Contacts of the helix formed by residues 227 - 251 (chain D) in PDB entry 4O9U
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 227 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C VAL* 4.4 7.3 - - - +
48C GLY* 5.0 4.2 - - - -
51C VAL* 4.6 4.3 - - - +
8D TYR* 4.2 12.7 + - - -
49D TRP* 3.6 29.0 - - - -
222D GLY* 2.7 11.0 + - - +
225D VAL* 3.3 24.3 - - + +
226D GLY* 1.3 75.7 - - - +
228D PRO* 1.3 65.3 - - - +
229D ALA* 3.5 17.6 + - - +
230D LEU* 3.5 21.2 + - + +
231D MET* 2.9 30.2 + - - +
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Residues in contact with PRO 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A TYR* 3.2 32.5 - - + +
1C MET* 4.9 4.3 - - - -
3C PHE* 3.6 20.6 - - + -
5D GLN* 3.4 26.2 - - - +
8D TYR* 4.3 13.0 - - + -
49D TRP* 6.3 0.2 - - + -
226D GLY 3.4 8.3 - - - +
227D ASN* 1.3 88.4 - - - +
229D ALA* 1.3 59.8 + - - +
231D MET* 3.3 12.7 - - + +
232D VAL* 2.9 37.0 + - + +
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Residues in contact with ALA 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A TYR* 4.0 5.1 + - - -
44C VAL* 5.3 5.4 - - + -
47C VAL* 5.9 1.1 - - + -
8D TYR* 3.6 34.2 - - + +
11D VAL* 4.3 16.2 - - + -
12D ALA* 5.6 2.5 - - - -
15D PHE* 5.2 2.9 - - + -
42D ALA* 5.9 1.3 - - + -
227D ASN* 3.4 6.9 - - - +
228D PRO* 1.3 78.9 - - - +
230D LEU* 1.3 63.5 + - + +
232D VAL* 4.9 1.8 - - - -
233D ALA* 2.8 37.0 + - - +
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Residues in contact with LEU 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C VAL* 3.4 31.9 - - + +
45C VAL* 4.7 7.0 - - + -
47C VAL* 4.6 4.5 - - + -
48C GLY* 4.4 14.6 - - - +
99D ILE* 4.1 25.8 - - + -
218D VAL* 3.0 52.0 - - + +
219D GLY* 3.3 3.6 - - - -
221D GLU* 4.9 2.2 - - + -
222D GLY* 3.7 17.5 - - - +
225D VAL* 5.5 2.7 - - + -
227D ASN* 3.5 22.3 + - + +
229D ALA* 1.3 79.2 - - + +
231D MET* 1.3 63.1 + - - +
233D ALA* 5.0 1.1 - - - -
234D GLY* 3.2 13.8 + - - +
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Residues in contact with MET 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C PHE* 3.6 35.7 - - + -
8C ALA* 3.8 17.7 - - + -
11C ILE* 4.4 10.3 - - + -
219D GLY* 4.0 6.4 - - - -
222D GLY 3.4 21.5 - - - +
223D PHE* 3.4 42.7 - - + +
226D GLY* 4.5 4.0 - - - -
227D ASN 2.9 28.0 + - - +
228D PRO* 3.3 17.0 - - + +
230D LEU* 1.3 80.5 - - - +
232D VAL* 1.3 62.4 + - + +
235D THR* 3.0 26.2 + - - +
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Residues in contact with VAL 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A TYR* 3.5 24.7 - - + -
14A LEU* 4.3 10.1 - - + -
11C ILE* 3.6 25.8 - - + -
15C THR* 3.4 21.6 + - - +
12D ALA* 3.9 23.8 - - + -
16D ILE* 4.3 6.3 - - + -
228D PRO* 2.9 23.7 + - + +
229D ALA 4.3 1.1 - - - +
231D MET* 1.3 72.5 - - + +
233D ALA* 1.3 55.4 + - - +
235D THR* 3.3 9.7 - - - +
236D LEU* 2.8 36.7 + - + +
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Residues in contact with ALA 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ILE* 4.7 8.7 - - + -
42C HIS* 6.0 0.7 - - - -
44C VAL* 4.2 15.5 - - + -
15D PHE* 3.8 31.2 - - + -
218D VAL* 5.2 0.2 - - - -
229D ALA 2.8 22.4 + - - +
232D VAL* 1.3 73.9 - - - +
234D GLY* 1.3 54.3 + - - +
236D LEU* 3.3 9.6 - - - -
237D VAL* 2.6 41.5 + - + +
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Residues in contact with GLY 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C HIS* 5.9 0.7 - - - -
215D GLY* 3.0 28.4 - - - +
218D VAL* 3.8 11.5 - - - +
219D GLY* 3.6 5.2 - - - -
230D LEU 3.2 21.9 + - - -
233D ALA* 1.3 77.5 - - - +
235D THR* 1.3 49.5 + - - +
237D VAL* 3.1 2.1 + - - -
238D GLY 2.8 31.2 + - - -
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Residues in contact with THR 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C PHE* 3.9 41.3 + - + +
15C THR* 3.4 22.0 - - + -
16C ALA* 4.2 12.1 - - - +
215D GLY 4.8 0.7 - - - -
216D MET* 5.8 2.0 - - - +
219D GLY* 4.0 7.3 - - - -
223D PHE* 5.0 0.9 - - + -
231D MET 3.0 22.4 + - - +
232D VAL 3.3 7.9 - - - +
234D GLY* 1.3 71.3 - - - +
236D LEU* 1.3 60.7 + - - +
237D VAL 3.2 0.4 - - - -
238D GLY* 4.0 2.9 - - - +
239D ALA* 3.5 25.8 + - - +
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Residues in contact with LEU 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C THR* 3.2 29.2 - - - +
18C LEU* 5.0 0.4 - - + -
19C GLY* 3.8 20.7 - - - +
22C LEU* 4.9 1.1 - - + -
41C ILE* 5.1 3.1 - - + -
15D PHE* 4.2 20.0 - - + +
16D ILE* 3.8 28.5 - - + -
19D LEU* 3.7 27.6 - - + +
232D VAL* 2.8 21.2 + - + +
233D ALA* 3.0 11.4 + - - +
235D THR* 1.3 77.3 - - - +
237D VAL* 1.3 63.4 + - + +
239D ALA* 5.4 0.8 - - - +
240D ALA* 3.6 17.3 + - - +
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Residues in contact with VAL 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C SER* 3.8 16.7 - - - +
41C ILE* 3.7 37.0 - - + -
42C HIS* 3.6 39.5 - - + +
211D ASN* 4.2 8.5 - - - +
212D ALA* 4.8 0.2 - - - -
215D GLY* 4.0 9.2 - - - -
233D ALA 2.6 21.5 + - - +
234D GLY 3.6 3.1 - - - +
236D LEU* 1.3 78.3 - - + +
238D GLY* 1.3 60.6 + - - +
239D ALA 3.4 0.4 - - - -
240D ALA* 3.3 5.5 + - - +
241D GLY* 2.8 27.5 + - - -
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Residues in contact with GLY 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212D ALA* 3.3 28.6 - - - +
215D GLY* 3.7 5.4 - - - -
216D MET* 4.1 7.0 - - - -
234D GLY 2.8 19.2 + - - -
235D THR* 4.5 2.0 - - - -
237D VAL* 1.3 73.7 - - - +
239D ALA* 1.3 49.5 + - - +
241D GLY 3.1 2.1 + - - -
242D THR* 2.7 40.1 + - - -
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Residues in contact with ALA 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ALA* 4.4 24.2 - - + +
19C GLY* 6.1 0.9 - - - -
20C TYR* 5.4 11.5 - - + +
235D THR* 3.5 22.2 + - - +
236D LEU 5.4 0.2 - - - +
238D GLY* 1.3 74.6 - - - +
240D ALA* 1.3 61.5 + - - +
242D THR* 3.3 9.9 - - - -
243D LEU* 3.1 24.9 + - - +
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Residues in contact with ALA 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C GLY* 5.3 5.3 - - - +
20C TYR* 5.5 1.7 - - - +
23C ILE* 4.1 30.1 - - + +
38C SER* 5.5 7.2 - - - -
19D LEU* 4.6 10.8 - - + -
236D LEU 3.6 16.8 + - - +
237D VAL* 3.3 10.4 + - - +
238D GLY 3.2 0.2 - - - -
239D ALA* 1.3 78.3 - - - +
241D GLY* 1.3 56.4 + - - +
243D LEU* 3.7 3.6 + - - +
244D LEU* 2.9 32.0 + - - +
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Residues in contact with GLY 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C SER* 5.8 1.2 - - - -
208D SER* 3.1 7.0 + - - -
211D ASN* 4.6 6.3 - - - -
212D ALA* 3.5 16.8 - - - -
237D VAL 2.8 14.5 + - - -
238D GLY 3.4 3.8 - - - -
240D ALA* 1.3 74.1 - - - +
242D THR* 1.3 54.9 + - - +
244D LEU* 3.7 12.3 - - - -
245D THR* 2.5 39.0 + - - -
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Residues in contact with THR 242 (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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212D ALA* 3.5 10.6 - - - +
216D MET* 4.7 15.1 - - + +
238D GLY 2.7 27.5 + - - -
239D ALA* 3.3 13.6 - - - -
240D ALA 3.2 0.2 - - - -
241D GLY* 1.3 69.9 - - - +
243D LEU* 1.3 66.9 + - - +
245D THR* 3.2 14.3 + - - -
246D VAL* 3.3 23.5 + - + +
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Residues in contact with LEU 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C TYR* 3.7 61.0 - - + +
23C ILE* 5.0 11.4 - - + +
24C THR* 4.5 9.9 - - + +
239D ALA 3.1 12.1 + - - +
240D ALA* 4.1 4.0 - - - +
242D THR* 1.3 79.4 - - - +
244D LEU* 1.3 53.0 + - - +
246D VAL* 3.2 8.9 + - + +
247D LEU* 2.8 60.0 + - + +
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Residues in contact with LEU 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ILE* 4.7 11.4 - - + +
26C VAL* 6.0 0.4 - - + -
31C HIS* 4.9 21.8 - - + +
34C LEU* 4.0 25.4 - - + -
35C MET* 4.4 29.8 - - + -
38C SER* 4.6 4.5 - - - +
208D SER* 3.7 15.5 - - - +
211D ASN* 4.5 7.0 - - - +
240D ALA* 2.9 20.3 + - + +
241D GLY* 3.4 13.7 - - - +
242D THR 3.1 0.2 - - - -
243D LEU* 1.3 77.2 - - - +
245D THR* 1.3 57.3 + - - +
247D LEU* 3.6 7.4 + - + +
248D MET* 3.0 41.2 + - + +
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Residues in contact with THR 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D VAL* 3.3 36.5 - - + +
208D SER* 2.8 25.4 + - - -
209D PHE* 3.3 23.2 + - + +
212D ALA* 4.5 0.9 - - - +
241D GLY 2.5 25.3 + - - -
242D THR* 3.2 7.3 + - - -
244D LEU* 1.3 72.2 - - - +
246D VAL* 1.3 59.2 + - - +
248D MET* 3.4 4.2 - - - +
249D ALA* 2.8 30.4 + - - +
256D VAL* 5.0 7.6 - - + -
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Residues in contact with VAL 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D THR* 3.4 20.9 - - + +
243D LEU* 3.2 10.9 + - + +
245D THR* 1.3 74.4 - - - +
247D LEU* 1.3 58.4 + - - +
249D ALA* 2.9 6.5 + - - -
250D ARG* 2.8 68.0 + - - +
256D VAL* 4.3 22.4 - - + -
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Residues in contact with LEU 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ILE* 4.8 8.3 - - + +
24C THR* 5.1 6.7 - - - +
26C VAL* 4.4 21.8 - - + -
31C HIS* 4.9 18.1 - - + +
243D LEU* 2.8 41.9 + - + +
244D LEU* 4.1 7.6 - - + +
246D VAL* 1.3 72.6 - - - +
248D MET* 1.3 57.6 + - - +
249D ALA 3.3 0.2 - - - -
250D ARG* 4.8 3.1 - - + +
251D ALA* 3.1 29.2 + - + +
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Residues in contact with MET 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C HIS* 4.1 35.9 - - + +
35C MET* 4.5 8.5 - - + -
204D PRO* 3.8 21.8 - - + +
205D VAL* 3.3 16.1 - - + +
208D SER* 4.7 11.4 - - - -
244D LEU* 3.0 26.6 + - + +
245D THR* 3.4 4.5 - - - +
247D LEU* 1.3 73.7 - - - +
249D ALA* 1.3 58.5 + - - +
251D ALA* 4.2 9.2 - - + -
252D MET* 3.4 16.9 - - + +
332D PRO* 5.6 5.8 - - + +
338D PRO* 3.0 45.5 - - + -
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Residues in contact with ALA 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D VAL* 3.7 22.2 - - + -
245D THR 2.8 18.3 + - - +
246D VAL* 2.9 8.5 + - - +
248D MET* 1.3 78.5 - - - +
250D ARG* 1.3 55.2 + - + +
251D ALA 3.3 0.2 - - - -
252D MET* 3.0 20.0 - - - +
254D ARG* 2.6 24.2 - - - +
255D SER 4.2 16.2 - - - +
256D VAL* 4.2 13.5 - - + -
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Residues in contact with ARG 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D VAL* 2.8 43.2 + - - +
247D LEU* 4.8 2.4 - - - +
249D ALA* 1.3 70.8 - - + +
251D ALA* 1.3 60.1 + - - +
252D MET 3.0 11.2 - - - +
254D ARG 3.6 11.4 - - - +
255D SER* 4.9 9.4 - - - +
256D VAL* 5.4 4.5 - - - -
393D GLY 4.8 1.7 - - - +
395D PRO* 3.7 11.3 - - - +
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Residues in contact with ALA 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C HIS* 5.6 4.5 - - + -
247D LEU* 3.1 24.9 + - + +
248D MET* 4.2 10.1 - - + -
250D ARG* 1.3 74.7 - - - +
252D MET* 1.3 61.2 + - - +
331D HIS* 4.6 3.1 - - - -
332D PRO* 4.0 27.9 - - + +
333D VAL* 3.3 13.7 - - + +
395D PRO* 3.3 21.7 - - - +
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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