Contacts of the helix formed by residues 201 - 242 (chain A) in PDB entry 4AVM
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A GLN* 4.2 1.2 + - - -
128A TYR* 4.3 8.0 - - - -
197A ILE* 3.1 14.2 + - - -
198A LEU* 2.5 34.3 + - - +
200A ASN* 1.4 71.9 - - - +
202A ARG* 1.3 62.1 + - - +
203A ILE 3.2 2.2 - - - -
204A GLY* 3.3 5.5 + - - +
205A CYS* 3.1 20.6 + - - +
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Residues in contact with ARG 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A GLN* 3.7 13.9 - - + +
56A GLU* 4.6 8.7 + - - -
128A TYR* 3.3 26.2 - - - +
198A LEU 3.7 0.6 + - - -
199A TYR* 2.9 66.9 + - - +
200A ASN* 3.2 7.1 + - - +
201A SER* 1.3 79.6 + - - +
203A ILE* 1.3 79.6 + - + +
205A CYS* 3.3 4.1 + - - +
206A TYR* 3.0 58.4 + - + +
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Residues in contact with ILE 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A ASN* 3.5 23.1 - - + +
202A ARG* 1.3 97.0 - - + +
204A GLY* 1.3 62.9 + - - +
206A TYR* 3.1 11.9 + - + +
207A VAL* 3.0 36.0 + - + +
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Residues in contact with GLY 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A ASN 4.4 0.4 + - - -
201A SER* 3.3 8.3 + - - +
203A ILE* 1.3 80.6 - - - +
205A CYS* 1.3 60.1 + - - +
207A VAL* 3.5 8.2 + - - +
208A THR* 2.9 30.3 + - - -
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Residues in contact with CYS 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A THR* 5.6 2.9 - - - -
125A MET* 3.6 27.4 - - - -
128A TYR* 3.6 47.3 - - + -
201A SER 3.1 12.1 + - - +
202A ARG 3.4 9.0 - - - +
203A ILE 3.1 0.2 - - - -
204A GLY* 1.3 76.6 - - - +
206A TYR* 1.3 61.9 + - - +
208A THR* 3.2 6.3 + - - -
209A ILE* 3.0 36.9 + - - +
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Residues in contact with TYR 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A GLN* 4.9 1.6 + - - +
56A GLU* 3.5 30.0 + - - +
57A GLY* 4.9 4.0 + - - -
60A LEU* 4.1 26.0 - - + -
125A MET* 4.8 5.4 - - + -
128A TYR* 4.5 5.7 + + - -
202A ARG* 3.0 44.8 + - + +
203A ILE* 3.6 8.3 - - + +
205A CYS* 1.3 83.2 - - + +
207A VAL* 1.3 67.3 + - + +
209A ILE* 3.5 2.0 + - - +
210A PHE* 3.0 41.3 + + + +
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Residues in contact with VAL 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A ILE* 3.0 32.4 + - + +
204A GLY* 3.7 8.7 - - - +
206A TYR* 1.3 76.0 - - + +
208A THR* 1.3 57.8 + - - +
210A PHE* 4.5 0.8 - - - +
211A GLN* 2.9 62.3 + - + +
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Residues in contact with THR 208 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A GLN 5.4 0.4 - - - +
124A THR* 4.1 24.0 - - + +
204A GLY 2.9 18.8 + - - -
205A CYS* 3.2 5.8 + - - -
207A VAL* 1.3 79.1 - - - +
209A ILE* 1.3 62.8 + - - +
211A GLN* 3.9 2.8 - - - -
212A ASN* 2.8 45.1 + - - +
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Residues in contact with ILE 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU* 4.7 2.9 - - + -
64A LEU* 3.9 19.5 - - + -
120A GLN 4.7 0.9 - - - +
121A ALA* 3.4 28.8 - - + +
124A THR* 3.7 26.0 - - + -
125A MET* 3.8 30.1 - - + +
205A CYS* 3.0 24.3 + - - +
206A TYR* 4.0 4.0 - - - +
208A THR* 1.3 77.6 - - - +
210A PHE* 1.3 76.5 + - + +
212A ASN* 3.4 4.9 + - - +
213A ILE* 3.0 39.1 + - + +
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Residues in contact with PHE 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU* 3.9 35.7 - - + -
64A LEU* 5.2 1.3 - - + -
206A TYR* 3.0 30.1 + + + +
207A VAL* 4.5 0.7 - - - +
209A ILE* 1.3 86.2 - - + +
211A GLN* 1.3 62.0 + - - +
213A ILE* 4.0 24.5 - - + +
214A SER* 3.0 28.4 + - - -
217A ARG* 6.4 0.2 - - - -
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Residues in contact with GLN 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A VAL* 2.9 42.5 + - + +
208A THR* 4.2 3.8 - - - +
210A PHE* 1.3 77.0 - - - +
212A ASN* 1.3 59.2 + - - +
214A SER* 3.5 6.1 + - - -
215A ASN* 2.9 30.1 + - - +
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Residues in contact with ASN 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A GLN* 2.9 54.2 + - + +
121A ALA* 5.1 2.2 - - + +
208A THR* 2.8 44.7 + - - +
209A ILE 3.6 4.0 - - - +
211A GLN* 1.3 76.3 - - - +
213A ILE* 1.4 63.6 + - - +
215A ASN* 3.3 5.7 + - - +
216A LEU* 3.0 31.3 + - - +
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Residues in contact with ILE 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU* 3.7 30.1 - - + -
67A PHE* 5.0 10.1 - - + -
117A LEU* 4.3 14.1 - - + -
121A ALA* 4.1 16.1 - - + +
209A ILE* 3.0 29.9 + - + +
210A PHE* 4.0 23.3 - - + +
212A ASN* 1.4 74.9 - - - +
214A SER* 1.3 61.8 + - - +
216A LEU* 3.4 6.4 + - - +
217A ARG* 3.0 59.5 + - + +
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Residues in contact with SER 214 (chain A).
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 3.0 20.2 + - - -
211A GLN* 3.7 7.0 - - - -
212A ASN 3.3 0.2 - - - -
213A ILE* 1.3 78.1 - - - +
215A ASN* 1.3 62.4 + - - +
217A ARG* 3.3 12.3 + - - +
218A ASP* 2.9 25.0 + - - +
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Residues in contact with ASN 215 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A GLN* 5.2 5.4 - - - +
211A GLN 2.9 21.1 + - - +
212A ASN* 3.8 7.0 - - - +
214A SER* 1.3 73.1 + - - +
216A LEU* 1.3 69.9 + - - +
218A ASP* 3.3 15.0 + - - +
219A VAL* 3.3 24.7 + - - +
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Residues in contact with LEU 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A TYR* 4.2 12.6 - - + +
116A LYS* 3.5 59.7 - - + +
117A LEU* 3.7 19.7 - - + +
120A GLN* 3.6 28.3 - - + +
121A ALA* 5.5 1.1 - - + +
212A ASN 3.0 21.8 + - - +
213A ILE* 3.8 4.7 - - - +
215A ASN* 1.3 78.3 - - - +
217A ARG* 1.3 60.2 + - - +
219A VAL* 3.5 3.6 + - + -
220A PHE* 3.0 18.0 + - - +
1246A EDO 2.8 26.6 + - - +
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Residues in contact with ARG 217 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A PHE* 4.3 17.9 - - - -
113A TYR* 3.3 27.8 - - + +
210A PHE* 6.4 0.2 - - - -
213A ILE* 3.0 41.3 + - + +
214A SER* 4.0 9.8 - - - +
216A LEU* 1.3 72.8 - - - +
218A ASP* 1.4 61.4 + - - +
220A PHE* 3.2 8.1 + - + +
221A TYR* 2.8 68.7 + - + -
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Residues in contact with ASP 218 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A SER* 2.9 15.6 + - - +
215A ASN* 3.3 11.2 + - - +
217A ARG* 1.4 76.5 - - - +
219A VAL* 1.4 63.1 + - + +
221A TYR* 3.4 11.8 + - - +
222A ARG* 3.0 40.9 + - - +
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Residues in contact with VAL 219 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LYS* 5.8 1.6 - - - +
215A ASN* 3.3 25.0 + - - +
216A LEU* 3.7 2.5 - - + +
217A ARG 3.3 0.2 - - - -
218A ASP* 1.4 75.8 - - + +
220A PHE* 1.4 57.6 + - - +
222A ARG* 3.3 28.4 + - - +
223A GLU* 2.9 41.8 + - + +
1246A EDO 3.6 32.5 - - - +
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Residues in contact with PHE 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A LEU* 4.3 9.2 - - + -
110A TRP* 3.5 40.4 - + - -
113A TYR* 3.7 43.5 - + + -
216A LEU 3.0 18.2 + - - +
217A ARG* 3.2 9.6 + - + +
219A VAL* 1.4 76.9 - - - +
221A TYR* 1.4 73.7 + + - +
223A GLU* 4.2 1.7 - - - +
224A MET* 2.9 71.7 + - + +
1246A EDO 4.0 11.6 + - - -
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Residues in contact with TYR 221 (chain A).
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* 2.8 64.6 + - + +
218A ASP* 3.8 12.6 - - - +
220A PHE* 1.4 87.9 - + - +
222A ARG* 1.4 58.4 + - - +
224A MET* 4.1 2.9 - - + +
225A SER* 2.8 33.0 + - - -
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Residues in contact with ARG 222 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ASP* 3.0 35.1 + - - +
219A VAL* 3.6 36.6 - - - +
221A TYR* 1.4 76.8 - - - +
223A GLU* 1.3 78.8 + - - +
225A SER* 3.4 6.7 + - - -
226A LYS* 3.3 34.0 + - + +
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Residues in contact with GLU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A LEU* 3.4 32.7 - - + +
219A VAL* 2.9 33.7 + - + +
220A PHE* 4.2 1.3 - - - +
222A ARG* 1.3 95.1 + - - +
224A MET* 1.3 64.9 + - - +
226A LYS* 3.2 45.1 + - - +
227A LEU* 3.3 15.8 + - - +
1246A EDO 5.8 0.2 - - - -
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Residues in contact with MET 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ASN* 3.3 28.7 - - - +
109A LEU* 3.8 25.6 - - + -
110A TRP* 3.4 28.7 - - + +
220A PHE* 2.9 54.2 + - + +
221A TYR* 4.1 4.0 - - + +
223A GLU* 1.3 74.4 - - - +
225A SER* 1.4 57.9 + - - +
227A LEU* 3.3 8.5 + - - +
228A ASN* 2.9 32.9 + - + +
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Residues in contact with SER 225 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A TYR 2.8 20.0 + - - -
222A ARG* 3.6 8.1 - - - -
223A GLU 3.3 0.2 - - - -
224A MET* 1.4 75.6 - - - +
226A LYS* 1.3 57.7 + - - +
228A ASN* 3.7 9.2 + - - +
229A HIS* 2.9 30.0 + - - +
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Residues in contact with LYS 226 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A ARG* 3.3 28.6 + - + +
223A GLU* 3.2 38.2 + - - +
225A SER* 1.3 77.1 - - - +
227A LEU* 1.4 63.9 + - + +
229A HIS* 3.2 8.5 + - - +
230A ASN* 3.1 30.1 + - - +
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Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ILE* 4.0 29.0 - - + +
105A ASN* 3.7 26.0 - - + +
106A ASN* 3.5 36.3 - - + +
109A LEU* 3.8 19.7 - - + -
223A GLU 3.3 8.2 + - - +
224A MET* 3.3 11.3 + - - +
226A LYS* 1.4 76.9 - - + +
228A ASN* 1.3 57.8 + - - +
230A ASN* 3.2 19.8 + - - +
231A LEU* 3.0 27.0 + - - +
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Residues in contact with ASN 228 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A MET 2.9 18.5 + - - +
225A SER* 3.7 9.2 + - - +
227A LEU* 1.3 73.0 - - - +
229A HIS* 1.4 66.2 + - - +
231A LEU* 3.3 27.2 + - - +
232A TYR* 3.3 12.0 + - - +
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Residues in contact with HIS 229 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A SER* 2.9 18.5 + - - +
226A LYS* 3.2 7.4 + - - +
228A ASN* 1.4 77.7 - - - +
230A ASN* 1.4 63.8 + - - +
232A TYR* 3.2 15.6 + + + +
233A GLU* 3.1 52.8 + - + +
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Residues in contact with ASN 230 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLU* 3.6 17.0 + - - +
102A ILE* 3.7 13.6 - - + +
226A LYS* 3.1 20.0 + - - +
227A LEU* 3.2 24.0 + - - +
229A HIS* 1.4 75.6 - - - +
231A LEU* 1.3 60.4 + - - +
233A GLU* 3.1 22.4 + - - +
234A VAL* 2.8 32.4 + - - +
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Residues in contact with LEU 231 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LEU* 4.3 15.0 - - + -
99A LEU* 4.4 13.2 - - + -
102A ILE* 3.6 16.1 - - + +
227A LEU 3.0 12.7 + - - +
228A ASN* 3.4 23.1 - - - +
229A HIS 3.2 0.2 - - - -
230A ASN* 1.3 73.8 - - - +
232A TYR* 1.3 65.9 + - - +
234A VAL* 3.2 5.3 + - + +
235A MET* 3.2 44.6 + - + +
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Residues in contact with TYR 232 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ASN 3.3 7.7 + - - +
229A HIS* 3.2 17.6 + + - +
231A LEU* 1.3 77.8 - - - +
233A GLU* 1.3 63.7 + - + +
235A MET* 3.2 9.8 + - - +
236A SER* 3.0 46.8 + - - -
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Residues in contact with GLU 233 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLU* 4.9 7.5 - - - +
229A HIS* 3.1 38.2 + - + +
230A ASN* 3.1 27.5 + - - +
232A TYR* 1.3 79.2 - - + +
234A VAL* 1.3 57.6 + - - +
236A SER* 3.2 10.2 + - - -
237A LYS* 3.0 39.0 + - - +
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Residues in contact with VAL 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TYR* 3.4 25.6 + - + +
94A ASP 4.5 0.2 - - - +
95A GLY* 3.9 14.4 - - - +
98A GLU* 3.4 39.0 - - + +
99A LEU* 4.2 10.3 - - + +
102A ILE* 3.7 15.0 - - + -
230A ASN 2.8 14.8 + - - +
231A LEU* 3.2 10.3 + - + +
233A GLU* 1.3 73.8 - - - +
235A MET* 1.3 72.3 + - + +
237A LYS* 3.2 9.2 + - - +
238A LEU* 3.0 26.0 + - - +
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Residues in contact with MET 235 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LEU* 4.0 28.9 - - + -
89A TYR* 4.0 11.7 - - + -
99A LEU* 5.3 0.2 - - + -
231A LEU* 3.2 24.1 + - + +
232A TYR* 3.2 9.6 + - - +
234A VAL* 1.3 97.8 - - + +
236A SER* 1.4 55.8 + - - +
238A LEU* 3.3 23.7 + - - +
239A GLU* 2.9 30.9 + - - +
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Residues in contact with SER 236 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A TYR* 3.0 34.9 + - - -
233A GLU* 3.2 12.1 + - - -
235A MET* 1.4 74.3 - - - +
237A LYS* 1.3 57.6 + - - +
239A GLU* 3.4 10.8 + - - +
240A ARG* 3.0 37.5 + - - +
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Residues in contact with LYS 237 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ASP* 4.2 19.8 - - + +
95A GLY* 4.5 12.3 - - - +
98A GLU* 2.7 34.7 + - - +
233A GLU* 3.0 21.6 + - - +
234A VAL* 3.5 8.5 - - - +
236A SER* 1.3 74.2 - - - +
238A LEU* 1.4 59.6 + - - +
240A ARG* 3.5 5.8 + - - +
241A GLN* 3.0 30.3 + - - +
1248A EPE 4.8 8.1 + - - +
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Residues in contact with LEU 238 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A TYR* 3.4 32.1 - - + +
93A TRP* 3.5 52.5 - - + -
94A ASP 4.2 5.5 + - - -
234A VAL 3.0 8.1 + - - +
235A MET* 3.5 22.2 - - - +
237A LYS* 1.4 77.1 - - - +
239A GLU* 1.4 61.5 + - - +
241A GLN* 3.5 4.0 + - - +
242A HIS* 2.9 43.5 + - + +
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Residues in contact with GLU 239 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A MET 2.9 18.0 + - - +
236A SER* 3.7 8.7 - - - +
237A LYS 3.4 0.2 - - - -
238A LEU* 1.4 77.4 - - - +
240A ARG* 1.4 62.5 + - + +
242A HIS* 3.2 7.1 + - - +
243A SER* 3.1 21.9 + - - +
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Residues in contact with ARG 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A SER* 3.0 23.4 + - - +
237A LYS* 3.9 6.3 - - - +
239A GLU* 1.4 72.3 - - + +
241A GLN* 1.3 66.5 + - - +
243A SER* 3.1 23.5 + - - +
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Residues in contact with GLN 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLU 3.3 21.4 + - - -
93A TRP* 3.4 4.1 - - - +
94A ASP* 2.8 48.8 + - - +
237A LYS 3.0 17.8 + - - +
238A LEU* 3.7 5.2 - - - +
239A GLU 3.4 0.2 - - - -
240A ARG* 1.3 75.3 - - - +
242A HIS* 1.3 85.3 + - + +
243A SER 3.6 2.6 + - - +
----------------------------------------------------------
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Residues in contact with HIS 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A TRP* 3.6 30.6 + + - -
238A LEU* 2.9 32.6 + - + +
239A GLU* 3.2 7.8 + - - +
240A ARG 3.2 0.6 - - - -
241A GLN* 1.3 104.1 + - + +
243A SER* 1.3 62.6 + - - +
244A ASN 3.8 0.9 + - - -
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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