Contacts of the helix formed by residues 140 - 171 (chain N) in PDB entry 2DYS
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 140 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119N GLU* 4.2 14.4 - - - -
135N ASN* 5.6 0.6 - - - +
138N HIS 4.1 0.4 - - - +
139N ALA* 1.3 77.5 - - - +
141N ALA* 1.3 59.3 + - - -
142N SER 3.4 2.9 + - - -
143N VAL 4.4 0.3 + - - -
213N ARG* 2.8 28.2 + - - +
36P HIS* 3.3 21.8 + - - -
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Residues in contact with ALA 141 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118N VAL* 4.1 8.5 - - + -
119N GLU* 4.1 6.2 + - + +
140N GLY* 1.3 71.9 - - - -
142N SER* 1.3 65.8 + - - +
143N VAL 3.4 0.2 - - - -
144N ASP* 2.9 4.9 + - - +
145N LEU* 2.8 32.8 + - + +
32P THR* 3.8 23.3 - - + -
36P HIS* 3.7 19.5 + - + +
37P PHE* 4.3 18.5 - - + -
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Residues in contact with SER 142 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115N SER* 2.7 31.2 + - - +
118N VAL* 3.0 25.0 + - - +
119N GLU* 3.7 6.9 - - - +
121N GLY* 3.2 30.9 + - - -
122N ALA* 3.7 2.5 - - - -
138N HIS* 5.3 1.8 - - - -
140N GLY 3.4 2.7 - - - -
141N ALA* 1.3 77.0 - - - +
143N VAL* 1.3 64.3 + - - +
145N LEU 3.1 0.9 + - - -
146N THR* 3.1 22.3 + - - -
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Residues in contact with VAL 143 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122N ALA* 4.0 6.3 - - + -
124N THR* 4.0 16.2 - - + -
128N VAL* 4.4 10.8 - - + -
133N ALA* 3.5 25.6 - - + +
138N HIS* 3.9 31.7 + - + +
140N GLY 4.4 0.2 + - - -
141N ALA 3.4 0.2 - - - -
142N SER* 1.3 79.3 - - - +
144N ASP* 1.3 62.3 + - - +
146N THR* 3.3 7.7 + - - -
147N ILE* 3.1 30.6 + - + +
209N LEU* 4.8 0.7 - - + -
213N ARG* 3.5 34.3 - - - +
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Residues in contact with ASP 144 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141N ALA 2.9 8.3 + - - +
143N VAL* 1.3 76.6 - - - +
145N LEU* 1.3 61.7 + - - +
147N ILE* 3.3 4.7 + - - +
148N PHE* 3.1 37.0 + - + -
210N LEU* 3.3 19.1 - - + +
213N ARG* 2.7 37.4 + - - +
214N ASN* 2.9 26.0 + - - -
32P THR* 4.8 2.7 - - + -
35P PHE* 5.2 1.6 - - + -
36P HIS* 2.6 34.0 + - + +
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Residues in contact with LEU 145 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111N LEU* 3.6 44.7 - - + +
114N ALA* 4.1 14.4 - - + -
115N SER* 3.8 11.9 - - - +
118N VAL* 4.0 22.2 - - + -
141N ALA* 2.8 30.7 + - + +
142N SER 3.1 6.0 + - - +
144N ASP* 1.3 76.3 - - - +
146N THR* 1.3 58.7 + - - +
148N PHE* 3.3 5.9 + - + +
149N SER* 3.0 27.9 + - - -
29P SER* 5.3 3.8 - - - +
32P THR* 3.8 26.9 - - + +
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Residues in contact with THR 146 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59N THR* 5.8 0.8 - - + +
63N PHE* 3.7 35.6 - - + -
112N LEU* 5.6 2.7 - - + +
115N SER* 2.9 26.4 + - - -
122N ALA* 3.7 12.5 - - + +
124N THR* 5.7 0.9 - - - +
128N VAL* 4.6 15.9 - - + -
142N SER 3.1 7.0 + - - -
143N VAL* 3.5 12.1 - - - +
144N ASP 3.2 0.2 - - - -
145N LEU* 1.3 78.5 - - - +
147N ILE* 1.3 60.8 + - + +
149N SER* 3.3 9.3 + - - -
150N LEU* 3.2 23.2 + - + +
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Residues in contact with ILE 147 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128N VAL* 5.3 4.7 - - + -
143N VAL* 3.1 27.7 + - + +
144N ASP* 3.6 9.9 - - - +
146N THR* 1.3 75.7 - - + +
148N PHE* 1.3 59.6 + - + +
150N LEU* 3.1 11.8 + - + +
151N HIS* 2.9 45.8 + - + +
206N ILE* 3.5 42.6 - - + +
209N LEU* 4.0 21.8 - - + -
210N LEU* 3.9 34.5 - - + +
213N ARG* 4.5 0.4 - - - -
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Residues in contact with PHE 148 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111N LEU* 3.6 16.4 - - + -
144N ASP* 3.1 28.0 + - + -
145N LEU* 3.6 9.4 - - + +
146N THR 3.3 0.2 - - - -
147N ILE* 1.3 76.8 - - + +
149N SER* 1.3 61.5 + - - +
151N HIS* 3.2 10.9 + - - +
152N LEU* 3.0 27.2 + - - +
210N LEU* 4.0 32.3 - - + -
609N PGV 3.7 31.9 - - + -
28P THR* 3.4 17.9 - - + +
31P LEU* 3.6 26.0 - - + -
32P THR* 3.1 34.5 - - - -
35P PHE* 4.9 4.0 - + - -
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Residues in contact with SER 149 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68N PHE* 3.8 6.2 - - - -
108N SER* 2.5 49.8 + - - +
111N LEU* 3.7 15.1 - - - +
112N LEU* 3.7 18.5 - - - +
145N LEU 3.0 13.6 + - - -
146N THR* 3.4 13.7 - - - -
147N ILE 3.2 0.2 - - - -
148N PHE* 1.3 75.7 - - - +
150N LEU* 1.3 58.5 + - - +
152N LEU 3.3 1.7 + - - -
153N ALA* 3.0 16.4 + - - +
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Residues in contact with LEU 150 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63N PHE* 3.8 40.4 - - + -
67N PHE* 3.9 30.0 - - + -
126N TRP 5.5 0.4 - - - +
128N VAL* 4.8 7.4 - - + -
146N THR* 3.2 16.8 + - + +
147N ILE* 3.1 11.8 + - + +
149N SER* 1.3 75.8 - - - +
151N HIS* 1.3 59.7 + - - +
153N ALA* 3.3 4.9 + - + +
154N GLY* 2.7 28.1 + - - -
202N LEU* 5.0 15.1 - - + +
206N ILE* 3.6 31.6 - - + -
235N PHE* 6.0 2.9 - - + -
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Residues in contact with HIS 151 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147N ILE* 2.9 35.2 + - + +
148N PHE* 3.2 21.0 + - - +
150N LEU* 1.3 76.5 - - - +
152N LEU* 1.3 59.8 + - + +
154N GLY* 3.2 2.3 + - - -
155N VAL* 3.0 33.8 + - - +
203N ALA* 3.9 9.5 + - + -
206N ILE* 3.8 18.2 - - + +
207N THR* 3.1 29.6 + - - -
210N LEU* 4.8 4.9 - - + -
609N PGV 4.2 13.8 - - + +
28P THR* 5.6 0.2 - - + -
305P PEK 3.2 45.3 - - + +
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Residues in contact with LEU 152 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104N LEU* 4.0 16.2 - - + +
107N PRO* 4.0 24.9 - - + -
108N SER* 3.7 16.4 - - - +
111N LEU* 3.6 24.2 - - + -
148N PHE 3.0 15.4 + - - +
149N SER 3.7 2.2 - - - +
151N HIS* 1.3 76.0 - - - +
153N ALA* 1.3 63.0 + - - +
155N VAL* 3.3 4.2 + - - +
156N SER* 3.0 23.8 + - - -
609N PGV 3.9 21.3 - - + -
24P ALA* 3.9 29.8 - - + +
25P LEU* 4.4 0.9 - - - +
28P THR* 4.1 18.2 - - + +
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Residues in contact with ALA 153 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67N PHE* 4.4 27.3 - - + +
68N PHE* 4.7 7.2 - - + -
105N LEU* 4.3 12.4 - - + +
108N SER* 3.6 10.7 + - - +
149N SER 3.0 17.5 + - - +
150N LEU* 3.6 8.7 - - + +
152N LEU* 1.3 75.5 - - - +
154N GLY* 1.3 57.9 + - - +
156N SER* 3.4 8.2 - - - -
157N SER* 3.1 30.3 + - - -
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Residues in contact with GLY 154 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67N PHE* 6.2 0.6 - - - -
150N LEU 2.7 17.2 + - - -
151N HIS* 3.6 1.8 - - - -
152N LEU 3.1 0.2 - - - -
153N ALA* 1.3 76.0 - - - +
155N VAL* 1.3 59.4 + - - +
157N SER* 3.3 2.3 + - - -
158N ILE* 2.9 38.0 + - - +
199N LEU* 3.7 24.8 - - - +
202N LEU* 6.2 0.2 - - - -
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Residues in contact with VAL 155 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104N LEU* 3.9 16.4 - - + -
151N HIS 3.0 20.3 + - - +
152N LEU* 3.9 4.3 - - - +
154N GLY* 1.3 72.1 - - - +
156N SER* 1.3 60.8 + - - +
158N ILE* 3.2 9.2 + - + +
159N LEU* 2.8 49.8 + - + +
609N PGV 3.9 52.5 - - + -
301P DCW 5.5 4.0 - - + -
305P PEK 4.2 20.4 - - + -
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Residues in contact with SER 156 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19N TYR* 4.1 3.1 + - - -
101N SER* 2.4 44.1 + - - +
104N LEU* 3.7 19.3 - - - +
105N LEU* 3.6 18.1 - - - +
152N LEU 3.0 13.1 + - - -
153N ALA 3.4 10.3 - - - -
155N VAL* 1.3 76.6 - - - +
157N SER* 1.3 56.7 + - - -
159N LEU* 4.7 0.4 - - - -
160N GLY* 2.9 23.0 + - - -
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Residues in contact with SER 157 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67N PHE* 6.1 0.7 - - - -
71N MET* 3.7 21.5 - - - +
153N ALA 3.1 15.9 + - - -
155N VAL 3.2 0.2 - - - -
156N SER* 1.3 74.3 + - - +
158N ILE* 1.3 60.9 + - - +
160N GLY* 3.3 2.8 + - - +
161N ALA* 2.8 28.8 + - - +
195N LEU* 4.1 15.4 - - - +
199N LEU* 3.4 26.5 - - - -
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Residues in contact with ILE 158 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154N GLY* 2.9 25.2 + - - +
155N VAL* 3.8 7.4 - - + +
157N SER* 1.3 71.1 - - - +
159N LEU* 1.3 69.9 + - + +
161N ALA* 3.2 6.8 + - - +
162N ILE* 3.1 40.0 + - + +
195N LEU 4.3 7.6 - - - +
196N LEU* 4.3 6.7 - - + -
199N LEU* 3.9 28.3 - - + -
200N PRO* 4.0 5.6 - - + -
203N ALA* 6.1 0.2 - - + -
609N PGV 6.5 0.7 - - + -
86P PHE* 5.9 1.8 - - + -
89P SER* 4.1 17.9 - - - +
301P DCW 3.4 35.4 - - + -
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Residues in contact with LEU 159 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97N MET* 3.2 41.2 - - + +
100N MET* 3.3 34.3 - - + -
101N SER* 3.4 15.5 - - - +
104N LEU* 4.2 9.6 - - + -
155N VAL* 2.8 35.2 + - + +
156N SER* 3.7 0.4 - - - +
158N ILE* 1.3 80.3 - - + +
160N GLY* 1.3 61.2 + - - +
162N ILE* 3.3 9.5 + - + -
163N ASN* 3.2 18.6 + - - +
609N PGV 4.4 31.6 - - + -
86P PHE* 6.1 0.7 - - + -
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Residues in contact with GLY 160 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19N TYR* 5.8 0.2 - - - -
75N ILE* 6.1 1.6 - - - -
98N ASN* 5.4 3.8 - - - -
101N SER* 3.2 13.0 + - - -
156N SER 2.9 13.4 + - - -
157N SER* 3.3 4.2 + - - -
158N ILE 3.3 0.2 - - - -
159N LEU* 1.3 77.2 - - - +
161N ALA* 1.3 55.6 + - - +
163N ASN* 3.3 7.0 + - - +
164N PHE* 2.9 44.6 + - - -
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Residues in contact with ALA 161 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157N SER 2.8 20.5 + - - +
158N ILE* 3.2 8.0 + - - +
160N GLY* 1.3 72.5 - - - +
162N ILE* 1.3 58.6 + - - +
164N PHE* 4.6 1.3 - - - -
165N ILE* 3.0 37.6 + - - +
192N ALA* 3.3 39.0 - - + +
195N LEU* 4.1 11.3 - - + +
196N LEU* 4.4 9.0 - - + +
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Residues in contact with ILE 162 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94N PHE* 4.2 3.4 - - + -
97N MET* 3.7 14.4 - - + -
158N ILE* 3.1 30.6 + - + +
159N LEU* 3.6 18.2 - - + +
160N GLY 3.3 0.2 - - - -
161N ALA* 1.3 76.4 - - - +
163N ASN* 1.3 60.6 + - - +
165N ILE* 4.9 0.4 - - - -
166N THR* 2.7 34.0 + - - +
196N LEU* 3.8 16.2 - - + -
609N PGV 5.0 5.4 - - + -
82P GLY* 3.8 29.8 - - - +
85P LEU* 4.0 15.7 - - + +
86P PHE* 4.1 31.4 - - + -
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Residues in contact with ASN 163 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92N MET* 3.5 11.6 - - + +
93N ALA 3.5 2.1 + - - -
94N PHE* 3.1 45.7 + - - +
97N MET* 4.3 3.1 - - + +
98N ASN* 3.0 44.7 + - - +
159N LEU 3.2 10.7 + - - +
160N GLY* 3.4 10.3 - - - +
162N ILE* 1.3 77.0 - - - +
164N PHE* 1.3 57.7 + - - +
166N THR* 3.4 1.9 + - - -
167N THR* 2.7 43.8 + - - -
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Residues in contact with PHE 164 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75N ILE* 3.2 48.5 - - + -
76N GLY* 5.1 0.4 - - - -
79N GLY* 3.5 24.7 - - - -
80N ASN* 3.5 24.0 - - - -
83N VAL* 4.3 11.2 - - + -
92N MET* 3.7 22.2 - - + -
98N ASN* 5.8 0.7 - - - -
160N GLY* 2.9 35.1 + - - +
161N ALA* 4.0 4.0 - - - +
163N ASN* 1.3 73.6 - - - +
165N ILE* 1.3 63.8 + - - +
167N THR* 3.3 1.9 + - - -
168N ILE* 2.9 31.8 + - + +
188N VAL* 3.6 25.4 - - + -
192N ALA* 4.3 9.6 - - + -
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Residues in contact with ILE 165 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G PEK 4.6 11.4 - - + -
161N ALA 3.0 20.9 + - - +
164N PHE* 1.3 76.4 - - - +
166N THR* 1.3 61.9 + - - +
168N ILE* 3.9 0.7 - - - +
169N ILE* 3.0 45.8 + - + +
189N MET* 4.1 22.0 - - + +
192N ALA* 3.3 27.4 - - + +
193N VAL* 3.7 23.8 - - + +
196N LEU* 4.4 13.5 - - + -
85P LEU* 3.8 30.1 - - + -
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Residues in contact with THR 166 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93N ALA* 3.7 18.6 - - + -
94N PHE* 3.7 15.4 - - + -
162N ILE 2.7 23.8 + - - -
163N ASN 3.8 2.5 - - - -
164N PHE 3.3 0.2 - - - -
165N ILE* 1.3 77.1 - - - +
167N THR* 1.3 59.1 + - - +
169N ILE* 4.0 2.1 - - - +
170N ASN* 2.8 37.6 + - + +
78P GLY* 3.3 34.8 - - - +
81P TYR* 4.0 10.7 - - + +
82P GLY* 3.7 6.4 + - - -
85P LEU* 3.7 12.1 - - - +
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Residues in contact with THR 167 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83N VAL* 4.9 7.4 - - + -
84N PRO* 5.2 2.2 - - + -
87N ILE* 3.8 18.0 - - + +
89N ALA* 4.9 1.1 - - + -
91N ASP 4.1 5.4 - - - +
92N MET* 3.6 28.3 - - - +
93N ALA 3.0 19.6 + - - -
163N ASN* 2.7 27.9 + - - -
164N PHE* 3.7 4.9 - - - -
166N THR* 1.3 76.9 - - - +
168N ILE* 1.3 59.6 + - - +
171N MET* 2.8 49.3 + - + +
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Residues in contact with ILE 168 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83N VAL* 3.7 27.4 - - + -
87N ILE* 4.6 5.8 - - + -
164N PHE* 2.9 22.3 + - + +
165N ILE 4.1 2.0 - - - +
167N THR* 1.3 76.4 - - - +
169N ILE* 1.3 61.0 + - - +
172N LYS* 3.4 16.5 - - + +
178N GLN* 3.3 25.4 - - - +
185N VAL* 3.5 42.6 - - + +
188N VAL* 4.2 11.0 - - + -
189N MET* 3.7 36.8 - - + +
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Residues in contact with ILE 169 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G GLY 4.5 2.2 - - - +
7G ASP 2.9 30.5 - - - +
8G HIS* 4.1 6.3 - - + -
9G GLY* 3.5 25.3 - - - +
102G PEK 5.5 3.4 - - + -
165N ILE* 3.0 36.3 + - + +
166N THR* 4.0 2.2 - - - +
168N ILE* 1.3 79.7 - - - +
170N ASN* 1.3 59.0 + - - +
171N MET 3.7 0.4 - - - -
172N LYS* 3.4 16.5 + - - -
178N GLN* 4.0 8.1 - - - +
189N MET* 3.3 28.3 - - + -
81P TYR* 3.8 33.0 - - + +
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Residues in contact with ASN 170 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93N ALA* 5.8 0.8 - - - +
166N THR* 2.8 19.1 + - + +
169N ILE* 1.3 78.6 - - - +
171N MET* 1.3 67.5 + - + +
172N LYS 3.7 3.9 + - - +
8P TYR* 3.2 18.1 + - - -
74P ALA* 3.0 26.7 + - - +
75P VAL* 5.2 0.2 - - - +
77P LYS* 3.6 26.7 - - - +
78P GLY* 3.5 18.8 - - - +
81P TYR* 4.0 14.4 - - + -
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Residues in contact with MET 171 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87N ILE* 3.5 17.4 - - - +
88N GLY 5.1 0.3 - - - -
89N ALA* 3.8 12.0 - - + +
90N PRO* 4.2 10.9 - - + +
91N ASP 3.2 26.2 - - - +
92N MET 3.9 4.3 - - - +
93N ALA* 3.5 37.7 - - - -
167N THR* 2.8 30.8 + - + +
170N ASN* 1.3 84.7 - - + +
172N LYS* 1.3 61.7 + - - +
8P TYR* 3.5 54.9 - - + -
10P MET* 5.7 1.3 - - + -
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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