Contacts of the helix formed by residues 221 - 247 (chain P) in PDB entry 3L73
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 PHE 221 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19P LEU* 3.1 49.1 - - + -
20P ILE 3.8 4.1 + - - +
22P LEU* 3.0 32.4 + - + +
24P ALA* 4.9 0.9 - - + -
219P ILE 3.5 0.8 + - - -
220P PRO* 1.3 70.0 - - - +
222P HIS* 1.3 57.4 + - - +
225P TYR* 2.7 59.1 + - + -
226P SER* 3.1 26.7 + - - -
229P ASP* 3.9 13.2 - - - -
3002P UQ 3.1 60.6 - + + -
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Residues in contact with HIS 222 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436N ARG* 3.0 38.3 + - - -
19P LEU 4.1 13.7 - - - +
20P ILE* 3.5 24.3 + - + +
220P PRO* 3.1 11.0 - - - +
221P PHE* 1.3 79.1 - - - +
223P PRO* 1.3 78.6 - - + +
226P SER* 2.9 25.9 + - - +
227P PHE* 4.0 10.8 - + - -
3008P PEE 2.8 32.7 + - - -
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Residues in contact with PRO 223 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433N ASP* 3.6 19.7 - - - +
435N ASN* 4.2 19.7 - - + +
436N ARG* 4.1 11.0 - - - -
222P HIS* 1.3 93.2 - - + +
224P TYR* 1.3 72.3 + - + +
225P TYR 3.5 0.2 - - - -
226P SER* 3.3 9.0 - - - +
227P PHE* 2.8 51.6 + - + +
3008P PEE 5.4 0.7 - - - +
226Q LYS* 4.2 20.6 - - + -
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Residues in contact with TYR 224 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433N ASP* 2.6 40.4 + - + -
435N ASN* 2.7 27.2 + - + -
219P ILE* 3.4 46.4 - - + -
220P PRO* 3.6 15.7 - - + +
221P PHE 3.5 1.2 + - - -
222P HIS 3.5 0.2 - - - -
223P PRO* 1.3 82.7 - - + +
225P TYR* 1.3 63.2 + - + +
227P PHE* 3.9 0.3 - - - +
228P LYS* 3.0 18.5 + - - +
226Q LYS* 3.8 12.8 - - + -
227Q TRP* 3.0 47.7 + + + +
229Q VAL* 4.1 12.5 - - - +
230Q LEU* 4.0 21.4 - - + +
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Residues in contact with TYR 225 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24P ALA* 3.5 25.4 - - + -
25P PRO 2.5 28.2 + - - -
26P SER 3.5 6.8 + - - -
28P ILE* 3.0 35.0 + - + +
219P ILE* 3.6 15.0 - - + -
221P PHE* 2.7 43.5 + - + +
224P TYR* 1.3 73.6 - - + +
226P SER* 1.3 63.7 + - - +
227P PHE 3.1 1.6 - - - -
228P LYS* 3.7 22.0 - - + -
229P ASP* 2.9 33.7 + - - +
3002P UQ 4.2 6.1 - - - +
227Q TRP* 3.4 30.2 - + - -
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Residues in contact with SER 226 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19P LEU 5.5 0.7 - - - -
221P PHE* 3.1 26.9 + - - -
222P HIS* 2.9 32.4 + - - -
223P PRO* 3.1 11.1 + - - +
225P TYR* 1.3 75.6 - - - +
227P PHE* 1.3 67.0 + - - +
229P ASP* 4.0 2.5 - - - +
230P ILE* 3.2 33.1 + - - +
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Residues in contact with PHE 227 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222P HIS* 4.0 13.5 - + - -
223P PRO* 2.8 50.9 + - + +
224P TYR* 3.9 2.5 - - - +
226P SER* 1.3 81.3 + - - +
228P LYS* 1.3 64.6 + - - +
230P ILE* 3.4 11.3 + - + +
231P LEU* 3.1 24.1 + - - +
3008P PEE 5.7 0.7 - - - -
219Q LEU* 5.7 6.9 - - + +
222Q MET* 4.0 38.4 - - + -
223Q LYS* 4.4 16.3 - - + +
226Q LYS* 4.1 26.5 - - + -
227Q TRP* 5.2 2.0 - - + +
3005R PEE 3.5 33.9 - - - -
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Residues in contact with LYS 228 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28P ILE* 3.8 13.5 + - + -
29P SER* 3.6 23.8 - - - +
30P ALA* 4.2 3.6 - - - +
33P ASN* 3.0 31.5 + - - +
224P TYR 3.0 18.7 + - - +
225P TYR* 3.4 31.2 + - + +
227P PHE* 1.3 76.4 - - - +
229P ASP* 1.3 58.3 + - - +
231P LEU* 3.5 3.3 + - + +
232P GLY 3.0 21.1 + - - -
223Q LYS* 4.0 38.6 - - - +
227Q TRP* 4.4 7.0 - - + +
3003Q CDL 4.2 21.1 + - - +
72S HIS* 6.0 1.8 + - - -
3004T CDL 5.0 2.6 + - - -
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Residues in contact with ASP 229 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32P TRP 4.9 1.4 - - - +
33P ASN* 3.6 22.6 + - - +
36P SER* 3.0 33.7 + - - +
37P LEU* 5.1 2.1 - - - +
221P PHE* 3.9 8.4 - - + -
225P TYR* 2.9 27.9 + - - +
226P SER* 4.0 3.4 - - - +
228P LYS* 1.3 77.0 - - - +
230P ILE* 1.3 55.2 + - + +
231P LEU 3.1 0.2 - - - -
232P GLY* 3.0 2.1 + - - -
233P LEU* 2.7 34.5 + - - +
3002P UQ 3.3 24.3 - - + +
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Residues in contact with ILE 230 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226P SER* 3.2 22.6 + - - +
227P PHE* 3.4 11.2 + - + +
229P ASP* 1.3 78.3 - - + +
231P LEU* 1.3 63.6 + - - +
233P LEU* 3.1 14.0 + - + +
234P THR* 3.1 22.5 + - - +
219Q LEU* 3.8 23.8 - - + -
3005R PEE 3.8 45.8 - - + +
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Residues in contact with LEU 231 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227P PHE 3.1 17.1 + - - +
228P LYS 3.5 4.0 - - - +
230P ILE* 1.3 80.6 - - - +
232P GLY* 1.3 63.0 + - - +
234P THR* 2.8 25.6 + - - +
235P LEU* 3.0 28.8 + - + +
216Q THR* 4.1 6.5 - - + +
219Q LEU* 3.8 13.7 - - + +
220Q TYR* 3.7 53.2 - - + +
223Q LYS* 3.8 27.8 - - + -
3003Q CDL 4.0 16.8 - - - +
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Residues in contact with GLY 232 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P ASN* 3.6 19.3 - - - -
37P LEU* 4.0 7.1 - - - +
228P LYS 3.0 11.5 + - - -
229P ASP 3.0 5.1 + - - -
231P LEU* 1.3 76.3 - - - +
233P LEU* 1.3 60.8 + - - +
235P LEU* 3.5 1.4 + - - +
236P MET* 3.2 28.4 + - - +
3003Q CDL 3.8 20.1 + - - +
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Residues in contact with LEU 233 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P LEU* 3.5 23.5 - - + +
40P VAL* 3.7 37.0 - - + -
90P PHE* 5.6 3.8 - - + -
229P ASP 2.7 16.7 + - - +
230P ILE* 3.3 16.6 - - + +
231P LEU 3.1 0.2 - - - -
232P GLY* 1.3 70.3 - - - +
234P THR* 1.3 59.5 + - - +
236P MET* 3.2 2.4 + - - +
237P LEU* 2.8 49.0 + - + +
3005R PEE 4.5 28.7 - - + -
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Residues in contact with THR 234 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230P ILE 3.1 7.5 + - - +
231P LEU* 2.8 27.2 + - - +
233P LEU* 1.3 76.3 - - + +
235P LEU* 1.3 61.3 + - - +
237P LEU* 3.7 9.4 - - + +
238P THR* 3.1 27.2 + - - -
215Q LEU* 5.1 6.7 - - + -
216Q THR* 4.0 18.1 + - - -
219Q LEU* 3.3 31.5 - - + +
3009Q BOG 6.4 2.7 - - + -
3005R PEE 4.3 21.8 - - + -
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Residues in contact with LEU 235 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231P LEU* 3.0 26.9 + - + +
232P GLY 3.8 4.9 - - - +
233P LEU 3.2 0.2 - - - -
234P THR* 1.3 85.2 + - - +
236P MET* 1.3 59.1 + - + +
238P THR* 4.1 3.4 - - - +
239P PRO* 3.1 22.7 - - - +
216Q THR* 3.4 33.2 - - + +
3003Q CDL 3.9 72.5 - - + +
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Residues in contact with MET 236 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34P PHE* 4.7 14.8 - - + -
37P LEU* 3.6 23.3 - - + -
90P PHE* 3.4 44.3 - - + -
93P ILE* 4.5 23.3 - - + -
94P CYS* 4.6 8.1 - - - -
97P LEU* 5.2 2.5 - - + -
232P GLY 3.2 12.5 + - - +
233P LEU 4.0 1.1 - - - +
235P LEU* 1.3 76.0 - - - +
237P LEU* 1.3 66.4 + - - +
238P THR 3.1 1.8 - - - -
239P PRO* 2.9 21.8 - - + +
240P PHE 3.4 7.8 + - - -
3003Q CDL 4.9 11.7 - - + -
3004T CDL 5.4 9.2 - - + -
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Residues in contact with LEU 237 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90P PHE* 4.2 7.4 - - + -
233P LEU* 2.8 35.9 + - + +
234P THR* 3.7 10.3 - - + +
236P MET* 1.3 77.5 - - - +
238P THR* 1.3 61.1 + - - +
240P PHE* 3.4 28.1 - - + +
241P LEU* 3.0 43.0 + - + +
3009Q BOG 4.5 14.8 - - + -
3005R PEE 4.0 29.6 - - + -
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Residues in contact with THR 238 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234P THR 3.1 15.4 + - - -
235P LEU* 4.1 3.6 - - - +
236P MET 3.1 1.8 + - - -
237P LEU* 1.3 76.4 - - - +
239P PRO* 1.3 76.5 - - + +
241P LEU* 3.9 3.5 - - - +
242P THR* 2.9 36.3 + - - +
208Q MET* 4.6 3.3 - - - +
209Q LEU* 4.9 7.9 - - + -
212Q SER* 2.6 32.4 + - - +
216Q THR* 4.1 6.1 + - - -
3009Q BOG 5.9 1.1 - - - +
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Residues in contact with PRO 239 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235P LEU 3.1 19.1 - - - +
236P MET* 2.9 26.2 - - + +
238P THR* 1.3 85.5 - - + +
240P PHE* 1.3 63.3 + - - +
242P THR* 3.2 7.7 + - + +
243P LEU* 2.8 26.1 + - - +
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Residues in contact with PHE 240 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44P THR* 5.5 11.9 - - + -
83P LEU* 3.6 33.4 - - + -
86P ASN* 3.6 19.7 - - + -
87P GLY* 3.5 29.2 - - - -
90P PHE* 3.9 29.4 - + + -
236P MET 3.4 10.7 + - - +
237P LEU* 3.4 26.9 - - + +
239P PRO* 1.3 76.2 - - - +
241P LEU* 1.3 78.3 + - + +
243P LEU* 2.9 12.5 + - + +
244P ALA* 2.8 28.7 + - + +
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Residues in contact with LEU 241 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83P LEU* 3.9 23.1 - - + -
237P LEU* 3.0 26.5 + - + +
240P PHE* 1.3 98.6 - - + +
242P THR* 1.3 55.2 + - - +
244P ALA* 4.3 3.6 - - - +
245P LEU* 2.7 45.4 + - + +
208Q MET* 3.7 35.0 - - + -
3009Q BOG 4.0 28.5 - - + -
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Residues in contact with THR 242 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238P THR* 2.9 27.5 + - - +
239P PRO* 3.4 7.4 - - + +
241P LEU* 1.3 76.6 - - - +
243P LEU* 1.3 60.5 + - - +
246P PHE* 2.9 44.6 + - + +
247P SER* 3.9 0.3 + - - -
208Q MET* 3.4 20.1 - - - +
209Q LEU* 3.9 14.0 - - + +
----------------------------------------------------------
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Residues in contact with LEU 243 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86P ASN* 3.7 25.6 - - + +
89P SER* 6.0 0.9 - - - -
239P PRO 2.8 14.3 + - - +
240P PHE* 3.3 11.7 - - + +
242P THR* 1.3 75.1 - - - +
244P ALA* 1.3 58.4 + - - +
245P LEU 3.0 5.2 + - - -
247P SER* 2.9 59.5 + - - +
250P LEU* 3.8 28.7 - - + -
251P LEU* 3.8 22.0 - - + -
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Residues in contact with ALA 244 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79P LEU* 6.4 0.2 - - + -
82P ASN* 3.4 30.5 - - + +
83P LEU* 4.7 11.9 - - + -
86P ASN* 3.7 33.4 - - + +
240P PHE* 2.8 24.9 + - + +
241P LEU* 4.2 6.1 - - - +
243P LEU* 1.3 72.7 - - - +
245P LEU* 1.3 66.5 + - + +
248P PRO* 4.1 7.9 - - - +
201Q ARG* 4.8 0.2 - - - -
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Residues in contact with LEU 245 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78P TRP* 4.4 6.3 - - + -
79P LEU* 4.3 23.8 - - + -
83P LEU* 6.3 1.1 - - + -
241P LEU* 2.7 29.6 + - + +
242P THR 4.5 0.7 - - - +
244P ALA* 1.3 86.5 - - + +
246P PHE* 1.3 63.6 + - + +
248P PRO* 4.3 1.1 - - - -
201Q ARG* 2.6 52.0 + - + +
202Q LYS 5.0 0.2 + - - -
204Q MET* 4.2 14.8 - - + -
205Q GLY* 3.8 33.2 - - - +
208Q MET* 4.1 22.7 - - + -
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Residues in contact with PHE 246 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242P THR* 2.9 38.5 + - + +
245P LEU* 1.3 81.5 - - - +
247P SER* 1.3 59.7 + - - +
248P PRO* 3.3 10.5 - - - +
17Q PRO* 3.4 49.0 - - + +
18Q LEU* 4.1 9.4 - - + -
201Q ARG* 3.7 8.7 + - - +
202Q LYS* 4.2 12.1 - - + -
205Q GLY* 3.3 40.6 - - - -
206Q LEU 3.9 1.1 - - - -
208Q MET* 4.2 5.6 - - + -
209Q LEU* 3.5 31.6 - - + -
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Residues in contact with SER 247 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86P ASN* 5.4 0.2 + - - -
242P THR 3.9 0.8 + - - -
243P LEU* 2.9 27.7 + - - +
246P PHE* 1.3 80.8 - - - +
248P PRO* 1.3 64.0 - - - +
249P ASN 3.1 3.0 + - - -
250P LEU* 3.1 45.7 + - - +
----------------------------------------------------------
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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