Contacts of the helix formed by residues 143 - 182 (chain C) in PDB entry 1CUN
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 THR 143 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C GLY 4.1 0.5 - - - -
142C ASP* 1.3 96.3 + - + +
144C LEU* 1.3 63.0 + - - +
145C ALA* 3.3 9.9 + - - +
146C ALA* 3.1 21.9 + - - +
147C ILE* 3.3 22.9 + - - +
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Residues in contact with LEU 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C THR* 1.3 73.6 - - - +
145C ALA* 1.3 59.2 + - - +
147C ILE* 2.9 28.0 - - + +
148C GLN* 3.2 27.3 + - - +
218C SER* 5.5 8.1 - - - +
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Residues in contact with ALA 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C THR* 3.2 7.9 + - - +
144C LEU* 1.3 79.2 - - - +
146C ALA* 1.3 63.0 + - - +
148C GLN* 3.4 17.5 - - - +
149C GLY* 3.3 17.2 + - - -
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Residues in contact with ALA 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C GLY* 4.0 3.8 - - - -
142C ASP* 4.0 25.8 - - - +
143C THR* 3.1 20.3 + - - +
145C ALA* 1.3 77.5 - - - +
147C ILE* 1.3 65.2 + - - +
149C GLY* 3.0 12.4 + - - -
150C LEU* 3.0 22.5 + - + +
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Residues in contact with ILE 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C TYR 3.0 31.4 - - - +
141C GLY* 4.0 1.9 - - - +
143C THR 3.3 10.3 + - - +
144C LEU* 2.9 43.3 - - + +
146C ALA* 1.3 79.0 - - - +
148C GLN* 1.3 59.7 + - + +
150C LEU* 3.3 4.0 + - - +
151C LEU* 3.0 43.1 + - + +
214C LEU* 3.6 20.6 - - + +
217C ASN* 3.7 15.0 - - + +
218C SER* 3.3 27.6 - - - -
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Residues in contact with GLN 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C LEU* 3.2 30.0 + - - +
145C ALA* 3.4 19.4 - - - +
147C ILE* 1.3 80.5 - - + +
149C GLY* 1.3 66.3 + - - +
150C LEU 3.2 0.2 - - - -
151C LEU* 3.7 10.4 - - + +
152C LYS* 3.0 26.4 + - - +
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Residues in contact with GLY 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C ALA 3.3 11.9 + - - -
146C ALA* 3.0 8.2 + - - -
148C GLN* 1.3 78.8 - - - +
150C LEU* 1.3 64.8 + - - +
152C LYS* 3.4 9.7 + - - +
153C LYS* 3.2 28.7 + - - +
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Residues in contact with LEU 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C ASP* 3.5 16.8 - - + +
140C TYR* 3.5 8.7 - - - +
141C GLY* 3.5 31.0 - - - +
146C ALA* 3.0 18.6 + - + +
147C ILE 3.4 7.6 - - - +
148C GLN 3.2 0.2 - - - -
149C GLY* 1.3 77.6 - - - +
151C LEU* 1.3 63.1 + - - +
153C LYS* 3.3 29.3 + - + +
154C HIS* 3.0 22.3 + - - +
210C ARG* 3.8 18.6 + - - +
214C LEU* 4.1 14.3 - - + +
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Residues in contact with LEU 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C ILE* 3.0 48.1 + - + +
148C GLN* 3.8 10.3 - - + +
149C GLY 3.4 0.2 - - - -
150C LEU* 1.3 76.5 - - - +
152C LYS* 1.3 57.6 + - - +
154C HIS* 3.1 5.3 + - + +
155C GLU* 2.9 48.2 + - - +
211C LYS* 3.9 22.0 - - + +
214C LEU* 3.6 28.9 - - + +
215C ASP* 3.9 20.9 - - - +
218C SER* 4.8 6.7 - - - +
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Residues in contact with LYS 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C GLN 3.0 17.9 + - - +
149C GLY* 3.5 9.4 - - - +
151C LEU* 1.3 78.0 - - - +
153C LYS* 1.3 63.3 + - + +
155C GLU* 3.3 17.0 + - - +
156C ALA* 3.3 21.0 + - - +
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Residues in contact with LYS 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C GLY 3.2 15.7 + - - +
150C LEU* 3.7 27.3 - - + +
151C LEU 3.3 0.2 - - - -
152C LYS* 1.3 79.1 - - + +
154C HIS* 1.3 63.1 + - - +
156C ALA* 3.4 7.0 + - - +
157C PHE* 3.0 21.7 + - - +
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Residues in contact with HIS 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C VAL* 4.6 4.0 - - + +
150C LEU 3.0 14.0 + - - +
151C LEU* 3.1 8.0 + - + +
153C LYS* 1.3 75.9 - - - +
155C GLU* 1.3 61.0 + - + +
157C PHE* 3.0 28.7 + + + +
158C GLU* 2.8 58.8 + - + +
207C ALA* 3.6 19.6 + - + +
210C ARG* 3.8 27.2 - - + +
211C LYS* 3.7 26.0 - - + +
214C LEU* 4.1 15.7 - - + -
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Residues in contact with GLU 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C LEU* 2.9 40.4 + - + +
152C LYS* 3.6 18.4 - - - +
153C LYS 3.3 0.2 - - - -
154C HIS* 1.3 77.5 - - + +
156C ALA* 1.3 61.0 + - - +
158C GLU* 3.3 20.8 + - - +
159C THR* 3.3 23.2 + - - -
211C LYS* 5.3 5.7 - - - -
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Residues in contact with ALA 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C LYS 3.3 9.3 + - - +
153C LYS* 3.8 9.4 - - - +
154C HIS 3.2 0.6 - - - -
155C GLU* 1.3 75.8 - - - +
157C PHE* 1.3 66.1 + - - +
159C THR* 3.2 7.7 + - - -
160C ASP* 3.1 31.1 + - - +
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Residues in contact with PHE 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C TRP* 3.8 18.8 - + - -
131C LYS* 3.7 39.9 - - + +
134C LEU* 6.0 2.9 - - + -
135C VAL* 4.1 10.3 - - + -
153C LYS 3.0 13.9 + - - +
154C HIS* 3.0 32.0 + + + +
156C ALA* 1.3 76.9 - - - +
158C GLU* 1.3 56.5 + - + +
160C ASP* 3.2 7.9 + - - +
161C PHE* 2.7 57.4 + + + +
203C LEU* 4.0 18.8 - - + -
207C ALA* 3.7 22.9 - - + -
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Residues in contact with GLU 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C HIS* 2.8 44.5 + - + +
155C GLU* 3.5 22.7 - - - +
156C ALA 3.2 0.2 - - - -
157C PHE* 1.3 82.8 - - + +
159C THR* 1.3 62.2 + - - +
161C PHE* 3.4 6.7 + - + +
162C THR* 3.0 25.7 + - - -
207C ALA* 6.4 0.2 - - + -
211C LYS* 3.8 19.9 + - - +
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Residues in contact with THR 159 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C GLU 3.3 11.0 + - - -
156C ALA* 3.2 10.3 + - - -
158C GLU* 1.3 77.2 - - - +
160C ASP* 1.3 67.5 + - - +
162C THR* 3.1 19.6 + - - -
163C VAL* 3.2 18.7 + - + +
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Residues in contact with ASP 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C TRP* 4.1 16.8 + - + +
131C LYS* 5.7 3.6 + - - -
156C ALA* 3.1 21.4 + - - +
157C PHE* 3.5 9.9 - - - +
159C THR* 1.3 82.2 - - - +
161C PHE* 1.3 62.2 + - - +
163C VAL* 3.1 10.0 + - - +
164C HIS* 3.0 32.6 + - + -
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Residues in contact with PHE 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C TRP* 3.6 26.0 - + + -
128C ILE* 5.5 2.0 - - + -
157C PHE* 2.7 40.1 + + + +
158C GLU* 3.7 8.3 - - + +
159C THR 3.2 0.2 - - - -
160C ASP* 1.3 72.9 - - - +
162C THR* 1.3 57.1 + - - +
164C HIS* 3.2 2.7 + - + -
165C LYS* 2.8 65.2 + - + +
200C VAL* 3.7 18.4 - - + -
203C LEU* 3.5 28.0 - - + -
204C GLU* 3.5 36.8 - - + -
207C ALA* 4.8 3.1 - - + -
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Residues in contact with THR 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ILE* 4.2 19.4 - - + +
158C GLU 3.0 15.9 + - - -
159C THR* 3.1 14.5 + - + -
161C PHE* 1.3 77.7 - - - +
163C VAL* 1.3 63.1 + - + +
165C LYS* 3.5 16.7 + - + +
166C ASP* 3.4 18.0 + - - +
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Residues in contact with VAL 163 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ILE* 3.8 24.9 - - + +
79B GLY* 3.9 22.7 - - - -
82B GLU* 4.9 4.9 - - - +
159C THR* 3.2 16.6 + - + +
160C ASP* 3.1 13.2 + - - +
162C THR* 1.3 76.6 - - - +
164C HIS* 1.3 64.9 + - + +
166C ASP* 3.0 7.3 + - - +
167C ARG* 2.9 59.9 + - - +
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Residues in contact with HIS 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C GLU 5.6 0.9 - - - -
124C GLU* 2.7 27.6 + - - +
127C TRP* 3.3 67.3 + + + -
128C ILE* 6.0 1.1 - - + -
160C ASP* 3.0 28.3 + - + +
161C PHE* 3.8 8.1 - - + +
163C VAL* 1.3 77.0 - - + +
165C LYS* 1.3 60.9 + - - +
167C ARG* 3.2 25.5 + - - +
168C VAL* 2.8 35.6 + - + +
200C VAL* 6.1 0.2 - - - -
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Residues in contact with LYS 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C PHE* 2.8 65.2 + - + +
162C THR* 3.8 16.4 + - + +
163C VAL 3.2 0.2 - - - -
164C HIS* 1.3 73.4 - - - +
166C ASP* 1.3 63.4 + - - +
168C VAL* 3.3 8.4 + - - +
169C ASN* 3.0 31.9 + - - +
200C VAL* 4.2 12.8 - - + -
204C GLU* 3.2 28.4 + - - +
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Residues in contact with ASP 166 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B THR* 4.9 4.2 - - - -
78B ILE* 3.5 52.5 + - + +
162C THR 3.4 8.7 + - - +
163C VAL 3.0 10.1 + - - +
165C LYS* 1.3 79.8 - - - +
167C ARG* 1.3 57.6 + - + +
169C ASN* 3.1 13.9 + - - +
170C ASP* 2.9 41.1 + - - +
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Residues in contact with ARG 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B VAL* 4.0 29.9 - - - +
9B HIS* 3.8 16.8 + - - +
12B PHE* 3.7 23.2 - - - -
78B ILE 4.9 4.9 + - - -
79B GLY* 5.8 1.0 - - - -
82B GLU* 3.5 23.6 + - - -
83B ILE* 6.0 0.6 - - - +
124C GLU* 3.6 22.1 + - - +
163C VAL* 2.9 40.4 + - - +
164C HIS* 3.2 29.5 + - - +
166C ASP* 1.3 75.7 - - + +
168C VAL* 1.3 60.3 + - - +
170C ASP* 3.0 11.2 + - - +
171C VAL* 2.8 33.6 + - - +
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Residues in contact with VAL 168 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C GLU* 4.0 22.4 - - + +
128C ILE* 4.7 3.4 - - + -
164C HIS* 2.8 21.2 + - + +
165C LYS 3.5 4.7 - - - +
167C ARG* 1.3 75.4 - - - +
169C ASN* 1.3 68.3 + - - +
171C VAL* 3.2 8.6 + - - +
172C CYS* 2.9 31.6 + - - -
196C LEU* 3.9 30.3 - - + +
197C LYS* 4.9 5.6 - - + +
200C VAL* 3.8 30.7 - - + -
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Residues in contact with ASN 169 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C LYS* 3.0 27.4 + - - +
166C ASP* 3.1 14.4 + - - +
168C VAL* 1.3 79.2 - - - +
170C ASP* 1.3 64.2 + - - +
172C CYS* 3.5 5.5 + - - +
173C ALA* 3.0 24.1 + - - +
197C LYS* 4.1 15.9 + - - -
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Residues in contact with ASP 170 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B MET 6.3 0.9 - - - +
8B VAL* 3.7 26.4 - - + +
9B HIS* 5.6 4.3 - - + -
77B THR* 5.9 2.1 - - - -
166C ASP* 2.9 31.2 + - - +
167C ARG* 3.0 12.5 + - - +
169C ASN* 1.3 76.2 - - - +
171C VAL* 1.3 66.6 + - + +
173C ALA* 3.2 8.7 + - - +
174C ASN* 3.0 23.0 + - - +
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Residues in contact with VAL 171 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B HIS* 3.6 24.7 - - + +
117C PHE* 3.6 26.1 - - + -
120C ASN* 3.8 18.2 - - + +
121C VAL* 3.7 21.8 - - + +
124C GLU* 4.3 10.5 - - + -
167C ARG 2.8 19.6 + - - +
168C VAL* 3.6 8.5 - - - +
170C ASP* 1.3 76.8 - - - +
172C CYS* 1.3 58.0 + - - +
174C ASN* 3.3 9.5 + - - +
175C GLY 3.0 22.0 + - - -
193C MET* 6.0 0.2 - - + -
196C LEU* 3.9 11.0 - - + -
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Residues in contact with CYS 172 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C VAL* 2.9 24.9 + - - +
169C ASN* 3.9 4.3 - - - +
171C VAL* 1.3 75.4 - - - +
173C ALA* 1.3 67.3 + - - +
175C GLY 3.0 1.6 + - - -
176C GLU* 2.9 28.7 + - - +
193C MET* 3.4 39.3 - - - +
196C LEU* 4.8 6.7 - - - -
197C LYS* 3.7 44.6 - - - +
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Residues in contact with ALA 173 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C ASN 3.0 18.2 + - - +
170C ASP* 3.2 8.2 + - - +
172C CYS* 1.3 74.4 - - - +
174C ASN* 1.3 57.7 + - - +
176C GLU* 3.2 16.2 + - - +
177C ASP* 3.0 34.3 + - - +
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Residues in contact with ASN 174 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C GLU* 4.5 6.6 + - - +
116C GLN* 5.7 1.2 - - - +
117C PHE* 3.7 29.8 + - - +
120C ASN* 4.9 4.9 - - - +
170C ASP 3.0 12.9 + - - +
171C VAL* 3.4 10.8 - - - +
173C ALA* 1.3 76.1 - - - +
175C GLY* 1.3 64.8 + - - +
177C ASP* 3.2 11.8 + - - +
178C LEU* 2.9 34.3 + - - +
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Residues in contact with GLY 175 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C PHE* 3.8 16.2 - - - -
171C VAL 3.0 11.5 + - - -
172C CYS 3.0 3.7 + - - -
174C ASN* 1.3 76.8 - - - +
176C GLU* 1.3 63.4 + - - +
178C LEU* 3.2 6.5 + - - +
179C ILE* 3.1 27.4 + - - +
189C ILE* 3.6 18.5 - - - +
193C MET* 3.9 7.6 - - - -
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Residues in contact with GLU 176 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C CYS* 2.9 23.5 + - - +
173C ALA* 3.5 13.8 - - - +
175C GLY* 1.3 75.7 - - - +
177C ASP* 1.3 64.5 + - - +
179C ILE* 3.3 9.2 + - + +
180C LYS* 2.9 36.2 + - - +
193C MET* 4.0 16.8 - - + +
197C LYS* 5.3 5.9 + - - -
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Residues in contact with ASP 177 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C ALA* 3.0 20.5 + - - +
174C ASN* 3.2 15.7 + - - +
176C GLU* 1.3 77.7 - - - +
178C LEU* 1.3 62.8 + - + +
180C LYS* 3.1 26.4 + - - +
181C LYS* 2.9 34.4 + - + +
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Residues in contact with LEU 178 (chain C).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C GLU* 5.1 5.2 - - + +
113C GLU* 3.6 46.4 - - + +
114C TYR* 4.0 10.8 - - + +
117C PHE* 3.7 32.1 - - + -
174C ASN* 2.9 25.9 + - - +
175C GLY* 3.2 7.6 + - - +
177C ASP* 1.3 76.1 - - - +
179C ILE* 1.3 63.4 + - - +
181C LYS* 3.3 10.1 + - + +
182C ASN* 3.1 31.3 + - - +
184C HIS 5.8 0.2 - - - -
189C ILE* 3.9 24.7 - - + -
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Residues in contact with ILE 179 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C GLY 3.1 11.3 + - - +
176C GLU* 3.6 9.0 - - + +
178C LEU* 1.3 76.1 - - - +
180C LYS* 1.3 64.3 + - - +
182C ASN 2.8 23.2 + - - +
184C HIS 5.7 0.2 - - - -
186C VAL* 4.0 24.2 - - + +
189C ILE* 3.7 31.0 - - + -
190C THR* 3.5 24.5 - - - +
193C MET* 3.9 13.5 - - + -
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Residues in contact with LYS 180 (chain C).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C GLU* 2.9 21.9 + - - +
177C ASP* 3.1 34.8 + - - +
179C ILE* 1.3 80.3 - - - +
181C LYS* 1.3 63.4 + - + +
182C ASN* 3.4 1.0 + - - -
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Residues in contact with LYS 181 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110C GLU* 6.2 2.9 - - - -
113C GLU* 2.5 41.2 + - - +
177C ASP* 2.9 26.4 + - + +
178C LEU* 3.3 12.8 + - + +
180C LYS* 1.3 78.5 - - + +
182C ASN* 1.3 66.5 + - - +
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Residues in contact with ASN 182 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110C GLU* 2.8 39.1 + - - +
178C LEU* 3.1 18.2 + - - +
179C ILE* 2.8 22.6 - - - +
180C LYS 3.3 2.0 - - - -
181C LYS* 1.3 86.7 - - - +
183C ASN* 1.3 63.4 + - - +
184C HIS* 2.9 28.9 + - + +
186C VAL* 3.9 0.7 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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