Contacts of the helix formed by residues 178 - 208 (chain H) 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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H TYR* 3.6 15.6 - - - +
109H THR* 3.5 32.4 + - - +
110H THR* 4.5 0.2 - - - -
125H GLY 4.6 6.3 - - - -
145H GLY* 3.7 11.0 - - - -
176H ASP 3.4 0.4 - - - -
177H GLU* 1.3 76.1 - - - +
179H ALA* 1.3 63.9 + - - +
180H GLY 3.2 4.2 + - - -
181H HIS* 3.7 3.1 + - - +
182H PHE* 3.5 13.7 + - - +
351H TRP* 4.2 1.7 - - - -
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Residues in contact with ALA 179 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145H GLY 4.8 0.8 - - - +
174H VAL* 3.9 4.7 - - + -
175H GLY* 3.8 20.7 - - - -
176H ASP 3.7 4.3 + - - +
177H GLU 3.4 2.6 + - - -
178H GLY* 1.3 75.1 - - - +
180H GLY* 1.3 60.1 + - - +
182H PHE* 3.4 3.1 + - - +
183H VAL* 3.0 30.1 + - - +
351H TRP* 3.7 22.0 - - + -
353H LEU* 3.6 31.0 - - + -
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Residues in contact with GLY 180 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H GLY 4.0 7.9 + - - -
127H GLY 4.5 2.0 - - - -
142H MET* 3.5 29.4 - - - +
144H GLY* 4.3 5.0 - - - -
174H VAL* 4.1 14.6 - - - +
178H GLY 3.2 1.2 - - - -
179H ALA* 1.3 76.2 - - - +
181H HIS* 1.3 60.8 + - - +
183H VAL* 3.1 6.5 + - - +
184H LYS* 2.8 25.8 + - - +
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Residues in contact with HIS 181 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100H ASP* 3.4 23.5 + - - -
102H GLY 2.9 28.7 + - - -
103H ASN* 4.6 1.8 - - - -
104H SER* 3.5 30.6 - - - +
106H TYR* 4.1 16.3 + - - -
109H THR* 2.9 26.2 + - - +
125H GLY* 3.4 34.3 + - - -
126H SER 3.4 10.3 + - - -
127H GLY* 4.3 4.3 - - - -
178H GLY 3.7 2.5 + - - +
179H ALA 3.4 0.2 - - - -
180H GLY* 1.3 72.6 - - - +
182H PHE* 1.3 60.8 + - - +
184H LYS* 3.1 9.1 + - + +
185H MET* 3.0 27.5 + - - +
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Residues in contact with PHE 182 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H TYR* 3.7 48.5 - + + +
178H GLY 3.5 7.4 + - - +
179H ALA 3.4 10.1 + - - +
180H GLY 3.2 0.6 - - - -
181H HIS* 1.3 78.6 - - - +
183H VAL* 1.3 57.4 + - - +
185H MET* 3.3 25.6 + - + +
186H VAL* 3.0 40.8 + - + +
270H SER* 4.7 1.1 - - - -
274H TYR* 4.0 13.7 - + - -
341H LEU* 4.0 24.0 - - + -
342H LEU* 3.6 28.7 - - + -
345H ALA* 3.6 29.4 - - + -
351H TRP* 4.3 12.3 - + + -
353H LEU* 6.0 1.8 - - + -
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Residues in contact with VAL 183 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142H MET* 3.8 10.3 - - - -
174H VAL* 3.6 19.5 - - + -
179H ALA* 3.0 19.6 + - + +
180H GLY* 3.1 9.4 + - - +
182H PHE* 1.3 74.3 - - + +
184H LYS* 1.3 61.0 + - - +
186H VAL* 4.5 4.9 - - - +
187H HIS* 2.8 28.4 + - - +
342H LEU* 4.3 12.1 - - + -
353H LEU* 5.8 2.5 - - + -
358H ILE* 3.7 31.0 - - + -
361H MET* 4.5 7.4 - - + -
362H TRP* 3.3 26.2 - - + +
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Residues in contact with LYS 184 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H ASN* 3.6 27.5 + - + +
127H GLY* 4.5 12.8 - - - -
128H VAL 3.7 15.0 - - - +
129H SER* 3.6 26.9 + - - -
142H MET* 3.9 26.0 - - + -
180H GLY 2.8 13.3 + - - +
181H HIS* 3.4 17.7 - - + +
183H VAL* 1.3 76.8 - - - +
185H MET* 1.3 61.6 + - - +
187H HIS* 3.4 5.0 + - - +
188H ASN* 3.1 55.5 + - - +
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Residues in contact with MET 185 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H TYR* 4.3 14.1 - - + -
181H HIS 3.0 12.2 + - - +
182H PHE* 3.6 35.4 - - + +
183H VAL 3.3 0.2 - - - -
184H LYS* 1.3 74.5 - - - +
186H VAL* 1.3 80.3 + - + +
188H ASN* 3.1 20.6 + - - +
189H GLY 3.2 0.7 + - - -
263H THR* 4.8 8.7 - - + +
266H TRP* 3.5 20.0 - - + +
267H THR* 2.7 37.0 + - - +
270H SER* 3.1 33.4 - - - +
341H LEU* 4.8 0.7 - - + -
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Residues in contact with VAL 186 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182H PHE* 3.0 41.2 + - + +
183H VAL 3.9 3.4 - - - +
185H MET* 1.3 84.3 - - + +
187H HIS* 1.3 63.6 + - - +
189H GLY* 3.0 9.9 + - - -
190H ILE* 3.0 32.0 + - + +
267H THR* 3.8 11.4 - - + +
338H GLY* 4.2 19.5 - - - +
341H LEU* 4.0 11.9 - - + -
342H LEU* 3.7 12.3 - - + -
362H TRP* 3.8 12.8 - - + -
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Residues in contact with HIS 187 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129H SER* 3.8 22.2 - - - -
142H MET* 4.3 3.4 - - + -
183H VAL 2.8 19.1 + - - +
184H LYS* 3.5 12.3 + - - +
185H MET 3.2 0.2 - - - -
186H VAL* 1.3 77.0 - - - +
188H ASN* 1.3 86.6 + - - +
189H GLY 3.3 0.2 + - - -
190H ILE* 3.4 4.8 + - - +
191H GLU* 3.2 30.7 + - - +
362H TRP* 3.4 33.5 - + - +
366H CYS* 4.0 22.1 - - - +
367H ILE* 4.1 15.4 + - + +
368H ILE* 3.8 24.4 - - + +
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Residues in contact with ASN 188 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184H LYS* 3.1 35.3 + - - +
185H MET* 3.1 7.9 + - - +
187H HIS* 1.3 105.1 + - - +
189H GLY* 1.3 59.2 + - - +
191H GLU* 3.7 14.0 + - - +
192H TYR* 3.2 30.7 + - + -
263H THR* 3.4 44.8 + - - +
264H GLY* 4.6 1.6 - - - +
267H THR* 4.3 0.7 - - - -
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Residues in contact with GLY 189 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185H MET 3.2 6.3 + - - -
186H VAL 3.0 7.9 + - - -
188H ASN* 1.3 76.7 - - - +
190H ILE* 1.3 65.2 + - - +
192H TYR* 3.1 14.4 + - - +
193H GLY 3.2 8.5 + - - -
264H GLY* 4.5 6.1 - - - -
267H THR* 3.5 24.0 + - - -
281H ILE* 3.6 21.0 - - - +
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Residues in contact with ILE 190 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186H VAL* 3.0 41.9 + - + +
187H HIS* 3.4 6.3 + - - +
189H GLY* 1.3 74.9 - - - +
191H GLU* 1.3 64.3 + - - +
193H GLY* 2.9 13.4 + - - +
194H ASP* 2.9 15.5 + - - +
267H THR* 5.7 1.6 - - + -
281H ILE* 4.6 10.5 - - + -
334H SER* 4.9 10.1 - - - +
335H TYR* 3.2 53.8 - - + +
338H GLY* 4.4 15.9 - - - -
339H PHE* 6.4 0.4 - - + -
362H TRP* 4.3 9.0 - - + -
368H ILE* 3.6 21.1 - - + -
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Residues in contact with GLU 191 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447G ARG* 4.7 15.8 + - - +
450G PHE* 4.4 4.5 - - - -
187H HIS* 3.2 17.7 + - - +
188H ASN* 3.7 16.5 - - - +
190H ILE* 1.3 77.3 - - - +
192H TYR* 1.3 67.1 + - + +
194H ASP* 3.5 1.9 + - - +
195H MET* 3.1 50.6 + - + +
232H LEU* 5.0 0.9 - - + -
288H ARG* 5.7 0.2 - - - -
367H ILE* 3.2 52.9 - - + +
368H ILE* 3.6 18.8 - - + -
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Residues in contact with TYR 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443G ILE* 5.6 0.9 - - - +
447G ARG* 4.2 9.0 - - - -
188H ASN* 3.2 20.4 + - + +
189H GLY* 3.1 11.1 + - - +
191H GLU* 1.3 84.3 - - + +
193H GLY* 1.3 63.2 + - - +
195H MET* 4.1 0.9 - - - +
196H GLN* 3.1 26.7 + - - +
261H LYS 3.1 10.2 + - - -
262H GLY* 3.1 25.6 - - - -
263H THR 4.4 2.2 - - - -
264H GLY* 3.5 22.0 - - - -
265H LYS* 5.1 2.1 + - + +
281H ILE 4.7 1.3 - - - +
284H ALA* 3.5 11.0 - - + +
285H VAL* 3.5 37.5 - - + -
288H ARG* 2.9 60.9 + - + +
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Residues in contact with GLY 193 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189H GLY 3.2 6.1 + - - -
190H ILE* 2.9 7.5 + - - -
192H TYR* 1.3 77.1 - - - +
194H ASP* 1.3 62.3 + - - +
196H GLN* 3.4 1.2 + - - +
197H LEU* 2.8 39.8 + - - +
280H LEU* 3.7 23.8 - - - -
281H ILE* 4.8 3.8 - - - +
284H ALA* 4.2 5.8 - - - +
334H SER* 5.5 1.8 - - - -
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Residues in contact with ASP 194 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190H ILE* 2.9 18.7 + - - +
191H GLU* 4.2 1.8 - - - +
193H GLY* 1.3 77.5 - - - +
195H MET* 1.3 63.2 + - - +
197H LEU* 3.7 5.3 - - - +
198H ILE* 3.1 32.2 + - + +
232H LEU* 4.1 17.2 - - + +
331H LYS* 3.3 37.8 + - - +
334H SER* 4.5 4.3 + - - -
335H TYR* 2.8 32.5 + - - -
368H ILE* 3.9 12.0 - - - +
370H SER* 6.0 0.7 - - - -
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Residues in contact with MET 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443G ILE* 3.7 31.0 - - + +
446G GLN* 3.3 32.3 - - + +
447G ARG* 4.5 10.5 - - + -
450G PHE* 6.3 1.8 - - + -
191H GLU* 3.1 40.0 + - - +
192H TYR 4.2 2.0 - - - +
194H ASP* 1.3 75.8 - - - +
196H GLN* 1.3 56.9 + - - +
198H ILE* 3.2 7.1 + - - +
199H CYS* 2.9 33.2 + - - -
232H LEU* 3.7 22.4 - - + -
288H ARG* 3.5 26.2 - - - +
367H ILE* 5.2 1.3 - - - -
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Residues in contact with GLN 196 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439G PRO* 4.9 4.7 - - - +
443G ILE* 4.4 16.6 - - + +
192H TYR 3.1 19.0 + - - +
193H GLY 4.0 1.3 - - - +
195H MET* 1.3 73.7 - - - +
197H LEU* 1.3 66.0 + - - +
199H CYS* 3.1 13.3 + - - +
200H GLU* 2.9 36.8 + - - +
284H ALA* 3.6 18.7 + - + +
287H ALA* 3.3 28.8 - - + +
288H ARG* 4.8 0.8 - - - +
421H PRO* 5.1 1.7 - - - +
422H CYS* 3.6 23.8 - - - -
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Residues in contact with LEU 197 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193H GLY 2.8 28.1 + - - +
194H ASP* 3.7 8.1 - - - +
196H GLN* 1.3 76.1 - - - +
198H ILE* 1.3 61.0 + - - +
200H GLU* 3.3 6.2 + - - +
201H ALA* 3.1 18.2 + - - +
280H LEU* 4.3 9.6 - - + -
327H LEU* 3.5 22.9 - - + +
330H SER* 3.6 17.0 - - - +
331H LYS* 3.8 35.9 - - + +
334H SER* 4.5 2.7 - - - +
422H CYS* 3.6 27.1 - - + -
423H PHE* 3.6 26.8 - - + -
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Residues in contact with ILE 198 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442G LEU* 4.6 2.9 - - + -
446G GLN* 4.5 4.7 - - - +
194H ASP 3.1 19.2 + - - +
195H MET* 3.2 5.1 + - - +
197H LEU* 1.3 73.1 - - - +
199H CYS* 1.3 65.0 + - - +
201H ALA* 3.4 6.0 + - - +
202H TYR* 3.0 22.7 + - - +
220H PHE* 3.8 15.2 - - + -
232H LEU* 3.9 40.4 - - + +
233H ILE* 4.1 15.3 - - + -
236H THR* 3.7 29.8 - - + +
327H LEU* 4.5 15.3 - - + -
331H LYS* 4.8 9.2 - - - +
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Residues in contact with CYS 199 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439G PRO* 3.3 47.7 - - + +
440G ALA* 5.2 0.2 - - - -
442G LEU* 3.8 18.6 - - - -
443G ILE* 3.5 28.0 - - - -
195H MET 2.9 24.1 + - - -
196H GLN* 3.1 18.6 + - - +
198H ILE* 1.3 76.8 - - - +
200H GLU* 1.3 56.5 + - - +
202H TYR* 3.4 5.5 + - - +
203H HIS* 2.9 23.2 + - - +
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Residues in contact with GLU 200 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439G PRO* 4.9 2.0 - - + -
196H GLN* 2.9 33.7 + - - +
197H LEU* 3.8 5.2 - - - +
198H ILE 3.3 0.2 - - - -
199H CYS* 1.3 73.4 - - - +
201H ALA* 1.3 65.8 + - - +
203H HIS* 3.2 9.2 + - - +
204H LEU* 3.1 26.9 + - - +
418H ILE* 5.2 0.9 - - - +
419H PRO 4.3 5.4 - - - +
420H MET* 3.5 25.9 - - + +
421H PRO* 3.0 13.8 - - + +
422H CYS* 2.8 35.7 + - - +
423H PHE* 3.0 38.5 + - + -
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Residues in contact with ALA 201 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197H LEU 3.1 14.0 + - - +
198H ILE* 3.7 7.2 - - - +
200H GLU* 1.3 73.9 - - - +
202H TYR* 1.3 65.1 + - - +
204H LEU* 3.3 11.7 + - - +
205H MET* 3.3 23.6 + - + +
220H PHE* 5.0 3.1 - - + -
323H ILE* 4.1 22.7 - - + +
324H ARG* 4.8 6.5 - - - +
327H LEU* 4.1 22.7 - - + -
423H PHE* 4.1 8.2 - - + -
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Residues in contact with TYR 202 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438G LEU 5.5 0.2 - - - -
439G PRO* 3.7 31.2 - - + -
441G SER* 4.9 8.0 + - - -
442G LEU* 4.4 20.9 - - + -
198H ILE 3.0 17.2 + - - +
199H CYS* 3.7 2.0 - - - +
201H ALA* 1.3 77.0 - - - +
203H HIS* 1.3 66.2 + + + +
205H MET* 3.3 13.0 + - - +
206H LYS* 3.2 44.5 + - + +
216H MET* 3.5 31.6 - - + -
220H PHE* 4.5 13.1 - + + -
240H LEU* 3.6 32.0 - - + +
251H LEU* 5.4 8.8 - - + +
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Residues in contact with HIS 203 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435G HIS* 3.9 20.5 - + - -
437G MET 4.1 7.9 + - - -
438G LEU* 4.6 1.8 - - + -
439G PRO* 3.8 29.0 - - + +
199H CYS 2.9 18.1 + - - +
200H GLU* 3.5 8.5 - - - +
201H ALA 3.2 0.2 - - - -
202H TYR* 1.3 81.9 - + - +
204H LEU* 1.3 61.6 + - - +
206H LYS* 3.4 13.1 + - - +
207H ASP* 2.8 55.3 + - - +
418H ILE* 3.3 19.7 - - + +
419H PRO* 3.5 37.0 + - + +
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Residues in contact with LEU 204 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200H GLU 3.1 13.1 + - - +
201H ALA 3.6 6.3 - - - +
202H TYR 3.3 0.4 - - - -
203H HIS* 1.3 74.1 - - - +
205H MET* 1.3 60.7 + - - +
208H VAL* 3.0 51.0 + - + +
209H LEU* 3.3 3.1 + - - +
319H PHE* 5.0 4.0 - - + -
323H ILE* 3.7 41.1 - - + -
409H ALA* 4.8 9.4 - - + +
413H GLY* 4.1 17.7 - - - +
418H ILE* 3.8 21.3 - - + -
420H MET* 4.0 15.9 - - + -
423H PHE* 3.9 21.8 - - + -
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Residues in contact with MET 205 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201H ALA 3.3 18.8 + - - +
202H TYR* 3.3 7.6 + - - +
204H LEU* 1.3 77.4 - - - +
206H LYS* 1.3 60.5 + - - +
209H LEU* 3.6 15.6 - - + +
210H GLY 3.4 5.9 + - - -
211H MET* 3.0 47.6 + - - +
216H MET* 3.9 35.7 - - + +
219H ALA* 4.7 4.0 - - + -
220H PHE* 4.2 17.0 - - + -
320H LEU* 4.9 5.8 - - + -
323H ILE* 4.9 7.4 - - + -
324H ARG* 3.1 47.3 - - - +
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Residues in contact with LYS 206 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437G MET* 4.1 31.5 + - - +
438G LEU 5.6 2.4 + - - -
202H TYR* 3.2 40.5 + - + +
203H HIS* 3.9 10.2 - - - +
204H LEU 3.2 0.4 - - - -
205H MET* 1.3 79.5 - - - +
207H ASP* 1.3 90.5 + - - +
210H GLY* 3.8 14.6 - - - -
211H MET 4.5 3.0 - - - +
216H MET* 3.6 24.2 - - + -
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Residues in contact with ASP 207 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435G HIS* 5.1 6.8 + - - -
203H HIS* 2.8 44.8 + - - +
206H LYS* 1.3 101.1 + - - +
208H VAL* 1.3 65.0 + - - +
210H GLY* 4.5 2.0 - - - -
310H PHE* 5.4 3.5 - - - -
416H ALA* 5.4 1.2 - - - +
418H ILE* 3.5 24.6 - - + +
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Residues in contact with VAL 208 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204H LEU* 3.0 30.3 + - + +
207H ASP* 1.3 77.6 - - - +
209H LEU* 1.3 63.8 + - - +
210H GLY 3.3 1.7 + - - -
310H PHE* 4.1 26.1 - - + -
312H PHE* 3.8 22.6 - - + +
319H PHE* 3.6 29.4 - - + -
412H THR* 4.2 5.2 - - + -
413H GLY* 4.7 0.9 - - - -
416H ALA* 3.8 10.3 - - + -
418H ILE* 3.5 29.4 - - + -
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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