Contacts of the helix formed by residues 201 - 237 (chain B) in PDB entry 4I1Q
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 SER 201 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B TYR* 4.2 8.6 - - - -
131B GLN* 5.0 0.9 + - - -
197B ILE* 3.1 13.5 + - - -
198B LEU* 2.7 34.0 + - - +
200B ASN* 1.3 77.8 - - - +
202B ARG* 1.3 62.6 + - - +
203B ILE 3.4 0.8 + - - -
204B GLY* 3.4 4.2 + - - +
205B CYS* 3.3 22.3 + - - +
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Residues in contact with ARG 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE* 4.5 11.3 + - - +
93A TRP* 4.7 9.1 - - - -
53B GLN* 3.8 23.8 - - - +
56B GLU* 2.7 44.1 + - - -
128B TYR* 3.6 21.1 - - - +
199B TYR* 3.4 40.3 + - - +
200B ASN 3.2 2.4 - - - -
201B SER* 1.3 79.1 + - - +
203B ILE* 1.3 84.7 + - + +
205B CYS* 3.5 1.6 + - - +
206B TYR* 3.1 56.0 + - + +
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Residues in contact with ILE 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE* 6.1 1.1 - - + -
93A TRP* 4.1 32.3 - - + -
238A LEU* 4.1 33.0 - - + +
200B ASN* 4.3 7.7 + - - +
201B SER 3.4 0.4 - - - -
202B ARG* 1.3 95.6 - - + +
204B GLY* 1.3 54.1 + - - +
206B TYR* 3.4 10.2 + - + +
207B VAL* 2.8 48.4 + - + +
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Residues in contact with GLY 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B ASN 5.0 1.4 + - - -
201B SER 3.4 8.1 + - - -
203B ILE* 1.3 75.8 - - - +
205B CYS* 1.3 59.8 + - - +
207B VAL* 3.7 6.9 - - - +
208B THR* 2.8 33.9 + - - -
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Residues in contact with CYS 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B THR* 5.3 4.9 - - + -
125B MET* 4.5 0.2 - - - -
128B TYR* 3.5 50.5 - - + -
201B SER* 3.3 15.8 + - - +
202B ARG 3.9 1.8 - - - +
203B ILE 3.3 0.4 - - - -
204B GLY* 1.3 73.8 - - - +
206B TYR* 1.3 70.4 + - - +
208B THR* 3.3 5.5 + - - -
209B ILE* 3.0 48.1 + - - +
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Residues in contact with TYR 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 5.7 1.3 - - + -
88A ILE* 3.5 38.8 - - + -
235A MET* 4.5 7.9 - - + -
238A LEU* 6.5 0.2 - - + -
53B GLN 4.7 0.2 + - - -
56B GLU* 2.5 41.2 + - - +
57B GLY* 3.6 12.5 + - - -
60B LEU* 3.4 28.5 - - + -
125B MET* 4.8 2.5 - - + -
128B TYR* 4.4 17.5 + + - -
202B ARG* 3.1 36.5 + - + +
203B ILE* 3.7 9.9 - - + +
205B CYS* 1.3 79.8 - - - +
207B VAL* 1.3 63.6 + - - +
209B ILE* 3.5 4.0 + - + -
210B PHE* 3.0 38.7 + - + -
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Residues in contact with VAL 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A MET* 3.6 37.0 - - + +
236A SER* 4.9 1.3 - - - -
238A LEU* 3.8 28.3 - - + +
203B ILE* 2.8 31.7 + - + +
204B GLY* 3.7 7.6 - - - +
206B TYR* 1.3 69.9 - - + +
208B THR* 1.3 67.4 + - - +
210B PHE* 3.2 1.9 + - - +
211B GLN* 3.0 45.1 + - + +
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Residues in contact with THR 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B THR* 4.8 13.2 - - + -
204B GLY 2.8 21.9 + - - -
205B CYS* 3.3 7.8 + - - +
207B VAL* 1.3 73.7 - - - +
209B ILE* 1.3 60.2 + - - +
211B GLN* 3.4 9.0 + - - +
212B ASN* 3.0 52.8 + - - +
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Residues in contact with ILE 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LEU* 5.1 1.8 - - + -
64B LEU* 3.7 22.7 - - + -
120B GLN 4.7 3.0 - - - +
121B ALA* 4.4 7.6 - - + +
124B THR* 3.9 27.1 - - + -
125B MET* 3.4 41.1 - - + +
205B CYS* 3.0 30.1 + - - +
206B TYR* 3.7 5.8 - - - +
208B THR* 1.3 75.5 - - - +
210B PHE* 1.3 67.5 + - + +
212B ASN* 3.4 8.1 + - - +
213B ILE* 3.1 38.3 + - + +
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Residues in contact with PHE 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A VAL* 4.1 24.2 - - + -
82A SER* 6.3 0.2 - - - -
85A LEU* 4.2 35.9 - - + -
231A LEU* 4.5 16.6 - - + +
235A MET* 3.8 31.4 - - + -
60B LEU* 4.0 39.7 - - + -
64B LEU* 4.9 3.8 - - + -
206B TYR* 3.0 32.1 + - + +
207B VAL 4.2 0.4 - - - +
209B ILE* 1.3 79.8 - - + +
211B GLN* 1.3 65.8 + - - +
213B ILE* 3.7 17.5 + - + +
214B SER* 3.0 27.7 + - - -
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Residues in contact with GLN 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A TYR* 3.7 42.7 + - + +
235A MET* 4.6 6.7 - - + -
236A SER* 3.2 35.8 - - - +
207B VAL* 3.0 38.2 + - + +
208B THR* 4.0 6.2 - - - +
210B PHE* 1.3 73.2 - - - +
212B ASN* 1.3 64.5 + - - +
214B SER* 3.1 1.6 + - - -
215B ASN* 2.8 37.4 + - - +
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Residues in contact with ASN 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B GLN* 3.3 50.4 + - + +
124B THR* 4.9 1.8 + - - -
208B THR* 3.0 42.2 + - - +
209B ILE 3.5 5.2 - - - +
211B GLN* 1.3 78.2 - - - +
213B ILE* 1.3 62.4 + - + +
215B ASN* 3.4 7.5 + - - +
216B LEU* 3.1 30.0 + - - +
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Residues in contact with ILE 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A VAL* 6.2 0.2 - - + -
231A LEU* 5.9 4.0 - - + -
64B LEU* 4.1 26.2 - - + -
67B PHE* 4.8 15.0 - - + -
117B LEU* 4.1 12.8 - - + -
121B ALA* 4.1 18.6 - - + -
209B ILE* 3.1 29.4 + - + +
210B PHE* 4.0 20.0 - - + +
211B GLN 3.3 0.2 - - - -
212B ASN* 1.3 73.3 - - - +
214B SER* 1.3 58.5 + - - +
216B LEU* 3.2 9.5 + - + +
217B ARG* 2.8 52.8 + - - +
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Residues in contact with SER 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ASN* 2.6 54.6 + - - +
229A HIS* 6.5 0.4 - - - -
231A LEU* 3.8 16.3 - - - +
232A TYR* 3.9 20.4 + - - -
210B PHE 3.0 17.6 + - - -
211B GLN 3.1 4.9 + - - -
213B ILE* 1.3 75.1 - - - +
215B ASN* 1.3 59.8 + - - +
218B ASP* 2.8 17.2 + - - +
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Residues in contact with ASN 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A TYR* 3.5 29.7 + - - -
120B GLN* 5.9 0.7 - - - +
211B GLN* 2.8 21.4 + - - +
212B ASN* 3.8 7.9 + - - +
214B SER* 1.3 78.0 - - - +
216B LEU* 1.3 63.1 + - + +
218B ASP* 3.5 8.1 - - - +
219B VAL* 3.3 26.3 + - - +
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Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B TYR* 4.0 17.9 - - + +
116B LYS* 3.7 37.0 - - + +
117B LEU* 3.7 41.3 - - + +
120B GLN* 3.8 24.2 - - + +
121B ALA* 6.0 0.4 - - + -
212B ASN 3.1 17.6 + - - +
213B ILE* 3.5 7.2 - - + +
215B ASN* 1.3 77.3 - - + +
217B ARG* 1.3 59.7 + - - +
219B VAL* 3.5 7.0 + - + +
220B PHE* 3.0 28.6 + - - +
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Residues in contact with ARG 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A MET* 5.9 1.2 - - - +
106A ASN* 5.0 9.3 + - - -
110A TRP* 5.6 4.4 - - - -
224A MET* 5.0 8.5 + - - +
227A LEU* 6.3 0.8 - - - +
228A ASN* 3.0 39.1 + - - +
231A LEU* 5.6 5.5 - - - +
67B PHE* 4.5 15.0 - - - -
113B TYR* 3.1 30.1 + - + +
213B ILE* 2.8 40.2 + - - +
216B LEU* 1.3 75.3 - - - +
218B ASP* 1.3 60.4 + - - +
220B PHE* 4.1 3.8 - - + -
221B TYR* 2.8 76.0 + - + -
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Residues in contact with ASP 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A SER* 4.0 12.9 + - - +
228A ASN* 3.3 7.6 + - - +
229A HIS* 3.3 38.0 + - + +
214B SER 2.8 18.0 + - - +
215B ASN* 3.5 10.1 - - - +
217B ARG* 1.3 78.0 - - - +
219B VAL* 1.3 64.9 + - - +
221B TYR* 4.0 4.5 - - - +
222B ARG* 3.1 49.2 + - - +
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Residues in contact with VAL 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LEU* 6.1 2.0 - - + -
112B ASP* 6.0 2.0 - - - +
116B LYS* 6.0 3.6 - - - +
215B ASN 3.3 15.2 + - - +
216B LEU* 4.0 6.1 - - + +
217B ARG 3.2 0.2 - - - -
218B ASP* 1.3 80.3 - - - +
220B PHE* 1.3 59.9 + - - +
222B ARG* 3.2 28.4 + - - +
223B GLU* 2.8 45.6 + - + +
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Residues in contact with PHE 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A TYR* 5.6 4.9 - + - -
109B LEU* 4.0 13.0 - - + -
110B TRP* 3.6 41.7 - + - -
113B TYR* 3.6 48.7 - + + -
216B LEU 3.0 18.7 + - - +
217B ARG* 3.1 4.7 + - + +
219B VAL* 1.3 77.2 - - - +
221B TYR* 1.3 82.1 + + - +
223B GLU* 3.2 6.0 + - - +
224B MET* 2.8 68.7 + - + +
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Residues in contact with TYR 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A TRP* 5.2 2.4 - - - -
220A PHE* 5.1 3.7 - + - -
221A TYR* 3.8 41.4 - + + +
224A MET* 3.6 42.6 - - + +
225A SER* 4.1 25.6 - - - +
228A ASN* 4.6 2.9 - - + -
217B ARG* 2.8 69.7 + - + +
218B ASP* 4.0 3.1 - - - +
220B PHE* 1.3 91.5 - + - +
222B ARG* 1.3 63.5 + - - +
224B MET* 3.7 3.4 - - - +
225B SER* 2.8 25.9 + - - -
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Residues in contact with ARG 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A SER* 5.3 1.5 + - - +
218B ASP* 3.1 34.9 + - - +
219B VAL* 3.2 33.5 + - - +
221B TYR* 1.3 79.8 - - - +
223B GLU* 1.3 78.7 + - - +
225B SER* 3.2 18.2 + - - -
226B LYS* 3.3 19.6 + - + +
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Residues in contact with GLU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LEU* 3.7 33.8 - - + +
219B VAL* 2.8 31.9 + - + +
220B PHE 3.8 2.7 - - - +
222B ARG* 1.3 85.3 + - - +
224B MET* 1.3 60.6 + - - +
225B SER 3.4 0.2 + - - -
226B LYS* 2.8 46.0 + - - +
227B LEU* 3.4 23.2 + - - +
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Residues in contact with MET 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ARG* 5.4 6.1 + - - -
221A TYR* 3.8 26.4 - - + +
106B ASN* 3.5 33.2 - - - +
109B LEU* 3.1 41.7 - - + -
110B TRP* 4.1 9.0 - - + +
220B PHE* 2.8 53.4 + - + +
221B TYR* 3.7 4.7 - - - +
223B GLU* 1.3 74.4 - - - +
225B SER* 1.3 60.1 + - - +
227B LEU* 3.5 10.8 + - - +
228B ASN* 2.8 29.3 + - - +
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Residues in contact with SER 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ASP* 4.0 15.8 + - - -
221A TYR* 4.0 22.6 - - - +
222A ARG 5.7 0.3 + - - -
221B TYR 2.8 12.5 + - - -
222B ARG* 3.2 15.3 - - - -
224B MET* 1.3 75.0 - - - +
226B LYS* 1.3 65.9 + - - +
228B ASN* 2.9 14.3 + - - +
229B HIS* 3.0 23.6 + - - -
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Residues in contact with LYS 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B ARG* 3.3 21.7 + - + +
223B GLU* 2.8 45.4 + - - +
224B MET 3.4 0.2 - - - -
225B SER* 1.3 75.2 - - - +
227B LEU* 1.3 61.3 + - + +
229B HIS* 3.0 14.2 + - + +
230B ASN* 2.9 36.0 + - - +
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Residues in contact with LEU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ARG* 6.0 1.1 - - - +
102B ILE* 4.0 23.0 - - + +
105B ASN* 3.7 23.3 - - + +
106B ASN* 3.4 43.3 - - + +
109B LEU* 4.0 11.9 - - + -
223B GLU 3.4 12.8 + - - +
224B MET* 3.7 11.7 - - - +
226B LYS* 1.3 78.4 - - + +
228B ASN* 1.3 57.6 + - - +
230B ASN* 3.7 19.7 - - - +
231B LEU* 2.8 31.2 + - - +
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Residues in contact with ASN 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A SER* 2.4 57.2 + - - -
217A ARG* 2.2 55.1 + - - +
218A ASP* 3.1 15.3 + - - +
221A TYR* 4.4 4.0 - - + -
224B MET 2.8 19.7 + - - +
225B SER* 2.9 13.0 + - - +
227B LEU* 1.3 73.3 - - - +
229B HIS* 1.3 64.1 + - - +
231B LEU* 3.4 4.2 + - - +
232B TYR 3.3 9.2 + - - -
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Residues in contact with HIS 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A SER* 5.0 1.0 + - - -
218A ASP* 2.9 36.8 + - - +
225B SER* 3.0 23.2 + - - -
226B LYS* 3.0 11.9 + - + +
228B ASN* 1.3 73.4 + - - +
230B ASN* 1.3 70.7 + - - +
232B TYR* 3.1 17.9 + - - +
233B GLU* 3.1 29.1 + - - +
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Residues in contact with ASN 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLU* 4.0 21.2 + - + +
102B ILE* 3.7 18.3 - - + +
226B LYS* 2.9 20.6 + - - +
227B LEU* 3.7 21.8 - - - +
229B HIS* 1.3 78.5 - - - +
231B LEU* 1.3 63.5 + - - +
233B GLU* 3.3 16.0 + - - +
234B VAL* 3.0 25.5 + - - +
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Residues in contact with LEU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A PHE* 4.4 19.7 - - + +
213A ILE* 5.3 3.6 - - + -
214A SER* 4.2 10.3 - - - +
217A ARG* 3.9 29.6 - - - +
85B LEU* 3.9 16.4 - - + -
99B LEU* 5.0 4.7 - - + -
102B ILE* 3.6 19.9 - - + +
227B LEU 2.8 17.9 + - - +
228B ASN* 3.6 6.5 - - - +
229B HIS 3.2 0.2 - - - -
230B ASN* 1.3 77.3 - - - +
232B TYR* 1.3 62.0 + - - +
234B VAL* 3.5 2.4 + - + +
235B MET* 3.0 55.5 + - + +
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Residues in contact with TYR 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A PHE 5.4 0.2 - - - -
211A GLN* 3.5 43.2 + - + -
214A SER* 3.3 24.4 + - - +
215A ASN* 3.6 35.6 + - - -
228B ASN 3.3 3.0 + - - +
229B HIS* 3.1 11.5 + - - +
231B LEU* 1.3 78.3 - - - +
233B GLU* 1.3 66.8 + - + +
235B MET* 3.3 5.4 + - - +
236B SER* 2.8 36.5 + - - -
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Residues in contact with GLU 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B HIS* 3.1 31.3 + - - +
230B ASN* 3.7 15.0 - - - +
232B TYR* 1.3 78.7 - - + +
234B VAL* 1.3 67.4 + - - +
236B SER* 2.5 26.2 + - - +
237B LYS* 3.4 14.0 - - + +
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Residues in contact with VAL 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TYR* 3.7 20.8 + - + +
95B GLY* 3.6 27.1 - - - +
98B GLU* 3.8 26.0 - - + -
99B LEU* 4.1 15.5 - - + +
102B ILE* 4.5 4.7 - - + -
230B ASN 3.0 15.6 + - - +
231B LEU* 3.7 5.6 - - - +
233B GLU* 1.3 76.6 - - - +
235B MET* 1.3 91.5 + - + +
237B LYS* 3.0 24.0 + - + +
238B LEU 4.0 0.2 + - - -
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Residues in contact with MET 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A TYR* 4.8 7.6 - - - +
207A VAL* 3.7 20.1 - - - +
210A PHE* 3.8 24.9 - - + -
211A GLN* 3.8 17.9 - - + -
85B LEU* 3.4 44.6 - - + -
89B TYR* 4.1 14.1 - - + -
99B LEU* 4.0 4.7 - - + -
231B LEU* 3.0 21.1 + - + +
232B TYR 3.6 6.5 - - - +
234B VAL* 1.3 103.3 - - + +
236B SER* 1.3 51.9 + - - +
237B LYS 2.7 13.0 + - - -
238B LEU* 2.9 25.2 + - - +
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Residues in contact with SER 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A VAL* 5.2 1.8 - - - -
211A GLN* 3.1 23.2 - - - +
232B TYR* 2.8 21.7 + - - -
233B GLU* 2.5 26.9 + - - -
235B MET* 1.3 68.7 - - - +
237B LYS* 1.3 58.8 + - - +
238B LEU* 3.4 8.1 - - - +
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Residues in contact with LYS 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ASP* 2.3 52.4 + - - +
95B GLY* 3.8 22.0 - - - -
233B GLU* 3.4 18.6 - - + +
234B VAL* 3.0 17.4 + - + +
235B MET 2.7 5.9 + - - -
236B SER* 1.3 76.1 - - - +
238B LEU* 1.3 65.7 + - - +
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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