Contacts of the helix formed by residues 187 - 220 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G VAL* 4.3 9.1 - - - +
151G TRP* 3.6 17.1 - - - -
181G LEU 5.7 0.4 - - - +
185G ALA* 3.2 10.6 + - + +
186G VAL* 1.3 75.1 - - - +
188G ASN* 1.3 86.4 + - - +
189G ALA* 3.4 5.8 - - + +
190G THR* 3.0 19.3 + - - +
191G LEU 3.1 8.0 + - - -
44L VAL* 6.0 1.4 - - - +
69L GLY* 5.9 5.5 - - - -
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Residues in contact with ASN 188 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G PRO 5.1 0.2 - - - -
72G HIS* 3.3 30.3 - - - +
73G VAL* 2.9 52.2 + - + +
187G ASP* 1.3 84.5 + - - +
189G ALA* 1.3 68.9 + - - +
190G THR 2.7 2.4 + - - -
191G LEU* 2.7 13.6 + - - +
192G ASN* 2.8 30.1 + - - +
70J THR* 5.0 0.8 + - - -
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Residues in contact with ALA 189 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181G LEU 4.1 8.5 - - - +
182G GLY 4.2 10.8 - - - +
187G ASP* 3.4 5.0 - - + +
188G ASN* 1.3 79.6 - - - +
190G THR* 1.3 61.4 + - - +
192G ASN* 3.8 7.8 - - - +
193G ARG* 2.9 46.3 + - - +
67J MET 4.5 3.1 - - - +
68J HIS* 6.1 3.1 - - + +
41L SER* 5.4 3.6 - - - +
44L VAL* 5.1 10.3 - - + -
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Residues in contact with THR 190 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G TRP* 5.4 0.4 - - - -
159G ALA* 5.8 0.7 - - + -
163G THR* 4.8 0.2 - - + -
180G LEU 3.9 15.5 - - - +
181G LEU* 3.0 31.3 + - + -
186G VAL* 3.7 13.4 - - + -
187G ASP* 3.0 25.8 + - - +
188G ASN 2.7 4.0 + - - -
189G ALA* 1.3 72.4 - - - +
191G LEU* 1.3 67.2 + - - -
193G ARG* 2.9 25.8 - - - +
194G PHE* 3.0 37.7 + - + -
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Residues in contact with LEU 191 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G TYR* 3.6 18.6 - - - +
71G PRO* 4.4 2.9 - - + -
72G HIS* 3.8 15.7 - - - +
73G VAL* 3.4 33.0 - - + +
76G ALA* 4.1 8.5 - - + -
148G VAL* 4.3 5.6 - - + -
149G LEU* 3.8 20.6 - - + +
151G TRP* 3.8 39.8 - - + -
187G ASP 3.1 4.3 + - - +
188G ASN* 2.7 13.2 + - - +
190G THR* 1.3 73.0 - - - +
192G ASN* 1.3 64.1 + - - +
194G PHE* 2.9 17.7 + - + +
195G PHE* 3.0 10.7 + - - +
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Residues in contact with ASN 192 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G PRO* 3.8 22.2 + - - +
188G ASN* 2.8 28.0 + - - +
189G ALA* 3.8 6.7 - - - +
191G LEU* 1.3 75.1 - - - +
193G ARG* 1.3 61.5 + - - +
195G PHE* 3.3 15.5 + - - +
196G SER* 3.4 9.0 + - - -
66J ALA 2.9 27.9 + - - +
67J MET* 3.0 24.9 + - - +
68J HIS* 3.8 7.2 - - - +
69J TYR 3.4 20.0 + - - +
70J THR* 3.8 8.3 + - - -
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Residues in contact with ARG 193 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179G TRP 3.3 5.5 + - - -
180G LEU 3.0 21.6 + - - -
182G GLY* 3.3 18.7 + - - -
189G ALA* 2.9 28.8 + - - +
190G THR* 2.9 22.2 - - - +
192G ASN* 1.3 76.8 - - - +
194G PHE* 1.3 75.0 + - + +
195G PHE 3.2 0.2 - - - -
196G SER* 3.5 2.3 + - - -
197G LEU* 3.1 30.0 + - + +
67J MET* 3.8 31.8 + - + +
68J HIS* 4.4 15.9 - - - -
38L MET* 2.9 71.6 + - + +
39L ASN 5.0 1.4 + - - -
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Residues in contact with PHE 194 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G PHE* 3.6 36.6 - + - -
145G MET* 3.7 22.5 - - + +
148G VAL* 3.7 30.7 - - + -
149G LEU* 4.6 8.3 - - + -
159G ALA* 4.5 5.6 - - + -
163G THR* 4.5 12.3 - - + -
180G LEU* 4.6 7.0 - - + -
190G THR* 3.0 36.6 + - + +
191G LEU* 2.9 11.3 + - - +
193G ARG* 1.3 85.2 - - + +
195G PHE* 1.3 55.7 + - - +
197G LEU* 3.1 3.2 + - + +
198G HIS* 2.6 39.2 + - - +
503G SMA 4.3 21.3 - - + -
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Residues in contact with PHE 195 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G ALA* 4.5 22.7 - - + -
69G TYR* 3.6 33.2 - + - -
71G PRO* 3.7 29.4 - - + -
149G LEU* 4.0 19.0 - - + +
191G LEU 3.0 8.2 + - - +
192G ASN 3.4 10.3 - - - +
193G ARG 3.2 0.2 - - - -
194G PHE* 1.3 75.6 - - - +
196G SER* 1.3 66.6 + - - +
198G HIS* 3.1 4.1 + + + +
199G TYR* 3.0 37.3 + + - +
502G HEM 4.2 20.9 - - + -
66J ALA 5.3 3.4 - - - -
195J PHE* 2.9 42.6 - + - -
199J TYR* 5.4 0.9 - + - -
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Residues in contact with SER 196 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192G ASN 3.4 4.4 + - - -
193G ARG 3.7 8.3 - - - -
194G PHE 3.3 0.2 - - - -
195G PHE* 1.3 83.2 - - - +
197G LEU* 1.3 58.7 + - - +
199G TYR* 3.5 0.5 - - - +
200G LEU* 3.2 13.7 + - - +
63J ILE* 2.9 33.8 + - - +
66J ALA* 3.5 14.6 - - - +
67J MET* 3.8 21.5 - - - -
199J TYR* 2.7 33.9 + - - -
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Residues in contact with LEU 197 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145G MET* 3.6 19.1 - - + -
193G ARG* 3.1 23.1 + - + +
194G PHE* 4.9 2.0 - - + -
195G PHE 3.1 0.4 - - - -
196G SER* 1.3 75.7 - - - +
198G HIS* 1.3 67.2 + - - +
199G TYR 3.0 2.0 + - - -
200G LEU* 3.2 23.2 + - + +
201G LEU* 3.0 33.6 + - + +
503G SMA 4.2 25.6 - - + -
63J ILE* 4.9 2.2 - - + -
67J MET* 3.6 25.1 - - + -
38L MET* 5.1 7.0 - - + -
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Residues in contact with HIS 198 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142G THR* 3.4 26.6 + - + +
145G MET* 4.2 14.1 - - + -
146G GLY* 3.5 12.9 + - - -
149G LEU* 3.6 17.9 - - + -
194G PHE 2.6 20.2 + - - +
195G PHE* 3.7 4.5 - + - +
197G LEU* 1.3 72.7 - - - +
199G TYR* 1.3 57.5 + - - +
202G PRO* 2.9 27.6 - - - +
502G HEM 2.0 96.6 + + + -
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Residues in contact with TYR 199 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63G ILE* 3.6 18.2 - - + +
66G ALA* 4.3 4.0 - - + -
195G PHE* 3.0 23.8 + + - +
196G SER 3.5 3.8 - - - +
197G LEU 3.0 0.2 - - - -
198G HIS* 1.3 76.2 - - - +
200G LEU* 1.3 65.4 + - - +
202G PRO* 3.0 15.8 - - - +
203G PHE* 3.6 33.3 - + - -
502G HEM 3.2 37.5 - - + +
195J PHE* 5.9 0.2 - + - -
196J SER* 2.9 36.2 + - - -
199J TYR* 3.3 61.0 - + + -
200J LEU* 3.7 7.4 - - - +
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Residues in contact with LEU 200 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196G SER 3.2 12.7 + - - +
197G LEU* 3.7 18.2 - - + +
199G TYR* 1.3 81.2 - - - +
201G LEU* 1.3 69.6 + - + +
203G PHE* 3.1 19.7 + - + +
204G VAL* 3.5 20.5 + - + -
63J ILE* 3.3 35.7 - - + -
199J TYR* 3.7 8.3 + - - +
203J PHE* 3.9 25.6 - - + -
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Residues in contact with LEU 201 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138G ALA* 3.9 12.6 - - + +
141G ALA* 3.8 13.2 - - + -
142G THR* 3.3 28.9 - - + +
145G MET* 3.7 25.4 - - + -
197G LEU* 3.0 21.7 + - + +
200G LEU* 1.3 76.0 - - + +
202G PRO* 1.3 64.0 - - + +
204G VAL* 2.7 45.0 + - + +
205G ILE* 2.8 14.9 + - + +
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Residues in contact with PRO 202 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G LEU* 4.5 4.9 - - + +
59G ILE* 4.3 16.9 - - + +
142G THR* 4.0 7.6 - - + +
198G HIS 2.9 28.7 - - - +
199G TYR 3.0 11.0 - - - +
201G LEU* 1.3 84.2 - - + +
203G PHE* 1.3 57.7 + - + +
205G ILE* 3.1 14.2 + - + +
206G ALA* 2.8 27.9 + - - +
502G HEM 3.6 48.9 - - + -
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Residues in contact with PHE 203 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59G ILE* 4.6 26.9 - - + -
63G ILE* 4.9 0.7 - - + -
199G TYR* 3.6 32.8 - + - -
200G LEU* 3.1 13.9 + - + +
202G PRO* 1.3 74.6 - - + +
204G VAL* 1.3 67.8 + - + +
206G ALA* 3.1 10.0 + - + +
207G ALA* 2.8 23.4 + - - +
502G HEM 5.5 2.5 - - + -
200J LEU* 3.9 24.0 - - + -
203J PHE* 3.2 61.5 - + + -
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Residues in contact with VAL 204 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138G ALA* 5.9 3.1 - - + -
200G LEU* 3.6 26.9 - - + +
201G LEU* 2.7 34.5 + - + +
203G PHE* 1.3 71.9 - - + +
205G ILE* 1.3 64.1 + - - +
207G ALA* 3.0 11.5 + - + +
208G LEU* 2.9 35.0 + - + +
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Residues in contact with ILE 205 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G LEU* 4.1 11.9 - - + -
104G PHE* 5.2 0.7 - - + -
135G ILE* 4.4 8.5 - - + -
138G ALA* 3.9 16.2 - - + -
139G MET* 3.9 35.9 - - + +
142G THR* 3.9 12.6 - - - +
201G LEU 2.8 18.5 + - - +
202G PRO* 3.1 9.9 - - + +
204G VAL* 1.3 76.2 - - - +
206G ALA* 1.3 65.7 + - - +
208G LEU* 2.8 13.4 + - - +
209G VAL* 2.8 39.4 + - + +
501G HEM 4.1 13.2 - - + -
502G HEM 4.1 18.2 - - + -
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Residues in contact with ALA 206 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G LEU* 3.7 21.1 - - + +
59G ILE* 4.9 7.2 - - + -
202G PRO 2.8 15.7 + - - +
203G PHE* 3.1 16.8 - - + +
205G ILE* 1.3 72.9 - - - +
207G ALA* 1.3 63.4 + - - +
209G VAL* 3.2 4.7 + - - +
210G ALA* 3.0 20.4 + - - +
505G ANJ 4.5 15.8 - - + +
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Residues in contact with ALA 207 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203G PHE 2.8 14.6 + - - +
204G VAL* 3.0 15.0 + - + +
206G ALA* 1.3 73.1 - - - +
208G LEU* 1.3 66.5 + - + +
210G ALA* 3.0 24.3 - - - +
211G ILE* 3.3 9.6 + - - +
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Residues in contact with LEU 208 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131G VAL* 4.0 11.1 - - + +
134G LEU* 3.9 36.3 - - + +
135G ILE* 3.8 22.4 - - + +
138G ALA* 5.2 4.5 - - + -
204G VAL* 2.9 28.3 + - + +
205G ILE* 2.8 15.5 + - - +
207G ALA* 1.3 73.6 - - + +
209G VAL* 1.3 51.9 + - - +
211G ILE* 2.8 22.6 + - + +
212G HIS* 2.7 34.2 + - - +
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Residues in contact with VAL 209 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G LEU* 3.9 9.6 - - + -
135G ILE* 4.0 3.1 - - + +
205G ILE* 2.8 33.1 + - + +
206G ALA* 3.3 7.9 - - - +
208G LEU* 1.3 71.1 - - - +
210G ALA* 1.3 65.3 + - - +
212G HIS* 3.3 9.6 - - + +
213G ILE* 3.0 33.4 + - + +
501G HEM 3.3 54.7 - - + -
505G ANJ 3.9 24.5 - - + +
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Residues in contact with ALA 210 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206G ALA 3.0 9.7 + - - +
207G ALA* 3.0 15.6 + - - +
208G LEU 3.0 0.2 - - - -
209G VAL* 1.3 75.2 - - - +
211G ILE* 1.3 57.6 + - + +
213G ILE* 2.7 29.4 + - - +
214G TRP* 2.8 13.2 + - - +
505G ANJ 4.3 16.3 + - + +
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Residues in contact with ILE 211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131G VAL* 4.2 18.8 - - + -
207G ALA 3.9 11.7 - - - +
208G LEU* 2.8 24.9 + - + +
210G ALA* 1.3 74.5 - - + +
212G HIS* 1.3 52.9 + - - +
214G TRP* 3.3 17.4 - - + +
215G ALA* 2.7 35.0 + - + +
23J LEU* 3.6 30.1 - - + -
25J ILE* 4.4 18.8 - - + -
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Residues in contact with HIS 212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G THR* 3.6 32.1 + - + +
131G VAL* 3.9 12.9 - - + +
132G GLY* 4.0 7.9 + - - -
135G ILE* 4.1 5.2 - - + -
208G LEU 2.7 14.9 + - - +
209G VAL* 3.3 15.7 - - - +
211G ILE* 1.3 73.1 - - - +
213G ILE* 1.3 65.4 + - - +
215G ALA* 3.2 5.0 + - - +
216G PHE* 3.0 24.6 + + - +
501G HEM 2.0 98.8 + + + -
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Residues in contact with ILE 213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G THR* 5.7 1.8 - - + -
209G VAL* 3.0 13.9 + - + +
210G ALA* 2.7 12.8 + - - +
212G HIS* 1.3 71.4 - - + +
214G TRP* 1.3 65.8 + - - +
216G PHE* 3.1 24.0 + - + -
217G HIS* 2.9 52.2 + - + +
501G HEM 5.1 2.7 - - + -
505G ANJ 2.9 73.8 - - + +
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Residues in contact with TRP 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210G ALA 2.8 14.8 + - - +
211G ILE* 3.3 23.3 - - + +
213G ILE* 1.3 74.3 - - - +
215G ALA* 1.3 60.5 + - - +
217G HIS* 3.3 8.4 - - + +
218G SER* 2.9 29.6 + - - -
23J LEU* 3.6 13.9 - - + -
24J PRO* 3.8 26.2 - - + +
25J ILE* 3.3 46.2 - - + -
28J LEU* 3.8 32.8 - - + -
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Residues in contact with ALA 215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127G VAL* 4.7 6.1 - - + -
128G THR* 3.9 26.4 + - - +
131G VAL* 5.7 0.9 - - + -
211G ILE* 2.7 20.8 + - + +
212G HIS* 3.5 5.6 - - - +
214G TRP* 1.3 71.4 - - - +
216G PHE* 1.3 57.4 + - - +
217G HIS 2.9 4.9 - - - -
218G SER* 3.0 18.9 + - - -
219G THR* 3.5 15.9 + - - +
22J ARG 3.9 3.2 - - - +
23J LEU* 3.6 24.4 - - + +
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Residues in contact with PHE 216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G THR* 3.9 8.3 + - + +
212G HIS* 3.0 28.6 + + - +
213G ILE* 3.1 35.2 - - + -
215G ALA* 1.3 76.8 - - - +
217G HIS* 1.3 76.8 + + - +
219G THR* 4.0 8.1 - - - -
220G GLY* 3.2 27.4 + - - -
221G ASN* 3.3 27.3 + - - -
501G HEM 3.7 65.5 - + + +
505G ANJ 3.2 25.8 - - - -
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Residues in contact with HIS 217 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G ILE* 4.9 5.9 - - - +
31G ASP 4.3 4.1 + - - -
32G THR* 3.2 50.1 + - + +
35G ILE* 4.2 37.7 - - + +
213G ILE* 2.9 37.6 + - + +
214G TRP* 3.3 12.1 - - + +
216G PHE* 1.3 103.2 - + - +
218G SER* 1.3 59.7 + - - +
219G THR 3.3 1.6 + - - -
220G GLY* 3.8 4.9 + - - -
505G ANJ 4.4 7.3 + - - -
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Residues in contact with SER 218 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G GLY* 5.5 6.4 + - - -
4G ILE* 5.7 2.7 - - - +
214G TRP* 2.9 30.1 + - - -
215G ALA* 3.0 4.9 + - - -
217G HIS* 1.3 79.3 - - - +
219G THR* 1.3 59.2 + - - +
21J SER 4.6 6.3 - - - +
22J ARG 3.3 26.4 + - - -
23J LEU* 4.5 0.2 - - - +
24J PRO* 3.9 12.4 - - - +
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Residues in contact with THR 219 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G ILE* 5.2 3.6 - - - -
124G PRO* 4.3 35.6 - - + +
125G ARG* 4.5 9.3 + - - +
128G THR* 4.8 3.6 + - - +
215G ALA 3.7 14.0 + - - +
216G PHE* 3.9 6.1 + - - -
217G HIS 3.3 0.2 - - - -
218G SER* 1.3 82.5 - - - +
220G GLY* 1.3 73.8 + - - +
228G GLU* 4.3 4.9 - - - +
231G ARG* 3.4 23.0 + - - +
501G HEM 4.3 4.9 + - - -
21J SER 4.5 3.8 - - - +
22J ARG* 3.9 23.8 - - + +
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Residues in contact with GLY 220 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G ILE* 4.7 14.3 - - - +
35G ILE* 4.8 8.1 - - - -
36G PRO 6.0 1.1 - - - -
125G ARG* 3.1 11.9 + - - -
216G PHE 3.2 14.4 + - - +
217G HIS 3.8 6.8 + - - -
218G SER 3.6 1.4 - - - -
219G THR* 1.3 92.4 + - - +
221G ASN* 1.3 63.0 + - - -
231G ARG* 4.9 3.6 - - - -
501G HEM 3.7 3.1 - - - +
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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