Contacts of the helix formed by residues 220 - 246 (chain P) in PDB entry 1PP9
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 220 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18P PHE* 3.2 35.7 - + - +
19P ILE 3.9 1.6 + - - -
21P LEU* 2.8 25.3 + - + +
23P ALA* 4.7 2.7 - - + -
218P ILE 3.6 1.0 + - - -
219P PRO* 1.3 72.2 - - - +
221P HIS* 1.3 56.4 + - - +
224P TYR* 2.8 52.1 + + + -
225P THR* 3.2 33.0 + - + -
228P ASP* 3.4 22.7 - - + -
3002P UQ 3.1 64.2 - + + -
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Residues in contact with HIS 221 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436N ARG* 3.2 33.8 + - - +
3012N PEE 2.9 37.4 + - - -
19P ILE* 3.3 43.7 + - + +
219P PRO* 3.3 10.8 - - - +
220P PHE* 1.3 78.8 - - + +
222P PRO* 1.3 69.4 - - + +
223P TYR 3.6 0.7 - - - -
225P THR* 2.9 36.6 + - + +
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Residues in contact with PRO 222 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435N ASN* 4.0 25.1 - - + +
436N ARG* 4.0 19.3 - - + -
3012N PEE 4.8 4.3 - - - +
220P PHE 3.8 0.2 - - - -
221P HIS* 1.3 96.2 - - + +
223P TYR* 1.3 79.3 + - + +
224P TYR 3.5 0.7 - - - -
225P THR* 3.1 20.6 + - - +
226P ILE* 3.2 18.2 + - + +
226Q LYS* 4.0 29.2 - - + +
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Residues in contact with TYR 223 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433N ASP* 2.5 39.4 + - - -
435N ASN* 2.8 21.9 + - - -
218P ILE* 3.9 20.9 - - + -
219P PRO* 3.5 24.9 - - + +
220P PHE 3.5 1.8 + - - -
222P PRO* 1.3 84.6 - - + +
224P TYR* 1.3 62.5 + - + +
226P ILE* 3.4 1.2 - - - +
227P LYS* 3.3 15.4 + - - +
226Q LYS* 3.4 22.9 - - + -
227Q TRP* 2.8 49.9 + + + +
229Q VAL* 3.8 11.3 - - - +
230Q LEU* 3.5 29.6 - - + +
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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
----------------------------------------------------------
23P ALA* 3.7 24.0 - - + -
24P PRO 2.6 28.5 + - - -
25P SER 3.2 18.4 + - - -
27P ILE* 3.2 38.4 + - + +
218P ILE* 3.6 15.3 - - + -
220P PHE* 2.8 41.3 + + + +
223P TYR* 1.3 74.1 - - + +
225P THR* 1.3 61.7 + - - +
226P ILE 3.3 0.7 - - - -
227P LYS* 3.7 23.1 - - + -
228P ASP* 2.8 39.3 + - - +
3002P UQ 4.6 4.0 - - - -
227Q TRP* 3.4 21.2 - + - -
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Residues in contact with THR 225 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18P PHE* 5.5 3.8 - - + -
19P ILE* 5.4 2.7 - - + -
220P PHE* 3.2 31.4 + - + +
221P HIS* 2.9 43.3 + - + +
222P PRO* 3.1 9.9 + - - +
224P TYR* 1.3 78.7 - - - +
226P ILE* 1.3 64.2 + - - +
228P ASP* 3.7 4.0 - - - +
229P ILE* 3.1 33.7 + - - +
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Residues in contact with ILE 226 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222P PRO* 3.2 18.6 - - + +
223P TYR 3.4 7.9 - - - +
225P THR* 1.3 80.8 + - - +
227P LYS* 1.3 67.1 + - - +
229P ILE* 3.3 18.6 + - + -
230P LEU* 3.1 21.5 + - - +
219Q VAL* 4.0 19.7 - - + +
222Q MET* 4.2 27.4 - - + +
223Q LYS* 3.8 34.5 - - + +
226Q LYS* 4.7 11.7 - - + -
227Q TRP* 4.1 10.1 - - + +
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Residues in contact with LYS 227 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27P ILE 3.1 27.1 + - - -
28P SER* 3.7 15.8 + - - +
29P SER* 4.0 3.7 + - - +
32P ASN* 3.2 20.2 + - - +
223P TYR 3.3 14.2 + - - +
224P TYR* 3.9 25.3 - - + +
225P THR 3.3 0.6 - - - -
226P ILE* 1.3 82.8 - - - +
228P ASP* 1.3 59.6 + - - +
230P LEU* 3.3 8.1 + - + +
231P GLY 3.0 21.3 + - - -
223Q LYS* 4.2 27.6 - - + +
227Q TRP* 4.3 10.2 - - + +
3003Q CDL 3.5 31.0 - - - +
3004T CDL 5.2 0.8 + - - -
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Residues in contact with ASP 228 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32P ASN* 3.7 20.4 + - - +
35P SER* 3.4 25.0 + - - +
36P LEU* 5.0 0.9 - - - +
39P ILE* 5.2 1.2 - - - +
220P PHE* 3.4 13.6 - - - -
224P TYR* 2.8 24.6 + - - +
225P THR* 3.7 5.8 - - - +
227P LYS* 1.3 75.4 - - - +
229P ILE* 1.3 56.2 + - + +
231P GLY* 3.2 1.0 + - - -
232P ALA* 2.8 34.2 + - - +
3002P UQ 3.0 33.5 - - - +
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Residues in contact with ILE 229 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225P THR* 3.1 27.1 + - - +
226P ILE* 3.6 18.6 - - + +
227P LYS 3.3 0.2 - - - -
228P ASP* 1.3 72.6 - - + +
230P LEU* 1.3 66.9 + - - +
232P ALA* 3.3 8.1 + - - +
233P LEU* 3.0 22.6 + - + +
219Q VAL* 4.1 23.1 - - + -
3006Q PEE 4.0 25.0 - - + +
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Residues in contact with LEU 230 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226P ILE 3.1 13.6 + - - +
227P LYS* 3.5 9.0 - - - +
229P ILE* 1.3 78.4 - - - +
231P GLY* 1.3 63.1 + - - +
233P LEU* 3.2 6.7 + - + +
234P LEU* 3.2 27.5 + - + +
216Q LEU* 4.2 25.4 - - + +
219Q VAL* 3.9 22.7 - - + -
220Q TYR* 3.8 39.7 - - + +
223Q LYS* 4.3 13.7 - - + -
3003Q CDL 4.0 29.2 - - - +
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Residues in contact with GLY 231 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32P ASN* 4.0 8.1 - - - -
36P LEU* 3.6 16.2 - - - +
227P LYS 3.0 13.2 + - - -
228P ASP 3.2 3.6 + - - -
230P LEU* 1.3 78.3 - - - +
232P ALA* 1.3 60.9 + - - +
234P LEU* 3.1 5.9 + - - +
235P LEU 2.9 18.4 + - - -
3003Q CDL 3.9 26.1 - - - +
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Residues in contact with ALA 232 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36P LEU* 3.7 11.6 - - - +
39P ILE* 3.4 27.1 - - + -
228P ASP 2.8 17.0 + - - +
229P ILE* 3.5 9.4 - - - +
231P GLY* 1.3 75.8 - - - +
233P LEU* 1.3 57.5 + - - +
235P LEU* 3.2 3.0 + - - +
236P ILE* 2.9 35.1 + - + +
3006Q PEE 4.4 19.3 - - + -
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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
----------------------------------------------------------
229P ILE* 3.0 14.4 + - + +
230P LEU* 3.5 8.1 - - - +
231P GLY 3.2 0.2 - - - -
232P ALA* 1.3 76.4 - - - +
234P LEU* 1.3 56.6 + - - +
236P ILE* 3.3 3.2 + - + -
237P LEU* 3.0 24.9 + - - +
212Q MET* 3.6 18.6 - - + +
215Q LEU* 4.0 21.3 - - + +
216Q LEU* 3.8 20.2 - - + -
219Q VAL* 3.5 40.6 - - + -
3006Q PEE 3.7 49.4 - - + -
47R VAL* 6.0 2.5 - - + -
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Residues in contact with LEU 234 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230P LEU* 3.2 15.9 + - + +
231P GLY 3.1 8.1 + - - +
233P LEU* 1.3 76.8 - - - +
235P LEU* 1.3 63.4 + - - +
237P LEU* 3.3 14.2 + - + +
238P ALA* 3.0 22.7 + - - +
216Q LEU* 3.7 30.5 - - + -
3003Q CDL 3.5 77.1 - - + +
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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
----------------------------------------------------------
36P LEU* 3.7 43.1 - - + +
39P ILE* 3.9 21.1 - - + -
40P CYS* 4.0 7.6 - - - -
43P LEU* 6.0 3.1 - - + -
89P MET* 3.7 35.4 - - + -
93P CYS* 4.0 18.4 - - - -
231P GLY 2.9 12.0 + - - +
232P ALA 3.2 8.0 + - - +
234P LEU* 1.3 77.9 - - - +
236P ILE* 1.3 59.7 + - + +
238P ALA* 3.3 3.8 + - - +
239P LEU* 2.9 30.3 + - + +
3003Q CDL 4.1 11.2 - - + +
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Residues in contact with ILE 236 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39P ILE* 5.6 2.9 - - + -
43P LEU* 5.4 5.6 - - + -
232P ALA* 2.9 21.7 + - + +
233P LEU* 3.7 6.3 - - - +
235P LEU* 1.3 79.5 - - + +
237P LEU* 1.3 59.0 + - - +
239P LEU* 4.3 7.9 - - + -
240P MET* 2.8 35.6 + - + +
212Q MET* 3.6 16.8 - - + -
3006Q PEE 3.8 96.0 - - + -
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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
----------------------------------------------------------
233P LEU 3.0 14.2 + - - +
234P LEU* 3.5 17.9 - - + +
235P LEU 3.2 0.2 - - - -
236P ILE* 1.3 76.5 - - - +
238P ALA* 1.3 57.3 + - - +
240P MET* 3.7 0.7 - - - +
241P LEU* 2.9 55.8 + - + +
208Q MET* 3.6 26.9 - - + -
209Q LEU* 4.5 7.2 - - + -
212Q MET* 3.7 25.5 - - + +
216Q LEU* 4.0 21.5 - - + -
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Residues in contact with ALA 238 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89P MET* 3.8 18.6 - - + -
234P LEU 3.0 11.2 + - - +
235P LEU* 3.6 8.3 - - - +
237P LEU* 1.3 77.2 - - - +
239P LEU* 1.3 62.7 + - - +
241P LEU* 3.4 13.2 + - - +
242P LEU* 3.3 26.3 + - - +
3003Q CDL 3.6 32.1 - - + -
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Residues in contact with LEU 239 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43P LEU* 3.9 28.0 - - + -
82P MET* 4.1 18.2 - - + +
85P ASN* 3.8 15.0 - - + -
86P GLY* 3.7 32.5 - - - +
89P MET* 3.9 15.9 - - + -
235P LEU* 2.9 20.2 + - + +
236P ILE* 3.7 8.5 - - - +
237P LEU 3.3 0.2 - - - -
238P ALA* 1.3 77.0 - - - +
240P MET* 1.3 75.9 + - - +
242P LEU* 3.1 8.0 + - - +
243P VAL* 2.9 32.4 + - + +
3006Q PEE 5.5 2.2 - - + -
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Residues in contact with MET 240 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78P ILE* 4.0 24.2 - - + -
82P MET* 4.2 12.3 - - + -
236P ILE* 2.8 37.0 + - + +
237P LEU 4.1 0.2 - - - +
239P LEU* 1.3 90.9 - - - +
241P LEU* 1.3 60.4 + - - +
243P VAL* 3.7 16.8 - - + +
244P LEU* 2.9 46.7 + - + +
208Q MET* 3.9 29.4 - - + +
3006Q PEE 3.9 32.1 - - + -
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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
----------------------------------------------------------
237P LEU* 2.9 43.6 + - + +
238P ALA* 3.7 11.2 - - - +
239P LEU 3.2 0.4 - - - -
240P MET* 1.3 77.1 - - - +
242P LEU* 1.3 59.9 + - + +
245P PHE* 3.0 48.2 + - + +
246P ALA* 3.5 2.5 + - - +
17Q LEU* 5.9 1.1 - - + -
208Q MET* 4.2 4.3 - - + -
209Q LEU* 4.0 27.1 - - + -
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Residues in contact with LEU 242 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85P ASN* 3.7 23.8 - - + +
89P MET* 3.9 28.5 - - + -
92P ILE* 5.7 0.7 - - + -
238P ALA 3.3 9.6 + - - +
239P LEU 3.1 7.5 + - - +
241P LEU* 1.3 80.4 - - + +
243P VAL* 1.3 54.9 + - - +
246P ALA* 2.7 48.5 + - + +
247P PRO* 2.7 7.9 - - - -
249P LEU* 4.3 15.9 - - + -
250P LEU* 3.8 38.1 - - + -
3008P JZR 6.1 2.0 - - + -
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Residues in contact with VAL 243 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77P TRP* 5.0 4.3 - - + -
78P ILE* 4.0 28.3 - - + -
81P TYR* 3.5 37.6 - - + +
82P MET* 3.8 19.3 - - + -
85P ASN* 4.1 7.6 - - + +
239P LEU* 2.9 33.1 + - + +
240P MET* 4.0 12.6 - - + +
242P LEU* 1.3 73.8 - - - +
244P LEU* 1.3 64.3 + - + +
247P PRO* 3.5 18.3 - - - +
201Q ARG* 3.8 6.6 - - - +
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Residues in contact with LEU 244 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77P TRP* 4.3 1.8 - - + -
78P ILE* 4.2 11.0 - - + -
240P MET* 2.9 38.8 + - + +
243P VAL* 1.3 79.3 - - + +
245P PHE* 1.3 60.4 + - + +
201Q ARG* 2.7 63.8 + - + +
202Q LYS 4.2 0.2 + - - -
204Q MET* 3.9 25.4 - - + +
205Q GLY* 3.5 28.7 - - - +
208Q MET* 3.9 18.8 - - + -
3006Q PEE 4.4 4.5 - - - +
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Residues in contact with PHE 245 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241P LEU* 3.0 33.2 + - + +
244P LEU* 1.3 85.5 - - - +
246P ALA* 1.3 64.7 + - + +
17Q LEU* 3.3 62.4 - - + +
18Q LEU* 3.7 13.7 - - + -
201Q ARG* 3.6 14.9 + - - +
202Q LYS* 4.3 7.5 - - + -
205Q GLY* 3.5 39.5 - - - -
208Q MET* 4.2 7.0 - - + -
209Q LEU* 3.8 30.7 - - + -
----------------------------------------------------------
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Residues in contact with ALA 246 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85P ASN* 4.6 1.0 - - - +
241P LEU 3.5 3.9 + - - +
242P LEU* 2.7 22.0 + - + +
245P PHE* 1.3 82.6 - - + +
247P PRO* 1.3 68.0 - - - +
248P ASP 3.2 4.2 + - - +
249P LEU* 3.2 36.4 + - + +
201Q ARG* 5.5 0.2 - - - +
----------------------------------------------------------
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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