Contacts of the helix formed by residues 225 - 250 (chain R) in PDB entry 1RZZ
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 GLY 225 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213R ASN* 4.3 5.2 - - - -
223R SER* 3.4 7.5 + - - -
224R ILE* 1.3 83.6 - - - +
226R THR* 1.3 66.7 + - - -
227R LEU 3.4 2.0 - - - -
228R GLY 3.8 0.4 - - - -
229R ILE* 3.0 23.1 + - - +
2009R U10 4.1 6.2 + - - +
44S ASN* 3.3 17.2 - - - +
173T GLU* 3.5 9.6 - - - -
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Residues in contact with THR 226 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190R HIS* 5.8 0.4 - - - -
209R PRO* 6.5 0.4 - - - -
212R GLU* 5.6 5.6 - - - -
225R GLY* 1.3 70.8 - - - -
227R LEU* 1.3 66.8 + - + +
229R ILE* 3.1 11.6 - - - +
230R HIS* 2.7 33.3 + - - -
232S GLU* 2.4 48.9 + - + +
233S CYS* 4.8 5.4 - - - +
234S GLU* 4.4 1.6 + - - +
173T GLU* 3.2 32.7 + - + +
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Residues in contact with LEU 227 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225R GLY 3.4 0.6 - - - -
226R THR* 1.3 86.0 - - + +
228R GLY* 1.3 62.3 + - - +
230R HIS* 3.5 2.5 + - + +
231R ARG* 3.1 53.1 + - - +
5S ASN* 3.7 18.4 - - - +
8S SER* 5.2 1.1 - - - +
223S ILE* 5.2 2.5 - - + -
224S LEU* 3.5 28.9 - - + +
227S SER* 4.3 1.8 - - - -
232S GLU* 3.3 34.8 - - + +
173T GLU* 4.5 1.4 + - - +
175T MET* 4.3 27.6 - - + -
194T GLN* 5.6 2.7 - - - +
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Residues in contact with GLY 228 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224R ILE* 3.7 25.1 + - - +
225R GLY 3.3 6.6 + - - -
226R THR 3.3 0.6 - - - -
227R LEU* 1.3 76.7 - - - +
229R ILE* 1.3 55.0 + - - +
231R ARG* 3.2 4.4 + - - +
232R LEU* 2.8 35.2 + - - +
42S PHE* 3.7 23.0 + - - -
43S GLY* 4.4 1.0 - - - -
175T MET* 5.9 0.6 - - - -
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Residues in contact with ILE 229 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186R ALA* 4.6 4.0 - - + +
190R HIS* 3.4 45.8 - - + +
224R ILE* 3.4 7.5 - - + +
225R GLY 3.0 16.0 + - - +
226R THR* 3.1 19.5 - - - +
228R GLY* 1.3 75.3 - - - +
230R HIS* 1.3 71.0 + - + +
232R LEU* 3.3 14.9 + - + +
233R GLY 2.9 23.6 + - - -
2009R U10 3.3 40.8 - - + +
216S PHE* 3.7 11.3 - - + -
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Residues in contact with HIS 230 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190R HIS* 3.0 15.3 + + - -
226R THR* 2.7 30.3 + - - -
227R LEU 3.5 5.5 + - - +
228R GLY 3.3 0.4 - - - -
229R ILE* 1.3 79.3 - - + +
231R ARG* 1.3 64.8 + - - +
233R GLY 4.5 0.2 - - - +
234R LEU* 3.3 20.1 + - - +
216S PHE* 4.6 2.2 - + - -
219S HIS* 3.3 20.0 - + - -
220S GLY* 3.6 29.6 - - - +
223S ILE* 3.4 30.2 - - + +
224S LEU* 4.7 6.1 - - + +
234S GLU* 2.8 28.9 + - - -
2007S FE2 2.2 26.4 - - - -
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Residues in contact with ARG 231 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227R LEU* 3.1 32.7 + - - +
228R GLY* 3.3 11.2 - - - +
230R HIS* 1.3 78.3 - - - +
232R LEU* 1.3 56.0 + - - +
234R LEU* 3.9 2.3 - - - +
235R LEU* 3.0 30.0 + - - +
5S ASN* 3.0 43.5 + - - +
6S ILE* 2.9 34.2 + - + +
8S SER* 3.2 27.5 + - - +
40S GLY 5.1 0.2 + - - -
41S TRP 3.3 13.9 + - - -
42S PHE* 2.9 46.7 + - + -
224S LEU* 4.1 19.7 - - + +
175T MET* 5.0 4.6 - - - +
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Residues in contact with LEU 232 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186R ALA* 4.7 2.9 - - + -
224R ILE* 4.1 16.8 - - + -
228R GLY 2.8 17.0 + - - +
229R ILE* 3.5 20.2 - - + +
231R ARG* 1.3 75.0 - - - +
233R GLY* 1.3 56.0 + - - +
235R LEU* 3.1 4.6 + - + +
236R LEU* 2.7 68.8 + - + +
2009R U10 3.9 35.7 - - + -
42S PHE* 3.8 21.7 - - + -
2011S LDA 5.8 4.0 - - + -
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Residues in contact with GLY 233 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183R ASN* 3.2 8.8 - - - +
229R ILE 2.9 11.3 + - - -
230R HIS 3.6 0.2 + - - -
231R ARG 3.5 0.2 - - - -
232R LEU* 1.3 76.3 - - - +
234R LEU* 1.3 62.5 + - - +
236R LEU* 4.7 1.6 - - - -
237R SER* 3.0 23.6 + - - -
216S PHE* 3.6 46.2 - - - +
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Residues in contact with LEU 234 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116R HIS* 4.9 7.0 - - + +
119R PHE* 6.0 3.4 - - + -
120R ALA* 3.7 11.2 - - + -
230R HIS 3.3 16.8 + - - +
231R ARG 3.9 3.4 - - - +
232R LEU 3.3 0.4 - - - -
233R GLY* 1.3 74.4 - - - +
235R LEU* 1.3 60.6 + - + +
237R SER* 3.2 5.0 + - - -
238R LEU* 2.9 70.7 + - + +
6S ILE* 4.7 11.4 - - + -
216S PHE 4.2 5.1 + - - -
217S ALA* 3.6 21.8 - - - +
221S ALA* 4.1 20.9 - - + +
224S LEU* 4.1 23.8 - - + -
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Residues in contact with LEU 235 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179R PHE* 5.4 5.2 - - + -
231R ARG 3.0 20.5 + - - +
232R LEU* 3.1 8.3 + - + +
234R LEU* 1.3 79.0 - - + +
236R LEU* 1.3 57.0 + - + +
238R LEU* 4.1 7.0 - - + +
239R SER* 2.7 51.4 + - - +
6S ILE* 4.8 14.4 - - + -
7S PHE* 6.0 3.1 - - + -
42S PHE* 4.0 25.6 - - + -
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Residues in contact with LEU 236 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179R PHE* 3.5 35.7 - - + +
182R THR* 3.9 28.0 - - + +
183R ASN* 3.6 37.7 - - + +
186R ALA* 4.0 11.2 - - + -
232R LEU* 2.7 51.8 + - + +
233R GLY* 4.8 0.2 - - - -
235R LEU* 1.3 75.0 - - + +
237R SER* 1.3 57.3 + - - +
239R SER* 3.3 0.9 + - - -
240R ALA* 2.9 29.7 + - - +
2009R U10 5.6 1.1 - - + -
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Residues in contact with SER 237 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183R ASN* 3.6 13.0 + - - -
233R GLY 3.0 16.3 + - - -
234R LEU 3.2 5.4 + - - -
236R LEU* 1.3 76.1 - - - +
238R LEU* 1.3 67.4 + - - +
240R ALA* 3.5 6.8 + - - +
241R VAL* 3.3 28.4 + - - +
2006R BPH 4.1 1.7 - - - +
213S ALA* 3.2 33.9 - - - +
217S ALA* 3.4 21.4 - - - +
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Residues in contact with LEU 238 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119R PHE* 4.7 9.4 - - + -
120R ALA* 3.9 26.5 - - + +
123R PHE* 3.8 42.4 - - + -
234R LEU* 2.9 54.0 + - + +
235R LEU* 4.1 8.5 - - + +
237R SER* 1.3 83.3 + - - +
239R SER* 1.3 57.1 + - - +
241R VAL* 3.4 3.8 + - - +
242R PHE* 3.0 27.8 + - - +
2006R BPH 4.3 7.4 - - + -
217S ALA* 4.2 6.5 - - + -
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Residues in contact with SER 239 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179R PHE* 3.7 28.7 - - - -
235R LEU* 2.7 40.2 + - - +
236R LEU 3.6 4.3 - - - -
237R SER 3.2 0.2 - - - -
238R LEU* 1.3 76.2 - - - +
240R ALA* 1.3 65.1 + - - +
242R PHE* 3.3 6.2 + - - +
243R PHE* 3.0 37.3 + - - -
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Residues in contact with ALA 240 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176R ALA* 3.7 8.0 - - - +
179R PHE* 3.6 21.3 - - + +
180R PHE* 3.6 36.6 - - + +
236R LEU 2.9 16.8 + - - +
237R SER* 3.6 8.7 - - - +
239R SER* 1.3 77.7 - - - +
241R VAL* 1.3 52.9 + - - +
243R PHE 3.5 0.3 + - - -
244R SER* 2.7 36.6 + - - -
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Residues in contact with VAL 241 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123R PHE* 3.6 23.1 - - + +
124R ALA* 4.4 1.8 - - - -
127R ALA* 3.5 28.0 - - + -
180R PHE* 4.4 8.3 - - + -
237R SER 3.3 9.3 + - - +
238R LEU 3.8 5.8 - - - +
239R SER 3.2 0.4 - - - -
240R ALA* 1.3 74.1 - - - +
242R PHE* 1.3 67.1 + - - +
244R SER* 3.2 7.2 + - - -
245R ALA* 3.0 23.3 + - + +
2002R BCL 4.5 8.1 - - - -
2006R BPH 3.2 45.8 - - + -
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Residues in contact with PHE 242 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123R PHE* 4.6 19.5 - + + -
238R LEU 3.0 17.9 + - - +
239R SER* 3.3 7.2 + - - +
241R VAL* 1.3 77.1 - - - +
243R PHE* 1.3 92.1 + + - +
245R ALA* 3.5 6.0 + - + +
246R LEU* 2.9 40.5 + - + +
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Residues in contact with PHE 243 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172R ALA* 3.6 11.5 - - + +
175R ILE* 3.7 36.1 - - + -
176R ALA* 3.8 19.5 - - + -
179R PHE* 3.7 23.8 - + - -
239R SER* 3.0 30.4 + - - +
242R PHE* 1.3 93.1 - + - +
244R SER* 1.3 60.1 + - - +
246R LEU* 3.6 29.4 - - + +
247R CYS* 2.9 29.6 + - - +
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Residues in contact with SER 244 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127R ALA* 5.7 0.2 - - - -
176R ALA* 3.8 6.0 - - - +
180R PHE* 3.6 4.2 - - - -
240R ALA 2.7 18.9 + - - -
241R VAL 3.2 9.6 + - - -
243R PHE* 1.3 73.8 - - - +
245R ALA* 1.3 66.3 + - - +
247R CYS* 3.0 15.6 + - - -
248R MET 3.1 3.3 + - - -
2002R BCL 3.0 75.4 + - - +
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Residues in contact with ALA 245 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126R LEU* 4.9 1.1 - - + +
127R ALA* 4.3 11.0 - - - -
130R THR* 3.6 28.8 - - + +
241R VAL* 3.0 12.9 + - + +
242R PHE* 3.7 7.2 - - + +
244R SER* 1.3 80.0 - - - +
246R LEU* 1.3 62.6 + - - +
248R MET 3.2 1.2 + - - -
249R ILE* 2.9 26.4 + - - +
2002R BCL 3.6 10.9 - - - -
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Residues in contact with LEU 246 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172R ALA* 4.3 11.2 - - + -
242R PHE* 2.9 34.4 + - + +
243R PHE* 3.8 33.9 - - + +
245R ALA* 1.3 77.4 - - - +
247R CYS* 1.3 61.3 + - - +
249R ILE* 3.1 31.1 - - + +
250R ILE* 3.3 23.0 - - + +
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Residues in contact with CYS 247 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167R PHE* 4.3 0.2 - - - -
170R ASN* 3.0 15.4 + - - +
172R ALA* 3.4 22.2 - - + +
173R HIS* 3.5 35.4 - - - +
176R ALA* 5.5 0.2 - - - -
243R PHE 2.9 16.5 + - - +
244R SER* 3.0 18.6 + - - -
246R LEU* 1.3 76.2 - - - +
248R MET* 1.3 61.0 + - - +
250R ILE* 3.4 6.7 - - - +
251R THR* 2.7 28.1 + - - -
2002R BCL 3.1 17.5 - - - -
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Residues in contact with MET 248 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130R THR* 4.9 3.1 - - + -
131R LEU* 3.9 13.7 - - + -
135R ARG* 3.3 39.4 - - - +
156R TRP* 4.0 17.3 - - + -
160R THR* 4.2 5.6 - - + -
167R PHE* 3.7 30.1 - - + -
244R SER 3.1 5.3 + - - +
245R ALA* 3.9 2.9 - - - +
247R CYS* 1.3 76.3 - - - +
249R ILE* 1.3 65.2 + - - +
250R ILE 3.1 2.2 - - - -
251R THR* 3.0 15.7 + - - +
2002R BCL 3.2 72.0 - - + +
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Residues in contact with ILE 249 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130R THR* 4.1 13.2 - - + +
134R PHE* 3.9 26.0 - - + -
135R ARG* 4.0 14.4 - - - +
138R MET* 3.7 30.9 - - + +
245R ALA 2.9 15.4 + - - +
246R LEU* 3.1 30.7 - - + +
248R MET* 1.3 77.0 - - - +
250R ILE* 1.3 59.6 + - + +
253R THR* 2.7 33.8 + - - +
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Residues in contact with ILE 250 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170R ASN* 4.2 7.6 - - - +
171R PRO* 5.3 3.8 - - + -
172R ALA* 4.5 7.9 - - + -
246R LEU* 3.3 31.2 - - + +
247R CYS* 3.4 13.0 - - - +
249R ILE* 1.3 85.4 - - + +
251R THR* 1.3 63.8 + - - +
253R THR* 3.4 7.2 - - - -
254R ILE* 3.2 32.3 + - + +
255R TRP* 3.1 27.2 + - - +
259R TRP* 3.6 26.2 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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