Contacts of the helix formed by residues 178 - 208 (chain G) in PDB entry 5UQ9
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 178 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106G TYR* 3.9 14.7 - - - +
109G THR* 3.6 36.1 + - - +
110G THR* 4.4 0.9 - - - -
113G CYS* 4.9 0.4 - - - +
125G GLY 5.3 0.2 - - - -
144G GLY 4.4 5.6 - - - -
145G GLY* 3.5 10.1 - - - -
176G ASP 3.5 0.4 - - - -
177G GLU* 1.3 75.0 - - - +
179G ALA* 1.3 62.1 + - - +
180G GLY 3.2 4.5 + - - -
181G HIS* 3.7 9.4 + - - +
182G PHE 3.8 6.6 + - - -
351G TRP* 4.0 3.3 - - - -
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Residues in contact with ALA 179 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145G GLY 4.7 2.0 - - - +
174G VAL* 3.6 2.2 - - + -
175G GLY* 3.9 13.9 - - - -
176G ASP 3.4 17.3 + - - +
177G GLU 3.1 2.2 + - - -
178G GLY* 1.3 74.6 - - - +
180G GLY* 1.3 63.5 + - - +
182G PHE* 3.5 4.1 + - - +
183G VAL* 3.1 25.1 + - - +
351G TRP* 3.6 30.0 - - + -
353G LEU* 3.9 20.2 - - + -
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Residues in contact with GLY 180 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G GLY 4.2 4.2 + - - -
142G MET* 3.7 26.4 - - - +
144G GLY* 4.2 7.7 - - - -
174G VAL* 3.6 19.9 - - - +
178G GLY 3.2 1.8 - - - -
179G ALA* 1.3 76.3 - - - +
181G HIS* 1.3 54.3 + - - +
183G VAL* 3.1 5.2 + - - +
184G LYS* 2.7 33.5 + - - +
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Residues in contact with HIS 181 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100G ASP* 3.5 17.9 + - - -
102G GLY 3.1 26.3 + - - -
103G ASN* 5.3 0.4 - - - -
104G SER* 3.7 23.2 + - - +
106G TYR* 4.1 15.2 + - + +
109G THR* 2.7 30.5 + - + +
125G GLY* 3.5 23.7 + - - -
126G SER 3.1 27.9 + - - -
127G GLY* 4.0 5.8 - - - -
178G GLY 3.7 4.2 + - - +
179G ALA 3.4 0.2 - - - -
180G GLY* 1.3 75.5 - - - +
182G PHE* 1.3 57.2 + - - +
184G LYS* 3.3 9.7 + - + +
185G MET* 2.8 27.0 + - - +
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Residues in contact with PHE 182 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106G TYR* 3.7 53.1 - + + +
178G GLY 3.8 1.2 + - - +
179G ALA 3.5 4.6 + - - +
180G GLY 3.2 0.6 - - - -
181G HIS* 1.3 75.6 - - - +
183G VAL* 1.3 61.2 + - + +
185G MET* 3.1 26.2 + - + +
186G VAL* 3.0 39.7 + - + +
270G SER* 4.3 6.7 - - - -
274G TYR* 4.4 4.7 - + - -
341G LEU* 4.1 19.3 - - + -
342G LEU* 4.0 16.4 - - + -
345G ALA* 3.5 31.4 - - + -
349G PHE* 5.2 0.2 - + - -
351G TRP* 3.7 25.6 - + + -
353G LEU* 5.9 2.0 - - + -
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Residues in contact with VAL 183 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142G MET* 4.1 11.7 - - + -
174G VAL* 3.6 19.5 - - + -
179G ALA 3.1 14.8 + - - +
180G GLY* 3.1 10.2 + - - +
182G PHE* 1.3 76.2 - - + +
184G LYS* 1.3 57.7 + - - +
186G VAL 3.3 1.0 + - - -
187G HIS* 2.8 27.7 + - - +
342G LEU* 4.2 16.2 - - + -
353G LEU* 4.7 6.1 - - + -
358G ILE* 3.7 36.6 - - + -
361G MET* 5.5 1.8 - - + -
362G TRP* 3.5 24.4 - - + +
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Residues in contact with LYS 184 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G ASN* 3.6 34.1 + - + +
127G GLY* 4.2 18.2 - - - -
128G VAL 3.3 24.2 + - - +
129G SER* 4.4 3.1 - - - +
142G MET* 3.7 23.3 - - + -
180G GLY 2.7 16.5 + - - +
181G HIS* 3.4 17.3 - - + +
183G VAL* 1.3 74.5 - - - +
185G MET* 1.3 61.6 + - - +
187G HIS* 3.3 32.9 + - - +
188G ASN* 3.1 39.7 + - - +
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Residues in contact with MET 185 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G GLU* 4.7 1.1 - - - +
106G TYR* 4.2 23.1 - - + -
181G HIS 2.8 14.0 + - - +
182G PHE* 3.1 34.7 + - + +
184G LYS* 1.3 77.2 - - - +
186G VAL* 1.3 72.2 + - + +
188G ASN* 3.2 10.1 + - - +
189G GLY 3.1 8.8 + - - -
263G THR* 4.7 4.4 - - - +
266G TRP* 3.4 37.5 - - + +
267G THR* 2.7 35.2 + - - +
270G SER* 3.2 22.7 - - - +
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Residues in contact with VAL 186 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182G PHE* 3.0 30.5 + - + +
183G VAL 3.9 3.8 - - - +
185G MET* 1.3 81.8 - - + +
187G HIS* 1.3 59.8 + - - +
189G GLY* 3.2 0.5 + - - -
190G ILE* 2.9 35.4 + - + +
267G THR* 3.5 11.4 - - + -
338G GLY* 3.9 23.8 - - - +
341G LEU* 3.9 14.4 - - + -
342G LEU* 3.6 21.5 - - + -
362G TRP* 3.9 17.7 - - + -
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Residues in contact with HIS 187 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129G SER* 3.4 22.0 + - - -
142G MET* 3.8 4.5 - - + -
183G VAL 2.8 18.1 + - - +
184G LYS* 3.3 21.8 - - - +
186G VAL* 1.3 77.1 - - - +
188G ASN* 1.3 81.0 + - - +
190G ILE* 3.6 4.3 + - - +
191G GLU* 3.1 39.1 + - - +
362G TRP* 3.5 26.4 - + - +
366G CYS* 3.5 31.2 - - - +
367G ILE 4.5 1.8 + - - -
368G ILE* 3.7 24.5 - - + +
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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
----------------------------------------------------------
103G ASN* 5.1 4.4 - - - +
184G LYS* 3.1 31.8 + - - +
185G MET* 3.2 9.3 + - - +
187G HIS* 1.3 98.2 + - - +
189G GLY* 1.3 64.9 + - - +
191G GLU* 3.2 14.3 + - - +
192G TYR* 3.1 33.4 + - + -
263G THR* 3.2 41.5 + - - +
264G GLY* 5.1 1.1 - - - +
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Residues in contact with GLY 189 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185G MET 3.1 10.9 + - - -
186G VAL 3.2 2.8 + - - -
188G ASN* 1.3 73.9 - - - +
190G ILE* 1.3 64.2 + - - +
192G TYR* 3.1 18.3 + - - +
193G GLY 3.2 8.7 + - - -
264G GLY* 4.9 4.0 - - - -
267G THR* 3.6 24.3 + - - -
281G ILE* 3.3 21.5 - - - +
285G VAL* 6.2 0.2 - - - -
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Residues in contact with ILE 190 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186G VAL* 2.9 24.8 + - + +
187G HIS 3.8 4.3 - - - +
189G GLY* 1.3 74.6 - - - +
191G GLU* 1.3 61.7 + - - +
193G GLY* 3.0 11.7 + - - +
194G ASP* 3.0 16.6 + - - +
267G THR* 5.3 0.2 - - - +
281G ILE* 4.6 7.9 - - + -
334G SER* 4.0 29.6 - - - +
335G TYR* 3.4 49.8 - - + +
338G GLY* 4.1 13.2 - - - -
362G TRP* 4.0 18.8 - - + -
368G ILE* 3.8 13.2 - - + -
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Residues in contact with GLU 191 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129G SER* 5.1 0.2 + - - -
187G HIS* 3.1 34.8 + - - +
188G ASN* 3.2 17.5 - - - +
189G GLY 3.2 0.4 - - - -
190G ILE* 1.3 77.8 - - - +
192G TYR* 1.3 66.8 + - + +
194G ASP* 3.8 1.3 + - - +
195G MET* 3.2 56.4 + - + +
232G LEU* 5.0 1.3 - - + +
288G ARG* 5.3 0.5 + - - -
367G ILE* 4.1 21.5 - - + +
368G ILE* 3.6 22.4 - - + +
447H ARG* 4.4 11.3 + - - -
450H PHE* 4.0 9.0 - - - -
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Residues in contact with TYR 192 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188G ASN* 3.1 28.7 + - + -
189G GLY* 3.1 9.4 + - - +
191G GLU* 1.3 83.3 - - + +
193G GLY* 1.3 62.2 + - - +
195G MET* 3.5 1.7 + - - +
196G GLN* 3.1 19.1 + - - +
259G GLY 5.6 1.6 + - - -
261G LYS 5.3 0.2 - - - -
262G GLY* 3.8 16.8 + - - -
263G THR* 4.0 5.4 + - - -
264G GLY* 3.5 34.5 + - - -
265G LYS* 5.5 3.2 - - + +
281G ILE* 5.1 1.1 - - + +
284G ALA* 3.5 19.9 - - + +
285G VAL* 3.8 31.6 - - + -
288G ARG* 3.1 59.2 + - + +
447H ARG* 4.5 8.7 + - - -
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Residues in contact with GLY 193 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G GLY 3.2 6.8 + - - -
190G ILE 3.0 6.8 + - - -
192G TYR* 1.3 78.1 - - - +
194G ASP* 1.3 67.2 + - - +
196G GLN* 3.9 1.2 - - - +
197G LEU* 3.0 33.9 + - - +
280G LEU* 3.8 22.6 - - - +
281G ILE* 4.8 2.9 - - - -
284G ALA* 4.2 6.4 - - - +
334G SER* 4.5 5.2 - - - -
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Residues in contact with ASP 194 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190G ILE* 3.0 15.7 + - - +
191G GLU* 4.4 2.9 - - - +
193G GLY* 1.3 76.8 - - - +
195G MET* 1.3 62.0 + - - +
197G LEU* 3.5 8.3 + - - +
198G ILE* 3.2 28.9 + - + +
232G LEU* 3.6 22.2 - - + +
327G LEU* 5.4 0.2 - - - +
331G LYS* 3.4 29.4 + - - +
334G SER* 4.8 3.5 + - - -
335G TYR* 2.8 40.5 + - - -
368G ILE* 4.1 12.0 - - + +
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Residues in contact with MET 195 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191G GLU* 3.2 49.0 + - + +
192G TYR 3.9 3.8 - - - +
193G GLY 3.2 0.8 - - - -
194G ASP* 1.3 75.8 - - - +
196G GLN* 1.3 65.3 + - - +
198G ILE* 3.0 8.7 + - - +
199G CYS* 3.0 23.6 + - - -
232G LEU* 4.2 17.9 - - + -
288G ARG* 3.3 25.8 - - - +
367G ILE* 5.0 0.2 - - + -
443H ILE* 3.5 22.2 - - + +
446H GLN* 3.7 20.5 - - - +
447H ARG* 4.5 6.5 - - + -
450H PHE* 3.4 29.6 - - + -
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Residues in contact with GLN 196 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192G TYR 3.1 15.1 + - - +
193G GLY 4.1 0.2 - - - +
195G MET* 1.3 79.7 - - - +
197G LEU* 1.3 61.7 + - - +
199G CYS* 3.3 14.9 + - - +
200G GLU* 3.0 49.0 + - - +
284G ALA* 3.9 8.4 - - + +
287G ALA* 3.7 29.8 - - + +
288G ARG* 5.7 2.9 - - - +
419G PRO 5.3 0.8 + - - -
421G PRO* 4.3 8.8 - - + +
422G CYS* 3.4 29.6 - - - -
439H PRO* 6.2 1.6 - - - +
440H ALA* 6.0 1.0 - - - -
443H ILE* 4.2 8.3 - - + +
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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
----------------------------------------------------------
193G GLY 3.0 26.4 + - - +
194G ASP* 3.7 8.3 - - - +
196G GLN* 1.3 77.5 - - - +
198G ILE* 1.3 61.7 + - - +
200G GLU* 3.4 5.0 + - - +
201G ALA* 3.1 22.2 + - - +
280G LEU* 4.4 9.6 - - + -
327G LEU* 3.6 18.4 - - + +
330G SER* 3.6 16.8 - - - +
331G LYS* 3.7 37.9 - - + +
334G SER* 4.6 2.7 - - - -
422G CYS* 3.6 26.2 - - + +
423G PHE* 3.5 28.4 - - + -
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Residues in contact with ILE 198 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194G ASP* 3.2 15.8 + - + +
195G MET 3.0 8.1 + - - +
197G LEU* 1.3 73.9 - - - +
199G CYS* 1.3 60.7 + - - +
201G ALA* 3.4 5.9 + - - +
202G TYR* 2.8 27.9 + - - +
220G PHE* 3.7 23.2 - - + -
230G SER* 5.1 0.2 - - - +
232G LEU* 3.6 36.3 - - + +
233G ILE* 3.8 24.9 - - + -
236G THR* 3.9 10.1 - - + +
327G LEU* 4.7 10.8 - - + -
442H LEU* 4.1 3.8 - - + -
446H GLN* 3.9 19.3 - - - +
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Residues in contact with CYS 199 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195G MET 3.0 17.2 + - - -
196G GLN* 3.3 20.2 + - - +
198G ILE* 1.3 77.9 - - - +
200G GLU* 1.3 51.6 + - - +
202G TYR* 3.3 7.3 + - - +
203G HIS* 2.6 36.1 + - - +
439H PRO* 3.4 39.7 - - + +
440H ALA* 5.1 0.2 - - - -
442H LEU* 3.9 16.6 - - - -
443H ILE* 3.5 26.5 - - - -
446H GLN* 4.6 0.4 - - - -
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Residues in contact with GLU 200 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196G GLN* 3.0 30.2 + - - +
197G LEU* 3.9 4.3 - - - +
199G CYS* 1.3 73.8 - - - +
201G ALA* 1.3 61.6 + - - +
203G HIS* 3.3 7.7 + - - +
204G LEU* 3.0 33.3 + - - +
418G ILE* 5.1 0.3 - - - +
419G PRO 4.0 13.9 - - - +
420G MET* 3.5 10.3 - - + -
421G PRO* 3.0 10.9 - - - +
422G CYS* 2.6 36.7 + - - +
423G PHE* 2.9 46.5 + - + +
439H PRO* 5.6 0.2 - - - -
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Residues in contact with ALA 201 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197G LEU 3.1 17.8 + - - +
198G ILE* 3.7 4.0 - - - +
200G GLU* 1.3 78.1 - - - +
202G TYR* 1.3 60.5 + - - +
204G LEU* 3.3 2.9 + - - +
205G MET* 3.1 30.5 + - + +
220G PHE* 4.7 1.3 - - + -
223G TRP* 4.2 17.0 - - + -
323G ILE* 3.8 25.4 - - + +
327G LEU* 4.3 12.6 - - + -
423G PHE* 3.9 9.5 - - + -
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Residues in contact with TYR 202 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198G ILE 2.8 21.7 + - - +
199G CYS* 3.6 2.5 - - - +
201G ALA* 1.3 73.6 - - - +
203G HIS* 1.3 62.3 + - - +
205G MET* 3.4 11.5 + - - +
206G LYS* 3.2 49.8 + - + +
213G GLN* 3.1 15.1 + - - -
216G MET* 3.7 25.8 - - + -
220G PHE* 4.2 9.9 - + + -
240G LEU* 3.6 35.0 - - + -
251G LEU* 4.5 8.9 - - + +
252G PRO* 5.9 0.7 - - - +
439H PRO* 3.8 30.5 - - + -
441H SER* 5.6 3.3 + - - -
442H LEU* 4.2 20.0 - - + -
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Residues in contact with HIS 203 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199G CYS 2.6 21.0 + - - +
200G GLU* 3.6 9.0 - - - +
201G ALA 3.2 0.2 - - - -
202G TYR* 1.3 73.8 - - - +
204G LEU* 1.3 64.2 + - - +
206G LYS* 3.3 15.1 + - - +
207G ASP* 3.0 49.0 + - - +
418G ILE* 3.5 25.6 - - + +
419G PRO* 3.6 30.9 - - + +
435H HIS* 4.0 15.4 - + - -
437H MET 4.7 3.3 + - - -
438H LEU* 4.7 0.2 - - - +
439H PRO* 3.4 32.7 - - + +
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Residues in contact with LEU 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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200G GLU 3.0 15.1 + - - +
201G ALA 3.8 2.0 - - - +
203G HIS* 1.3 76.3 - - - +
205G MET* 1.3 62.2 + - - +
208G VAL* 3.1 41.9 + - + +
209G LEU* 3.4 4.0 + - - +
319G PHE* 5.2 3.1 - - + -
323G ILE* 3.6 32.8 - - + -
409G ALA* 4.3 13.2 - - + +
413G GLY* 3.8 26.0 - - - +
418G ILE* 3.8 20.6 - - + -
420G MET* 3.8 20.6 - - + -
423G PHE* 3.9 21.8 - - + -
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Residues in contact with MET 205 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201G ALA 3.1 28.9 + - - +
202G TYR* 3.7 4.3 - - - +
203G HIS 3.3 0.4 - - - -
204G LEU* 1.3 77.6 - - - +
206G LYS* 1.3 57.9 + - - +
209G LEU* 3.8 4.8 - - - +
210G GLY 3.7 3.1 + - - -
211G MET* 3.2 45.6 + - - +
216G MET* 3.7 16.2 - - + +
219G ALA* 3.8 16.4 - - - -
220G PHE* 3.5 38.1 - - + -
223G TRP* 3.7 16.4 - - + -
320G LEU* 3.5 34.3 - - + -
323G ILE* 4.2 7.6 - - + -
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Residues in contact with LYS 206 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202G TYR* 3.2 44.7 + - + +
203G HIS* 3.3 18.3 + - - +
204G LEU 3.2 0.4 - - - -
205G MET* 1.3 79.6 - - - +
207G ASP* 1.3 82.3 + - - +
208G VAL 3.7 0.2 - - - -
210G GLY* 3.7 18.8 - - - -
211G MET 4.4 6.5 - - - +
213G GLN* 5.3 3.4 - - - +
216G MET* 3.7 21.3 - - + -
437H MET* 5.2 14.6 + - - +
438H LEU 5.5 4.0 - - - -
439H PRO* 5.4 3.4 - - - +
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Residues in contact with ASP 207 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203G HIS* 3.0 34.9 + - - +
206G LYS* 1.3 99.8 - - - +
208G VAL* 1.3 63.6 + - - +
210G GLY* 4.4 2.5 - - - -
310G PHE* 5.6 2.9 - - - -
416G ALA* 5.6 1.4 - - - +
418G ILE* 3.7 23.3 - - + +
435H HIS* 4.4 7.4 + - - -
----------------------------------------------------------
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Residues in contact with VAL 208 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204G LEU* 3.1 30.5 + - + +
207G ASP* 1.3 80.0 - - - +
209G LEU* 1.3 58.2 + - - +
210G GLY 3.4 0.6 + - - -
310G PHE* 4.8 10.1 - - + -
312G PHE* 3.7 40.3 - - + +
319G PHE* 3.6 29.4 - - + -
412G THR* 5.2 3.1 - - - -
413G GLY* 4.8 2.2 - - - -
416G ALA* 3.9 13.9 - - + -
418G ILE* 3.8 28.0 - - + -
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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