8 4.2 + - - -
233B ASN* 1.3 76.2 - - - +
235B GLU* 1.3 62.0 + - + +
236B THR 3.4 0.4 - - - -
237B VAL* 2.8 47.5 - - + +
238B LEU* 3.6 5.0 + - - +
1018B CLA 3.7 23.6 - - + -
1020B CLA 4.1 31.3 - - + +
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Residues in contact with GLU 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ILE* 4.8 5.1 - - + +
233B ASN* 2.5 30.1 + - - +
234B ILE* 1.3 79.3 - - + +
236B THR* 1.3 59.9 + - - +
238B LEU* 3.0 19.4 + - - +
239B SER* 3.6 5.9 + - - -
469B HIS* 3.2 19.2 - - - +
472B ARG* 2.7 57.8 + - - +
473B THR* 3.2 31.0 + - - +
1020B CLA 4.2 17.2 - - - +
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Residues in contact with THR 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 4.5 4.0 - - + -
229B LEU* 2.9 23.8 - - + +
230B ARG 4.5 0.7 - - - -
231B MET* 3.4 31.9 - - + -
233B ASN 2.7 23.7 + - - +
235B GLU* 1.3 75.3 - - - +
237B VAL* 1.3 60.2 + - + +
239B SER 3.4 0.7 + - - -
240B SER* 2.4 43.2 + - - +
473B THR* 3.4 24.9 - - - +
1016B CLA 3.4 10.0 - - - +
1018B CLA 4.6 3.4 - - + -
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Residues in contact with VAL 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 4.7 5.2 - - + -
234B ILE* 2.8 54.1 - - + +
236B THR* 1.3 80.5 - - + +
238B LEU* 1.3 59.6 + - - +
239B SER 3.3 0.4 - - - -
240B SER* 3.9 7.4 - - - -
241B SER* 3.0 21.9 + - - +
1018B CLA 3.3 60.1 - - + +
1020B CLA 3.3 16.7 - - + +
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Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B ILE 4.2 4.3 - - - +
235B GLU* 3.0 15.1 + - - +
237B VAL* 1.3 79.2 - - - +
239B SER* 1.3 53.3 + - - +
241B SER* 4.9 0.4 - - - -
242B ILE* 2.8 41.7 + - + +
469B HIS* 3.2 34.8 - - + +
1019B CLA 3.7 42.6 - - + -
1020B CLA 3.4 61.7 - - + +
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Residues in contact with SER 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B GLU 3.6 1.9 + - - -
236B THR 3.4 1.2 + - - -
238B LEU* 1.3 77.9 - - - +
240B SER* 1.3 56.7 + - - +
241B SER 2.9 10.2 + - - -
242B ILE* 4.3 4.9 - - - +
243B ALA* 3.5 7.3 + - - +
466B HIS* 2.7 35.1 + - - -
469B HIS* 2.9 16.9 + - - +
470B GLY* 2.8 39.4 + - - -
473B THR* 3.5 4.2 + - - -
1016B CLA 3.6 15.0 - - - -
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Residues in contact with SER 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B THR* 2.4 35.7 + - - -
237B VAL* 3.9 4.0 + - - -
238B LEU 3.6 0.2 - - - -
239B SER* 1.3 75.2 - - - +
241B SER* 1.3 57.3 + - - +
243B ALA* 4.7 1.8 - - - -
244B ALA* 4.6 1.6 - - - +
1016B CLA 3.5 29.5 + - - +
1018B CLA 2.9 72.4 - - - +
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Residues in contact with SER 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B VAL 3.0 18.9 + - - -
238B LEU 4.6 1.3 - - - -
239B SER 2.9 0.4 - - - -
240B SER* 1.3 78.0 - - - +
242B ILE* 1.3 68.1 + - - +
243B ALA 2.9 1.3 - - - -
244B ALA* 2.7 18.5 + - - +
245B VAL* 2.8 18.4 + - - +
1018B CLA 3.4 31.5 + - - -
1020B CLA 3.0 31.8 + - - -
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Residues in contact with ILE 242 (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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238B LEU* 2.8 31.8 + - + +
239B SER 4.1 4.5 - - - +
241B SER* 1.3 78.2 - - - +
243B ALA* 1.3 55.2 + - - +
245B VAL* 3.1 9.2 + - - +
246B PHE* 2.8 33.1 + - + +
462B PHE* 3.5 25.0 - - + +
465B GLY 4.0 14.8 - - - +
466B HIS* 3.5 21.3 - - + -
469B HIS* 3.9 27.4 - - + -
1019B CLA 4.1 33.9 - - + -
1020B CLA 4.9 2.4 - - - +
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Residues in contact with ALA 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B SER 3.5 4.8 + - - +
240B SER 4.8 0.7 - - - -
241B SER 2.9 0.6 - - - -
242B ILE* 1.3 82.3 - - - +
244B ALA* 1.3 56.1 + - - +
246B PHE* 3.4 17.5 - - + -
247B PHE* 3.0 26.3 + - - +
466B HIS* 3.3 32.8 - - + +
1016B CLA 3.5 35.5 - - + +
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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
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240B SER 4.6 1.3 + - - +
241B SER* 2.7 12.4 + - - +
243B ALA* 1.3 74.2 - - - +
245B VAL* 1.3 66.8 + - - +
247B PHE* 3.3 8.3 - - - +
248B ALA* 3.1 24.4 + - - +
1011B CLA 3.9 30.7 - - + +
1013B CLA 5.8 0.7 - - + -
1016B CLA 5.0 0.2 - - - +
1018B CLA 4.2 37.0 - - + -
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Residues in contact with VAL 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B SER 2.8 20.8 + - - +
242B ILE* 3.5 8.7 - - - +
244B ALA* 1.3 75.1 - - + +
246B PHE* 1.3 61.2 + - - +
248B ALA* 3.6 1.8 + - - +
249B ALA* 2.8 29.0 + - - +
462B PHE* 4.1 9.6 - - + -
1012B CLA 3.6 15.0 - - + +
1018B CLA 5.0 6.3 - - + +
1020B CLA 3.9 48.5 - - + +
1021B CLA 3.8 29.2 - - + -
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Residues in contact with PHE 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ILE* 2.8 10.2 + - + +
243B ALA* 3.4 33.4 - - + -
245B VAL* 1.3 75.0 - - - +
247B PHE* 1.3 74.5 + - - +
249B ALA* 3.1 8.1 - - - +
250B PHE* 3.0 34.5 + + - -
459B ALA 3.8 5.8 - - - +
462B PHE* 3.3 29.8 - - + -
463B PHE* 3.4 37.2 - + + -
466B HIS* 4.2 11.0 - + + -
1010B CLA 4.0 13.9 - - + -
1016B CLA 3.5 43.3 - + + -
1058H DGD 5.2 2.9 - - + -
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Residues in contact with PHE 247 (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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243B ALA 3.0 19.2 + - - +
244B ALA* 3.3 7.6 - - - +
246B PHE* 1.3 92.5 - - - +
248B ALA* 1.3 70.7 + - - +
250B PHE* 3.5 9.0 + - - +
251B VAL* 3.2 23.2 - - + +
1010B CLA 3.5 71.8 - + + -
1011B CLA 3.4 49.8 - - + -
1016B CLA 4.5 16.6 - - + -
42H LEU* 4.0 21.8 - - + -
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Residues in contact with ALA 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 3.1 12.0 + - - +
245B VAL* 4.2 1.8 - - - +
247B PHE* 1.3 79.8 - - - +
249B ALA* 1.3 71.2 + - - +
251B VAL* 3.0 17.7 + - - +
252B VAL* 3.0 17.0 + - - +
1011B CLA 3.4 49.5 - - + +
1012B CLA 4.2 8.5 - - + -
1020B CLA 5.6 0.7 - - + -
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Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B VAL 2.8 20.3 + - - +
246B PHE* 3.1 12.1 - - - +
248B ALA* 1.3 80.6 - - - +
250B PHE* 1.3 56.2 + - - +
251B VAL 2.7 9.0 + - - -
252B VAL* 2.7 14.9 + - - +
253B ALA* 3.2 8.5 + - - +
455B HIS* 4.4 7.7 - - + +
459B ALA* 3.9 13.9 - - + -
1012B CLA 3.1 37.2 - - + +
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Residues in contact with PHE 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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246B PHE* 3.0 31.9 + + - -
247B PHE* 3.5 10.1 - - - +
249B ALA* 1.3 79.7 - - - +
251B VAL* 1.3 61.2 + - + +
253B ALA* 3.6 5.6 - - - +
254B GLY 3.5 12.0 + - - -
455B HIS 4.4 5.2 - - - -
456B ALA 4.8 0.4 - - - -
459B ALA* 3.1 44.8 - - + +
460B LEU* 3.8 1.8 - - + -
1010B CLA 2.9 57.2 - - + -
159D ILE* 4.4 8.3 - - + -
1058H DGD 3.1 67.0 - - + +
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Residues in contact with VAL 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B PHE* 3.2 32.8 - - + +
248B ALA* 3.0 7.6 + - - +
249B ALA 2.7 5.1 + - - -
250B PHE* 1.3 72.5 - - + +
252B VAL* 1.3 59.0 + - + +
253B ALA 3.2 1.1 - - - -
254B GLY* 2.8 1.7 + - - -
255B THR* 2.8 33.4 + - + +
1010B CLA 3.4 60.8 - - + +
1011B CLA 5.0 0.9 - - - -
49H TYR* 5.7 0.4 - - + -
1058H DGD 3.3 29.4 - - + -
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Residues in contact with VAL 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 ALA 3.0 16.8 + - - +
249B ALA 2.7 10.2 + - - +
251B VAL* 1.3 67.2 - - - +
253B ALA* 1.3 60.1 + - - +
254B GLY 2.8 7.7 + - - -
255B THR* 2.4 28.1 + - - +
256B MET* 3.3 10.9 + - + +
451B PHE* 3.3 22.9 - - + -
455B HIS* 4.7 3.6 - - + -
1011B CLA 3.5 24.7 - - + +
1012B CLA 3.0 53.4 - - + +
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Residues in contact with ALA 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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249B ALA 3.2 2.5 + - - +
250B PHE 3.6 9.6 - - - +
251B VAL 3.2 0.4 - - - -
252B VAL* 1.3 77.3 - - - +
254B GLY* 1.3 56.6 + - - +
256B MET 4.5 0.2 - - - -
257B TRP* 4.6 0.2 - - - +
451B PHE* 4.5 1.8 - - - -
452B THR* 3.5 37.5 - - - +
455B HIS* 2.9 47.7 - - + +
1058H DGD 2.9 21.9 - - + +
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Residues in contact with GLY 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 PHE 3.5 0.2 + - - -
251B VAL 2.8 8.4 + - - -
252B VAL 2.8 1.0 - - - -
253B ALA* 1.3 78.6 - - - +
255B THR* 1.3 63.0 + - - +
256B MET 3.3 0.9 - - - -
257B TRP 3.3 1.4 + - - -
258B TYR* 2.3 52.8 + - - -
49H TYR* 5.6 0.2 - - - -
1058H DGD 3.8 21.5 - - - -
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Residues in contact with THR 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B VAL* 2.8 17.3 + - + +
252B VAL* 2.4 33.8 + - - +
254B GLY* 1.3 77.4 - - - +
256B MET* 1.3 58.5 + - - +
258B TYR 2.3 29.8 - - - +
260B SER* 3.0 27.6 - - - +
262B THR* 4.6 7.8 + - + +
263B THR* 3.3 20.6 + - - +
448B ARG* 3.8 0.2 + - - -
1010B CLA 5.1 10.8 - - - +
1011B CLA 5.0 8.0 + - + +
49H TYR* 4.2 11.2 - - + +
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Residues in contact with MET 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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65B PHE* 5.6 0.2 - - - -
252B VAL 3.3 7.3 + - - +
254B GLY 3.3 0.6 - - - -
255B THR* 1.3 76.4 + - - +
257B TRP* 1.3 60.8 + - - +
263B THR* 3.6 9.6 - - + -
268B PHE* 3.0 33.9 - - + -
448B ARG* 2.3 97.9 + - - +
451B PHE* 3.3 41.1 - - + -
452B THR* 3.0 20.4 - - - +
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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