Contacts of the helix formed by residues 187 - 220 (chain P) in PDB entry 2QJK
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 ASP 187 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44O VAL* 5.4 6.9 - - - +
66O LYS* 5.9 0.3 + - - -
69O GLY* 6.0 4.3 - - - -
73P VAL* 4.6 8.8 - - - +
151P TRP* 3.5 16.6 - - - -
181P LEU 5.7 0.4 - - - +
185P ALA* 3.1 10.8 + - + +
186P VAL* 1.3 75.4 - - - +
188P ASN* 1.3 81.9 + - - +
189P ALA* 3.4 6.1 - - + +
190P THR* 3.0 12.1 + - - +
191P LEU 3.1 13.3 + - - -
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Residues in contact with ASN 188 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70M THR* 4.9 1.0 + - - -
72P HIS* 3.2 31.0 - - - +
73P VAL* 2.9 51.8 + - + +
187P ASP* 1.3 83.1 + - - +
189P ALA* 1.3 70.7 + - - +
190P THR 2.6 4.0 + - - -
191P LEU* 2.6 15.2 + - - +
192P ASN* 2.8 30.0 + - - +
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Residues in contact with ALA 189 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67M MET 4.4 2.4 - - - +
68M HIS* 6.1 3.1 - - - +
41O SER* 5.3 7.2 - - - +
44O VAL* 5.5 7.0 - - + -
181P LEU 4.2 8.5 - - - +
182P GLY 4.3 10.8 - - - +
187P ASP* 4.5 4.4 - - + +
188P ASN* 1.3 80.5 - - - +
190P THR* 1.3 60.1 + - - +
192P ASN* 3.8 7.7 - - - +
193P ARG* 2.9 45.1 + - - +
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Residues in contact with THR 190 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151P TRP* 5.4 0.7 - - - -
159P ALA* 5.8 1.1 - - + -
163P THR* 4.8 0.9 - - + -
180P LEU 3.8 17.3 - - - +
181P LEU* 2.9 34.2 + - + -
186P VAL* 3.7 13.0 - - + -
187P ASP 3.0 26.9 + - - -
188P ASN 2.6 4.4 + - - -
189P ALA* 1.3 73.2 - - - +
191P LEU* 1.3 66.1 + - - -
193P ARG* 2.9 23.7 - - - +
194P PHE* 3.0 35.3 + - + -
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Residues in contact with LEU 191 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69P TYR* 3.6 18.8 - - - +
71P PRO* 4.4 3.8 - - + -
72P HIS* 3.8 14.6 - - - +
73P VAL* 3.4 33.2 - - + +
76P ALA* 4.0 9.2 - - + -
148P VAL* 4.3 5.6 - - + -
149P LEU* 3.7 22.4 - - + -
151P TRP* 3.8 37.2 - - + -
187P ASP 3.1 4.4 + - - +
188P ASN* 2.6 15.5 + - - +
190P THR* 1.3 74.2 - - - +
192P ASN* 1.3 63.5 + - - +
194P PHE* 3.0 17.1 + - - +
195P PHE* 3.0 11.4 + - - +
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Residues in contact with ASN 192 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66M ALA 3.0 14.8 + - - +
67M MET* 2.9 36.6 + - - +
68M HIS* 3.8 8.0 - - - +
69M TYR 3.3 19.9 + - - +
70M THR* 3.6 12.5 + - - -
71P PRO* 3.8 17.4 - - - +
188P ASN* 2.8 28.2 + - - +
189P ALA* 3.8 7.6 - - - +
191P LEU* 1.3 76.0 - - - +
193P ARG* 1.3 62.6 + - - +
195P PHE* 3.2 15.8 + - - +
196P SER 3.3 8.8 + - - -
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Residues in contact with ARG 193 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67M MET* 3.8 31.5 + - + +
68M HIS* 4.3 15.6 - - - -
38O MET* 3.1 71.4 + - + +
39O ASN 5.0 1.0 + - - -
179P TRP 3.3 5.7 + - - -
180P LEU* 3.1 21.2 + - - -
182P GLY* 3.3 18.9 + - - -
189P ALA* 2.9 27.6 + - - +
190P THR* 2.9 22.6 + - - +
192P ASN* 1.3 77.9 - - - +
194P PHE* 1.3 74.3 + - + +
196P SER* 3.4 2.8 + - - -
197P LEU* 3.1 28.5 + - + +
503P SMA 6.4 0.2 - - - -
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Residues in contact with PHE 194 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144P PHE* 3.6 35.7 - + - -
145P MET* 3.7 25.0 - - + +
148P VAL* 3.7 27.1 - - + -
149P LEU* 4.6 7.9 - - + -
159P ALA* 4.5 6.7 - - + -
163P THR* 4.5 9.2 - - + -
180P LEU* 4.6 6.7 - - + -
190P THR* 3.0 38.2 + - + +
191P LEU* 3.0 11.3 + - - +
193P ARG* 1.3 85.3 - - + +
195P PHE* 1.3 55.7 + - - +
197P LEU* 3.1 2.5 + - + +
198P HIS* 2.6 39.5 + - - +
503P SMA 3.8 27.1 - - + -
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Residues in contact with PHE 195 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66M ALA 5.4 3.1 - - - -
195M PHE* 2.9 44.0 - + - -
199M TYR* 5.5 0.2 - + - -
66P ALA* 4.4 21.3 - - + -
69P TYR* 3.6 33.4 - + - -
71P PRO* 3.7 31.0 - - + -
149P LEU* 4.0 18.5 - - + +
191P LEU 3.0 8.4 + - - +
192P ASN* 3.2 10.5 + - - +
194P PHE* 1.3 77.3 - - - +
196P SER* 1.3 66.9 + - - +
198P HIS* 3.1 3.9 + - + +
199P TYR* 3.0 36.9 + + - +
502P HEM 4.0 18.8 - - + -
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Residues in contact with SER 196 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63M ILE* 2.9 27.5 + - - +
66M ALA* 3.3 17.9 - - - +
67M MET* 3.7 21.5 - - - -
199M TYR* 2.7 37.0 + - - -
192P ASN 3.3 4.1 + - - -
193P ARG 3.6 8.5 - - - -
195P PHE* 1.3 82.5 - - - +
197P LEU* 1.3 62.3 + - - +
199P TYR* 3.4 0.9 - - - +
200P LEU* 3.2 11.4 + - - +
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Residues in contact with LEU 197 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63M ILE* 4.9 2.7 - - + -
67M MET* 3.5 25.8 - - + -
38O MET* 5.2 7.6 - - + -
145P MET* 3.7 17.9 - - + -
193P ARG* 3.1 22.2 + - + +
194P PHE* 5.0 0.7 - - + -
196P SER* 1.3 76.7 - - - +
198P HIS* 1.3 66.1 + - - +
199P TYR 2.9 2.0 + - - -
200P LEU* 3.1 21.7 + - + -
201P LEU* 3.0 33.2 + - + +
503P SMA 3.8 26.9 - - + -
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Residues in contact with HIS 198 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142P THR* 3.4 19.6 + - + +
145P MET* 4.2 12.7 - - + -
146P GLY* 3.5 19.7 + - - -
149P LEU* 3.5 19.1 - - + -
194P PHE 2.6 22.1 + - - +
195P PHE* 3.1 4.2 + + + +
197P LEU* 1.3 73.3 - - - +
199P TYR* 1.3 56.1 + - - +
202P PRO* 3.0 25.4 - - - +
502P HEM 2.0 97.5 + + + -
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Residues in contact with TYR 199 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196M SER* 3.0 26.8 + - - -
199M TYR* 3.3 56.1 - + + -
200M LEU* 3.5 13.4 - - - +
63P ILE* 3.8 14.5 - - + +
66P ALA* 4.2 12.8 - - + -
195P PHE* 3.0 26.2 + + + +
196P SER 3.4 10.5 - - - +
197P LEU 2.9 0.2 - - - -
198P HIS* 1.3 78.7 - - - +
200P LEU* 1.3 64.4 + - - +
202P PRO* 3.0 15.8 - - - +
203P PHE* 3.4 34.3 - + - -
502P HEM 3.1 35.0 - - + +
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Residues in contact with LEU 200 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63M ILE* 3.3 37.2 - - + -
199M TYR* 3.7 8.5 + - - +
203M PHE* 3.9 26.0 - - + -
196P SER 3.2 12.5 + - - +
197P LEU* 3.1 17.0 + - + +
199P TYR* 1.3 80.7 - - - +
201P LEU* 1.3 68.8 + - + +
203P PHE* 3.0 23.5 + - + +
204P VAL* 3.5 17.9 + - + -
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Residues in contact with LEU 201 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138P ALA* 3.8 12.8 - - + +
141P ALA* 3.7 12.6 - - + -
142P THR* 3.3 37.7 - - + +
145P MET* 3.7 16.2 - - + -
197P LEU* 3.0 22.0 + - + +
200P LEU* 1.3 74.9 - - + +
202P PRO* 1.3 71.2 - - + +
204P VAL* 2.7 34.6 + - + +
205P ILE* 2.8 14.4 + - + +
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Residues in contact with PRO 202 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55P LEU* 4.5 5.6 - - + +
59P ILE* 4.3 13.8 - - + +
142P THR* 4.0 6.3 - - + -
198P HIS 3.0 19.7 - - - +
199P TYR 3.0 21.5 - - - +
201P LEU* 1.3 84.6 - - + +
203P PHE* 1.3 51.9 + - + +
205P ILE* 3.0 15.1 - - + +
206P ALA* 2.7 33.7 + - - +
502P HEM 3.7 50.0 - - + -
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Residues in contact with PHE 203 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200M LEU* 3.8 25.4 - - + -
203M PHE* 3.3 60.1 - + + -
59P ILE* 4.6 25.4 - - + -
63P ILE* 4.9 1.8 - - + -
199P TYR* 3.4 31.9 - + - -
200P LEU 3.0 14.7 + - - +
202P PRO* 1.3 73.4 - - + +
204P VAL* 1.3 68.7 + - + +
206P ALA* 3.1 9.4 + - + +
207P ALA* 2.8 23.8 + - - +
502P HEM 5.6 4.0 - - + -
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Residues in contact with VAL 204 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138P ALA* 5.8 2.9 - - + -
200P LEU* 3.7 26.5 - - + +
201P LEU* 2.7 29.5 + - + +
203P PHE* 1.3 74.6 - - + +
205P ILE* 1.3 65.5 + - + +
207P ALA* 3.0 10.5 + - + +
208P LEU* 3.0 35.7 + - + +
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Residues in contact with ILE 205 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55P LEU* 4.1 13.5 - - + -
104P PHE* 5.3 0.7 - - + -
135P ILE* 4.4 8.7 - - + -
138P ALA* 3.9 16.2 - - + -
139P MET* 3.9 35.2 - - + +
142P THR* 3.9 12.6 - - - +
201P LEU 2.8 17.9 + - - +
202P PRO* 3.0 10.1 - - + +
204P VAL* 1.3 76.4 - - - +
206P ALA* 1.3 66.7 - - - +
208P LEU* 2.8 13.5 + - - +
209P VAL* 2.8 38.5 + - + +
501P HEM 4.3 10.8 - - + -
502P HEM 3.9 18.8 - - + -
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Residues in contact with ALA 206 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55P LEU* 3.7 20.4 - - + +
59P ILE* 4.9 7.6 - - + -
202P PRO 2.7 15.7 + - - +
203P PHE* 3.1 16.6 - - + +
205P ILE* 1.3 74.6 - - - +
207P ALA* 1.3 63.1 + - - +
209P VAL* 3.2 5.2 + - - +
210P ALA* 3.0 19.4 + - - +
505P ANJ 4.2 13.8 - - + +
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Residues in contact with ALA 207 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203P PHE 2.8 15.0 + - - +
204P VAL* 3.1 14.8 - - + +
206P ALA* 1.3 72.2 - - - +
208P LEU* 1.3 66.5 + - + +
210P ALA* 3.0 24.1 - - - +
211P ILE* 3.3 10.2 + - - +
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Residues in contact with LEU 208 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131P VAL* 3.9 11.9 - - + +
134P LEU* 3.9 35.0 - - + +
135P ILE* 3.8 24.9 - - + +
138P ALA* 5.2 4.7 - - + -
204P VAL* 3.0 27.9 + - + +
205P ILE* 2.8 15.7 + - - +
207P ALA* 1.3 73.6 - - + +
209P VAL* 1.3 52.5 + - - +
211P ILE* 2.8 23.4 + - + +
212P HIS* 2.7 33.1 + - - +
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Residues in contact with VAL 209 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55P LEU* 3.9 9.6 - - + -
135P ILE* 3.9 3.8 - - + +
205P ILE* 2.8 34.2 + - + +
206P ALA* 3.3 7.6 - - - +
208P LEU* 1.3 71.3 - - - +
210P ALA* 1.3 66.5 + - - +
212P HIS* 3.2 10.2 - - + +
213P ILE* 3.0 25.9 + - + +
501P HEM 3.6 51.1 - - + -
505P ANJ 4.1 25.4 - - + +
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Residues in contact with ALA 210 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206P ALA 3.0 10.1 + - - +
207P ALA* 3.0 15.8 + - - +
208P LEU 3.0 0.2 - - - -
209P VAL* 1.3 75.2 - - - +
211P ILE* 1.3 57.7 + - + +
213P ILE* 2.7 32.4 + - - +
214P TRP* 2.8 12.8 + - - +
505P ANJ 4.8 6.3 + - - -
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Residues in contact with ILE 211 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23M LEU* 3.8 28.3 - - + -
25M ILE* 4.6 16.4 - - + -
131P VAL* 4.2 19.3 - - + -
207P ALA 3.8 11.7 - - - +
208P LEU* 2.8 24.4 + - + +
210P ALA* 1.3 74.1 - - + +
212P HIS* 1.3 54.2 + - - +
214P TRP* 3.0 17.6 + - + +
215P ALA* 2.7 34.4 + - + +
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Residues in contact with HIS 212 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128P THR* 3.6 31.2 + - + +
131P VAL* 3.9 12.3 - - + +
132P GLY* 3.9 8.0 + - - -
135P ILE* 4.2 5.6 - - + -
208P LEU 2.7 15.6 + - - +
209P VAL* 3.2 15.9 - - + +
211P ILE* 1.3 73.1 - - - +
213P ILE* 1.3 63.3 + - + +
215P ALA* 3.2 6.0 + - - +
216P PHE* 3.1 24.3 + + - +
501P HEM 1.9 99.9 + + + -
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Residues in contact with ILE 213 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32P THR* 5.7 2.9 - - + -
209P VAL* 3.0 16.6 + - + +
210P ALA* 2.7 14.0 + - - +
212P HIS* 1.3 72.2 - - + +
214P TRP* 1.3 66.7 + - - +
216P PHE* 3.2 23.6 + - + -
217P HIS* 2.9 52.4 + - + +
501P HEM 5.3 1.3 - - + -
505P ANJ 3.0 69.1 - - + +
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Residues in contact with TRP 214 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23M LEU* 3.6 15.7 - - + -
24M PRO* 3.9 24.7 - - + +
25M ILE* 3.3 46.9 - - + -
28M LEU* 3.7 32.5 - - + -
210P ALA 2.8 15.6 + - - +
211P ILE* 3.4 21.8 - - + +
213P ILE* 1.3 73.9 - - - +
215P ALA* 1.3 59.3 + - - +
217P HIS* 3.4 7.7 + - + +
218P SER* 2.8 31.1 + - - -
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Residues in contact with ALA 215 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22M ARG 4.0 2.9 - - - +
23M LEU* 3.6 23.3 - - + -
127P VAL* 4.7 7.9 - - + -
128P THR* 3.8 26.7 + - - +
131P VAL* 5.7 0.9 - - + -
211P ILE* 2.7 21.6 + - + +
212P HIS* 3.5 5.4 - - - +
214P TRP* 1.3 70.0 - - - +
216P PHE* 1.3 59.1 + - - +
217P HIS 3.0 4.5 - - - -
218P SER* 3.0 19.0 + - - -
219P THR* 3.5 15.6 + - - +
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Residues in contact with PHE 216 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128P THR* 4.0 6.7 - - + +
212P HIS* 3.1 28.5 + + - +
213P ILE* 3.2 35.6 + - + -
215P ALA* 1.3 76.9 - - - +
217P HIS* 1.3 76.5 + + - +
218P SER 3.3 0.2 - - - -
219P THR* 4.0 7.9 - - - -
220P GLY* 3.2 26.7 + - - -
221P ASN* 3.4 26.8 + - - -
501P HEM 3.5 68.2 - + + +
505P ANJ 3.4 22.4 - - - -
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Residues in contact with HIS 217 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31P ASP 4.5 2.4 + - - -
32P THR* 3.2 44.4 + - + +
35P ILE* 3.7 42.7 - - + +
213P ILE* 2.9 44.0 + - + +
214P TRP* 3.5 11.0 - - + +
215P ALA 3.0 0.2 - - - -
216P PHE* 1.3 96.4 - + - +
218P SER* 1.3 60.9 + - - +
219P THR 3.2 1.4 + - - -
220P GLY* 3.8 4.3 + - - -
505P ANJ 4.1 10.1 + - - -
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Residues in contact with SER 218 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21M SER 4.6 6.1 - - - +
22M ARG 3.2 24.6 + - - +
23M LEU* 4.4 0.5 - - - +
24M PRO* 3.9 12.8 - - - +
3P GLY* 5.0 11.9 + - - -
214P TRP* 2.8 33.7 + - - -
215P ALA* 3.0 6.5 + - - -
217P HIS* 1.3 78.5 - - - +
219P THR* 1.3 59.5 + - - +
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Residues in contact with THR 219 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21M SER 4.6 3.4 - - - +
22M ARG* 3.9 24.5 - - + +
3P GLY* 5.9 2.7 - - - -
4P ILE* 5.8 0.2 - - - -
124P PRO* 4.3 34.7 - - + +
125P ARG* 4.1 15.0 + - - +
128P THR* 4.9 2.0 + - - +
215P ALA 3.7 14.0 + - - +
216P PHE* 3.9 6.8 + - - -
218P SER* 1.3 82.4 - - - +
220P GLY* 1.3 73.8 + - - +
228P GLU* 4.2 5.2 - - - +
231P ARG* 3.5 23.5 + - - +
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Residues in contact with GLY 220 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3P GLY* 6.1 0.4 - - - -
4P ILE* 4.6 19.3 - - - -
35P ILE* 4.8 8.3 - - - -
36P PRO 6.0 0.4 - - - -
125P ARG* 3.3 7.3 + - - -
216P PHE 3.2 14.5 + - - +
217P HIS 3.8 6.5 + - - -
218P SER 3.7 0.8 - - - -
219P THR* 1.3 95.5 + - - +
221P ASN* 1.3 64.9 + - - -
231P ARG* 4.9 1.8 - - - -
501P HEM 3.7 3.3 - - - +
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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