Contacts of the helix formed by residues 153 - 179 (chain B) in PDB entry 1K6O
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 ASN 153 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A VAL* 6.2 2.4 - - - +
151B ILE* 3.2 3.5 - - + +
152B ASP* 1.3 76.4 - - - +
154B LYS* 1.3 64.4 + - - +
155B LEU* 2.9 17.2 - - - +
156B ARG* 2.9 47.0 + - + +
157B ARG* 2.8 35.7 + - - +
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Residues in contact with LYS 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ASP 3.3 6.0 + - - +
153B ASN* 1.3 75.1 - - - +
155B LEU* 1.3 58.3 + - - +
157B ARG* 3.6 19.1 - - - +
158B TYR* 2.7 67.0 + - + +
190B GLU* 4.8 2.2 - - - +
106D G 5.6 4.7 + - - -
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A TYR* 4.6 29.2 - - + +
368A VAL* 4.0 30.5 - - + -
369A LYS* 5.9 3.6 - - + -
153B ASN* 2.9 13.2 - - - +
154B LYS* 1.3 79.1 - - - +
156B ARG* 1.3 68.1 + - + +
157B ARG 3.1 1.1 - - - -
158B TYR* 4.5 9.9 - - + -
159B THR* 2.8 44.2 + - + +
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Residues in contact with ARG 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ILE* 4.0 28.3 - - - +
151B ILE* 3.9 28.6 - - + +
152B ASP 5.7 0.2 - - - +
153B ASN* 2.9 32.9 + - + +
155B LEU* 1.3 77.5 - - + +
157B ARG* 1.3 55.7 + - - +
159B THR* 2.5 23.3 + - - -
160B THR* 2.7 23.5 + - - -
212E G 4.6 3.6 + - - -
213E G 2.9 40.9 + - - +
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Residues in contact with ARG 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B PHE* 3.6 28.7 - - - -
151B ILE* 2.7 37.4 + - + +
152B ASP* 2.9 30.5 + - - +
153B ASN 2.8 13.6 + - - +
154B LYS* 3.5 21.1 - - - +
156B ARG* 1.3 77.4 - - - +
158B TYR* 1.3 59.1 + - - +
160B THR* 3.0 4.3 + - - -
161B PHE* 2.8 28.7 + - + +
190B GLU* 2.6 49.4 + - - -
179C THR* 3.9 27.4 - - + +
181C THR* 6.2 0.2 - - - -
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Residues in contact with TYR 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B LYS* 2.7 55.4 + - + +
155B LEU* 3.3 12.8 + - + +
157B ARG* 1.3 80.9 - - - +
159B THR* 1.3 63.4 + - - +
161B PHE* 3.4 9.3 + - - +
162B SER* 3.2 23.2 + - - -
190B GLU* 2.8 53.8 + - + +
191B THR* 3.7 30.5 - - + +
106D G 6.2 0.2 - - - -
107D A 4.4 17.3 - - - -
108D T 6.2 0.4 - - - -
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Residues in contact with THR 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B LEU* 2.8 33.7 + - + +
156B ARG* 2.5 28.5 + - - -
158B TYR* 1.3 73.3 - - - +
160B THR* 1.3 62.4 + - - +
162B SER* 3.0 17.2 + - - -
163B LYS* 3.1 19.1 + - - +
108D T 5.6 7.2 - - + +
213E G 6.5 1.6 - - - -
214E A 6.1 2.0 - - - +
215E C 5.4 10.3 - - + +
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Residues in contact with THR 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ILE* 6.6 0.2 - - + -
151B ILE* 4.0 20.5 - - + +
156B ARG* 2.7 22.2 + - - +
157B ARG 3.4 3.6 - - - -
159B THR* 1.3 83.3 + - - +
161B PHE* 1.3 62.5 + - - +
163B LYS* 3.5 3.0 + - - +
164B ARG* 3.0 30.3 + - + +
178C LEU* 4.4 13.2 - - + -
179C THR* 4.8 4.9 - - + -
212E G 3.3 44.1 + - - +
213E G 5.1 4.5 + - - -
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Residues in contact with PHE 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ARG* 2.8 16.5 + - + +
158B TYR* 3.5 12.8 - - - +
159B THR 3.2 0.2 - - - -
160B THR* 1.3 72.6 - - - +
162B SER* 1.3 70.3 + - - +
164B ARG* 4.1 0.3 - - - +
165B LYS* 3.0 46.8 + - + +
187B VAL* 3.4 34.3 - - + -
189B SER* 3.9 23.6 - - - -
190B GLU* 5.2 2.2 - - + -
195B TYR* 4.2 11.2 - + - -
175C LEU* 4.3 6.4 - - + +
179C THR* 3.6 32.5 - - + +
181C THR* 3.6 23.3 - - + -
108D T 5.8 0.4 - - - -
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Residues in contact with SER 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B TYR 3.2 13.0 + - - -
159B THR 3.0 8.1 + - - -
161B PHE* 1.3 85.9 - - - +
163B LYS* 1.3 67.6 + - - +
164B ARG 3.1 0.2 + - - -
165B LYS* 3.7 8.6 - - - +
166B THR* 2.8 27.9 + - - -
107D A 5.1 1.9 - - - +
108D T 3.6 44.0 + - - +
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Residues in contact with LYS 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B THR* 3.1 15.6 + - - +
160B THR* 3.5 11.2 + - - +
162B SER* 1.3 79.8 - - - +
164B ARG* 1.3 62.9 + - - +
166B THR* 3.3 14.3 - - - -
167B GLY 3.4 3.6 + - - -
109D G 4.9 7.4 - - - +
110D T 3.1 34.3 + - + +
111D C 3.9 2.6 - - - +
211E T 3.6 39.4 + - + +
212E G 3.4 30.3 + - + +
213E G 3.1 25.1 + - - +
214E A 4.3 4.7 - - - +
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Residues in contact with ARG 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ARG* 4.5 9.7 - - - +
146B ILE* 5.3 7.3 - - - +
148B MET* 5.6 1.0 - - - -
160B THR* 3.0 23.5 + - + +
163B LYS* 1.3 72.0 - - + +
165B LYS* 1.3 55.6 + - - +
166B THR 2.6 5.1 + - - -
167B GLY* 2.3 29.1 + - - -
168B ILE* 2.8 14.0 + - + -
171C LYS* 3.7 21.4 - - + +
174C GLU* 3.2 39.6 + - - +
175C LEU* 3.7 25.6 - - + +
178C LEU* 3.6 28.0 - - + +
179C THR* 5.9 0.2 - - + -
211E T 3.5 27.6 + - - +
212E G 3.0 28.2 + - - +
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Residues in contact with LYS 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B PHE* 3.0 33.2 + - + +
162B SER* 4.3 7.7 + - - +
164B ARG* 1.3 78.1 - - - +
166B THR* 1.3 63.2 + - - +
168B ILE* 3.3 14.9 - - - +
169B MET* 3.0 37.6 - - + +
187B VAL* 4.1 23.6 - - + -
195B TYR* 3.2 49.3 - - + -
175C LEU* 4.2 4.3 - - + +
108D T 2.7 34.1 + - - +
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Residues in contact with THR 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B SER 2.8 19.4 + - - -
163B LYS* 3.3 9.9 - - - -
164B ARG 2.6 4.6 + - - -
165B LYS* 1.3 83.2 - - - +
167B GLY* 1.3 57.8 + - - -
169B MET* 4.3 3.2 - - - +
170B LYS* 3.8 15.8 + - - +
108D T 6.3 0.4 - - - -
109D G 5.0 11.9 - - - -
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Residues in contact with GLY 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LYS 3.4 2.2 + - - -
164B ARG 2.3 20.5 + - - -
166B THR* 1.3 69.6 - - - +
168B ILE* 1.3 58.8 + - - -
169B MET 3.2 1.6 - - - -
170B LYS* 2.9 25.0 + - - +
171B LYS* 2.9 18.1 + - - +
171C LYS* 5.7 1.6 - - - -
210E A 4.9 8.0 + - - +
211E T 3.5 17.7 - - - -
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Residues in contact with ILE 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ARG* 2.8 11.9 + - + +
165B LYS* 3.3 29.6 - - + +
167B GLY* 1.3 68.2 - - - -
169B MET* 1.3 79.3 + - + +
171B LYS* 3.0 8.3 + - + +
172B ALA* 2.9 21.5 + - - +
185B LEU* 3.5 28.9 - - + -
187B VAL* 4.7 1.8 - - + -
168C ILE* 3.3 36.1 - - + +
171C LYS* 3.4 31.8 - - + +
172C ALA* 4.0 9.2 - - + +
175C LEU* 4.1 20.0 - - + -
211E T 4.7 0.4 + - - -
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Residues in contact with MET 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LYS* 3.0 32.7 + - + +
166B THR* 4.3 4.7 - - - +
168B ILE* 1.3 85.2 - - + +
170B LYS* 1.3 65.7 + - - +
172B ALA* 3.3 3.7 + - - +
173B TYR* 3.1 19.1 + - - +
185B LEU* 3.4 25.8 - - + -
187B VAL* 5.2 2.0 - - - -
195B TYR* 4.1 12.3 - - + +
196B THR* 3.2 43.3 - - - +
197B PHE* 3.5 18.9 - - + +
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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
----------------------------------------------------------
166B THR 3.8 8.8 + - - +
167B GLY* 2.9 21.0 + - - +
169B MET* 1.3 78.2 - - - +
171B LYS* 1.3 62.7 + - + +
173B TYR* 2.9 15.0 + - + +
174B GLU* 2.9 44.0 + - + +
209E T 5.2 1.0 - - - -
210E A 3.2 40.1 + - - +
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Residues in contact with LYS 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLY 2.9 18.5 + - - +
168B ILE* 3.0 11.2 + - - +
170B LYS* 1.3 75.1 - - - +
172B ALA* 1.3 56.1 + - - +
174B GLU* 3.0 17.5 + - - +
175B LEU* 2.7 35.7 + - - +
143C ARG* 5.3 3.8 - - - +
164C ARG* 5.0 6.4 + - + +
167C GLY 6.1 0.4 - - - -
168C ILE* 3.7 26.0 - - + +
171C LYS* 4.5 24.0 - - + +
117D T 3.0 17.3 + - - -
118D A 2.6 34.8 + - - +
209E T 5.4 0.4 + - - -
210E A 4.0 31.5 + - - +
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Residues in contact with ALA 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ILE 2.9 11.2 + - - +
169B MET 3.4 8.7 - - - +
171B LYS* 1.3 75.8 - - - +
173B TYR* 1.3 54.0 + - - +
175B LEU* 3.8 1.5 - - - +
176B SER* 2.8 36.0 + - - -
183B VAL* 4.1 14.2 - - + +
185B LEU* 4.3 13.2 - - + -
197B PHE* 3.1 29.4 - - + -
168C ILE* 3.5 15.4 - - + +
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Residues in contact with TYR 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B MET 3.1 8.1 + - - +
170B LYS* 2.9 17.6 + - + +
172B ALA* 1.3 79.2 - - - +
174B GLU* 1.3 69.3 + - + +
176B SER* 3.1 2.6 - - - -
177B THR* 2.7 63.2 + - + +
197B PHE* 3.4 25.9 - + + -
148C MET* 3.9 29.5 + - + +
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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 42.3 + - + +
171B LYS* 3.3 15.0 + - - +
173B TYR* 1.3 81.2 - - + +
175B LEU* 1.3 56.2 + - - +
178B LEU* 2.4 41.1 + - - +
143C ARG* 5.9 0.5 + - - -
148C MET* 3.5 36.1 - - - +
164C ARG* 3.1 32.8 + - - +
210E A 4.0 12.6 + - - -
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Residues in contact with LEU 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B LYS 2.7 18.6 + - - +
172B ALA 3.8 2.0 - - - +
174B GLU* 1.3 74.4 - - - +
176B SER* 1.3 68.8 + - - +
178B LEU* 4.3 4.7 - - - -
179B THR* 2.9 43.7 + - + +
181B THR* 4.3 2.0 - - - +
183B VAL* 4.3 9.9 - - + -
161C PHE* 4.0 30.5 - - + +
164C ARG* 4.3 22.9 - - + +
165C LYS* 4.7 7.0 - - - +
168C ILE* 4.3 23.6 - - + -
187C VAL* 3.8 33.4 - - + -
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Residues in contact with SER 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ALA 2.8 24.4 + - - -
173B TYR 3.1 4.9 - - - -
175B LEU* 1.3 72.1 - - - +
177B THR* 1.3 57.4 + - - +
180B GLY* 2.8 30.0 + - - -
181B THR* 2.8 32.8 + - - -
183B VAL* 3.8 9.8 - - - +
197B PHE* 3.6 14.2 - - - -
199B THR* 3.3 24.5 + - - +
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Residues in contact with THR 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B TYR* 2.7 45.0 + - + +
176B SER* 1.3 78.3 - - - +
178B LEU* 1.3 63.2 + - - +
179B THR 3.3 0.5 + - - -
180B GLY* 3.3 9.1 + - - +
197B PHE* 6.0 0.2 - - + -
199B THR* 6.2 1.8 - - + -
148C MET* 2.6 38.2 - - - +
149C GLU* 5.8 0.7 - - - -
150C PHE* 3.4 21.7 + - - +
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Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B GLU 2.4 32.9 + - - +
175B LEU* 4.0 2.9 - - - +
177B THR* 1.3 69.6 + - - +
179B THR* 1.3 59.9 - - + +
146C ILE* 4.3 16.6 - - + +
147C LYS 3.8 20.4 - - - +
148C MET* 3.5 23.8 - - - -
149C GLU 3.8 11.0 - - - +
150C PHE* 3.6 0.7 - - - -
151C ILE* 3.1 45.0 + - + +
160C THR* 4.0 14.4 - - + -
164C ARG* 3.5 39.3 - - + +
119D G 4.3 6.5 - - - +
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Residues in contact with THR 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B LEU* 2.9 27.1 + - + +
178B LEU* 1.3 80.7 - - + +
180B GLY* 1.3 66.3 + - - +
181B THR* 2.9 12.8 - - - +
150C PHE* 4.1 8.5 - - - -
157C ARG* 3.7 36.4 - - + +
160C THR* 4.4 10.3 - - + -
161C PHE* 3.4 51.3 - - + +
190C GLU* 4.8 4.2 - - - +
----------------------------------------------------------
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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