Contacts of the helix formed by residues 169 - 201 (chain B) in PDB entry 1T7S
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 ALA 169 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B GLN* 1.3 78.3 - - - +
170B LYS* 1.3 55.6 + - - +
171B ARG* 4.5 6.5 - - + +
172B ASN* 2.9 18.3 + - + +
173B ARG* 2.8 31.0 + - - +
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Residues in contact with LYS 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ALA* 1.3 71.0 - - - +
171B ARG* 1.3 62.7 + - + +
173B ARG* 2.9 51.6 + - + +
174B GLU* 2.9 45.5 + - + +
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Residues in contact with ARG 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ALA* 3.4 5.1 - - + +
170B LYS* 1.3 80.6 - - + +
172B ASN* 1.3 63.7 + - - +
174B GLU* 4.0 19.6 - - - +
175B LYS* 3.4 33.9 + - - +
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Residues in contact with ASN 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B GLN* 4.4 19.7 + - + +
169B ALA* 2.9 24.0 + - - +
171B ARG* 1.3 84.0 + - - +
173B ARG* 1.3 64.7 + - - +
175B LYS* 3.7 22.1 + - - +
176B ARG* 3.3 25.4 + - - +
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Residues in contact with ARG 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B PRO 3.8 21.1 - - - +
166B GLU* 4.1 15.4 + - - +
168B GLN* 2.6 37.7 + - + +
169B ALA* 2.8 20.1 + - - +
170B LYS* 2.9 53.3 + - + +
172B ASN* 1.3 73.8 - - - +
174B GLU* 1.3 59.9 + - - +
175B LYS 3.1 1.8 - - - -
176B ARG* 3.2 14.4 + - - +
177B LYS* 2.8 44.1 + - + +
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Residues in contact with GLU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LYS* 2.9 50.9 + - - +
171B ARG* 4.0 22.0 - - - +
173B ARG* 1.3 77.1 - - - +
175B LYS* 1.3 63.4 + - + +
177B LYS* 3.5 12.0 - - - +
178B THR* 3.1 26.5 + - - -
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Residues in contact with LYS 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ARG* 3.4 25.2 + - - +
172B ASN* 3.7 23.9 + - - +
173B ARG 3.1 0.6 - - - -
174B GLU* 1.3 86.2 - - + +
176B ARG* 1.3 61.9 + - - +
177B LYS 3.4 0.2 + - - -
178B THR* 3.5 16.6 + - - -
179B LEU* 3.5 14.4 + - + +
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Residues in contact with ARG 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B PRO* 3.3 40.9 + - - +
168B GLN* 2.8 43.6 - - - +
172B ASN 3.3 13.4 + - - +
173B ARG* 3.2 20.3 + - - +
175B LYS* 1.3 76.4 - - - +
177B LYS* 1.3 73.6 + - - +
179B LEU* 3.5 8.2 + - + +
180B VAL* 2.9 48.7 + - + +
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Residues in contact with LYS 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ARG* 2.8 39.1 + - + +
174B GLU* 3.5 10.5 - - - +
176B ARG* 1.3 89.4 - - - +
178B THR* 1.3 67.9 + - - +
180B VAL* 3.1 8.8 + - + -
181B ASN* 2.8 43.9 + - - +
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Residues in contact with THR 178 (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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174B GLU 3.1 12.3 + - - -
175B LYS* 3.5 11.6 - - - -
176B ARG 3.3 0.2 - - - -
177B LYS* 1.3 77.9 - - - +
179B LEU* 1.3 72.1 + - + +
181B ASN* 4.0 4.1 - - - +
182B GLY* 2.8 29.8 + - - -
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Residues in contact with LEU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B LYS* 3.5 12.7 + - + +
176B ARG* 3.5 12.0 + - + +
177B LYS 3.3 0.6 - - - -
178B THR* 1.3 93.5 - - + +
180B VAL* 1.3 63.5 + - + +
182B GLY* 3.2 2.1 + - - -
183B ILE* 3.0 32.3 + - + +
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Residues in contact with VAL 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ARG* 2.9 46.3 + - + +
177B LYS* 3.1 10.1 + - + +
179B LEU* 1.3 74.0 - - + +
181B ASN* 1.3 76.9 + - - +
182B GLY 3.1 0.2 + - - -
183B ILE* 3.3 7.5 + - + +
184B GLN* 2.9 27.8 + - + +
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Residues in contact with ASN 181 (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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177B LYS* 2.8 33.6 + - - +
178B THR* 4.0 3.4 - - - +
180B VAL* 1.3 82.1 - - - +
182B GLY* 1.3 59.0 + - - +
184B GLN* 3.0 8.9 + - - +
185B THR* 2.8 37.4 + - - +
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Residues in contact with GLY 182 (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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178B THR 2.8 18.9 + - - -
179B LEU* 3.4 3.4 - - - -
180B VAL 3.0 1.2 - - - -
181B ASN* 1.3 80.4 - - - +
183B ILE* 1.3 61.2 + - - -
185B THR* 3.4 6.8 + - - -
186B LEU* 3.4 23.4 + - - +
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Residues in contact with ILE 183 (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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179B LEU* 3.0 20.5 + - + +
180B VAL* 3.8 8.7 - - - +
182B GLY* 1.3 69.9 - - - -
184B GLN* 1.3 71.8 + - - +
186B LEU* 3.3 14.5 + - + +
187B LEU* 3.0 39.9 + - + +
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Residues in contact with GLN 184 (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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180B VAL* 2.9 18.7 + - + +
181B ASN* 3.1 15.5 - - - +
183B ILE* 1.3 81.1 - - + +
185B THR* 1.3 64.4 + - - +
187B LEU* 2.9 32.3 + - - +
188B ASN* 2.8 48.3 + - - +
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Residues in contact with THR 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ASN* 2.8 21.8 + - - +
182B GLY* 3.7 6.3 - - - -
184B GLN* 1.3 72.9 - - - +
186B LEU* 1.3 65.8 + - + +
188B ASN* 3.4 13.4 + - - +
189B GLN* 2.9 48.4 + - + +
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Residues in contact with LEU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B GLY 3.4 18.9 + - - +
183B ILE* 3.3 16.8 + - + +
184B GLN 3.1 0.8 - - - -
185B THR* 1.3 80.1 - - + +
187B LEU* 1.3 54.4 + - - +
189B GLN* 2.8 25.4 + - + +
190B ASN* 2.5 38.9 + - + +
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Residues in contact with LEU 187 (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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183B ILE* 3.0 34.8 + - + +
184B GLN* 2.9 32.6 + - - +
186B LEU* 1.3 75.1 - - + +
188B ASN* 1.3 63.9 + - - +
190B ASN* 3.0 10.4 + - + +
191B ASP* 2.9 29.6 + - - +
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Residues in contact with ASN 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B GLN* 2.8 44.5 + - - +
185B THR* 3.5 16.4 + - - +
187B LEU* 1.3 74.7 - - - +
189B GLN* 1.3 64.2 + - + +
191B ASP* 3.0 29.7 + - - +
192B ALA* 3.1 8.3 + - - +
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Residues in contact with GLN 189 (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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185B THR* 2.9 33.6 + - + +
186B LEU* 2.8 35.1 + - + +
188B ASN* 1.3 77.8 - - + +
190B ASN* 1.3 61.7 + - - +
191B ASP 3.0 0.6 + - - -
192B ALA* 3.3 9.3 + - - +
193B LEU* 3.0 22.2 + - - +
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Residues in contact with ASN 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LEU* 2.5 20.4 + - + +
187B LEU* 3.5 11.7 - - + +
189B GLN* 1.3 72.6 - - - +
191B ASP* 1.3 58.3 + - - +
193B LEU* 3.5 20.7 - - - +
194B LEU* 3.0 25.6 + - - +
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Residues in contact with ASP 191 (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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187B LEU* 2.9 20.1 + - - +
188B ASN* 3.0 19.9 + - - +
190B ASN* 1.3 75.2 - - - +
192B ALA* 1.3 55.5 + - - +
193B LEU 2.9 1.1 - - - -
194B LEU* 2.7 27.5 + - - +
195B ARG* 2.7 27.5 + - + +
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Residues in contact with ALA 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ASN 3.1 6.7 + - - +
189B GLN* 3.7 9.9 - - - +
191B ASP* 1.3 79.7 - - - +
193B LEU* 1.3 52.7 + - - +
195B ARG* 3.4 21.2 - - - +
196B ARG* 2.8 34.5 + - - +
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Residues in contact with LEU 193 (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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189B GLN 3.0 15.9 + - - +
190B ASN* 3.5 23.1 - - - +
191B ASP 2.9 0.4 - - - -
192B ALA* 1.3 76.0 - - - +
194B LEU* 1.3 63.4 + - + +
196B ARG* 4.2 23.6 - - + +
197B LEU* 3.0 34.6 + - + +
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Residues in contact with LEU 194 (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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190B ASN* 3.0 15.4 + - - +
191B ASP* 2.7 19.6 + - - +
193B LEU* 1.3 73.4 - - + +
195B ARG* 1.3 69.1 + - + +
197B LEU* 3.3 15.9 + - + +
198B GLN* 3.1 58.2 + - + +
201B GLN* 5.7 0.4 - - - +
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Residues in contact with ARG 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ASP* 2.7 18.9 + - + +
192B ALA* 3.4 22.7 - - - +
194B LEU* 1.3 83.5 - - + +
196B ARG* 1.3 64.7 + - - +
198B GLN* 3.3 5.9 + - - +
199B GLU* 2.9 39.0 + - - +
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Residues in contact with ARG 196 (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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192B ALA 2.8 18.6 + - - +
193B LEU* 3.8 24.4 - - + +
195B ARG* 1.3 78.6 - - - +
197B LEU* 1.3 67.2 + - - +
199B GLU* 3.2 20.4 + - - +
200B TYR* 3.2 13.1 + - + +
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Residues in contact with LEU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LEU* 3.0 28.8 + - + +
194B LEU* 3.6 20.0 - - + +
195B ARG 3.3 0.2 - - - -
196B ARG* 1.3 77.7 - - - +
198B GLN* 1.3 57.7 + - - +
200B TYR* 3.2 13.4 + - + +
201B GLN* 2.9 47.9 + - + +
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Residues in contact with GLN 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LEU* 3.1 47.7 + - + +
195B ARG* 3.9 4.7 - - - +
197B LEU* 1.3 69.3 - - - +
199B GLU* 1.3 63.1 + - - +
200B TYR 2.8 6.9 + - - -
201B GLN* 2.8 41.2 + - + +
202B SER* 3.9 4.9 + - - -
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Residues in contact with GLU 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ARG* 2.9 38.5 + - + +
196B ARG* 3.2 12.6 + - - +
198B GLN* 1.3 76.6 - - - +
200B TYR* 1.3 55.1 + - - +
202B SER* 3.3 16.2 + - - -
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Residues in contact with TYR 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B ARG* 3.2 10.1 + - + +
197B LEU* 3.2 14.9 + - + +
198B GLN 2.8 0.6 - - - -
199B GLU* 1.3 78.4 - - - +
201B GLN* 1.3 56.4 + - + +
202B SER* 2.7 24.0 + - - -
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Residues in contact with GLN 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LEU* 5.7 0.4 - - - +
197B LEU* 2.9 41.9 + - + +
198B GLN* 2.8 42.4 + - - +
200B TYR* 1.3 78.8 - - + +
202B SER* 1.3 56.9 + - - +
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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