Contacts of the helix formed by residues 159 - 180 (chain B) in PDB entry 1KNY
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 159 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A MET 4.2 2.0 - - - +
153B ILE* 4.3 13.5 - - + +
157B GLY* 4.1 1.7 - - - -
158B PRO* 1.3 66.9 - - - +
160B THR* 1.3 58.0 + - - +
161B PHE 2.9 6.1 - - - -
162B LEU* 2.8 30.4 + - + +
163B PRO* 2.9 14.2 - - - +
220B SER* 4.2 25.6 - - - +
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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
----------------------------------------------------------
189A ALA 4.4 4.3 + - - -
192A LEU* 4.4 6.3 - - - +
193A THR* 3.7 25.4 + - + +
213A MET* 3.3 56.3 - - + +
158B PRO* 3.9 16.3 - - + +
159B THR* 1.3 78.3 - - - +
161B PHE* 1.3 59.7 + - - +
162B LEU 3.6 0.2 - - - -
163B PRO* 4.2 2.1 - - - +
164B SER* 4.0 9.0 + - - -
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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
----------------------------------------------------------
171A MET* 4.9 10.3 - - + -
188A SER* 3.7 29.4 - - - -
189A ALA* 3.2 47.3 - - + +
192A LEU* 5.5 3.1 - - + -
149B LYS* 4.8 14.1 - - + -
153B ILE* 4.0 13.9 - - + -
158B PRO 3.1 10.6 + - - +
159B THR 2.9 1.0 - - - -
160B THR* 1.3 79.7 + - - +
162B LEU* 1.3 52.4 + - - +
163B PRO* 3.4 2.5 - - - -
164B SER* 3.3 20.7 + - - -
165B LEU* 2.7 54.9 + - + +
168B GLN* 3.8 24.7 - - - -
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Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B TRP* 4.9 2.9 - - + -
153B ILE* 4.0 22.2 - - + +
158B PRO 3.8 2.2 + - - -
159B THR* 2.8 19.4 + - + +
161B PHE* 1.3 74.0 - - - +
163B PRO* 1.3 78.0 - - + +
165B LEU* 3.1 7.0 + - + -
166B THR* 2.9 36.3 + - - +
220B SER* 4.0 31.9 - - - +
223B LEU* 4.0 15.0 - - + -
224B LEU* 4.0 27.1 - - + -
227B LEU* 4.1 17.0 - - + -
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Residues in contact with PRO 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A VAL* 5.2 1.1 - - + -
212A VAL* 3.6 20.4 - - + +
213A MET 4.1 4.7 - - - +
214A SER 4.4 1.1 - - - +
215A GLY* 3.6 32.3 - - - +
217A LEU* 4.6 6.5 - - + -
159B THR 2.9 14.6 - - - +
160B THR 4.2 1.8 - - - -
161B PHE 3.6 2.2 - - - -
162B LEU* 1.3 96.0 - - + +
164B SER* 1.3 63.7 + - - +
166B THR* 3.0 11.8 + - - +
167B VAL* 3.3 15.6 + - - +
217B LEU* 4.0 29.4 - - + +
223B LEU* 5.1 0.7 - - + -
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Residues in contact with SER 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A VAL* 3.7 28.9 - - - +
171A MET* 4.5 5.6 - - - -
192A LEU* 3.9 8.8 - - - +
212A VAL* 3.6 25.6 + - - +
160B THR 4.0 6.2 + - - -
161B PHE* 3.3 20.3 + - - -
162B LEU 3.3 0.2 - - - -
163B PRO* 1.3 76.6 - - - +
165B LEU* 1.3 63.9 + - - +
167B VAL* 3.4 9.4 + - - +
168B GLN* 2.9 23.8 + - - -
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B TYR* 3.6 40.4 - - + +
149B LYS* 3.9 12.6 - - + -
150B TRP* 3.5 44.2 - - + +
153B ILE* 4.7 9.2 - - + -
161B PHE* 2.7 39.2 + - + +
162B LEU* 3.7 7.2 - - + +
164B SER* 1.3 73.7 - - - +
166B THR* 1.3 56.1 + - - +
168B GLN* 2.8 41.7 + - - +
169B VAL* 3.1 10.4 + - + +
227B LEU* 5.6 1.1 - - + -
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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 LEU* 2.9 26.1 + - - +
163B PRO 3.3 9.4 - - - -
165B LEU* 1.3 77.9 - - - +
167B VAL* 1.3 55.4 + - - +
169B VAL* 3.5 8.8 + - - +
170B ALA* 2.9 26.7 + - - +
208B LEU* 4.0 22.6 - - + +
211B PHE* 5.4 1.1 - - + -
212B VAL* 3.6 20.0 - - + -
217B LEU* 4.0 13.9 - - + -
223B LEU* 4.4 13.2 - - + +
227B LEU* 3.8 11.8 - - + +
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Residues in contact with VAL 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A PRO 4.8 0.7 - - - +
164A SER* 4.1 32.1 - - - +
167A VAL* 4.3 25.8 - - + -
168A GLN* 6.2 1.6 - - - +
163B PRO 3.3 11.3 + - - +
164B SER* 3.5 9.2 - - - +
165B LEU 3.1 0.2 - - - -
166B THR* 1.3 74.2 - - - +
168B GLN* 1.3 65.8 + - + +
170B ALA* 3.9 2.0 - - - +
171B MET* 3.1 34.6 + - + +
212B VAL* 4.1 24.9 - - + -
217B LEU* 4.7 9.6 - - + -
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Residues in contact with GLN 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A VAL* 4.7 9.1 - - - +
171A MET* 5.7 5.3 - - - +
146B TYR* 4.4 27.3 + - + +
161B PHE* 3.8 23.6 - - - -
164B SER* 2.9 30.7 + - - +
165B LEU* 2.8 19.9 + - + +
167B VAL* 1.3 82.3 - - + +
169B VAL* 1.3 62.3 + - - +
171B MET* 3.3 8.0 + - - +
172B ALA* 3.1 23.3 + - - +
559B KAN 4.6 12.6 - - - +
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Residues in contact with VAL 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU* 4.3 4.8 - - + +
146B TYR* 3.8 33.4 - - + -
150B TRP* 3.8 17.7 - - + -
165B LEU* 3.1 15.6 + - + +
166B THR 3.6 7.9 - - - +
168B GLN* 1.3 79.1 - - - +
170B ALA* 1.3 58.9 + - - +
172B ALA* 3.0 9.3 + - - +
173B GLY* 2.8 27.2 + - - -
208B LEU* 4.1 6.7 - - + -
227B LEU* 3.8 21.3 - - + -
230B PHE* 3.9 26.9 - - + -
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Residues in contact with ALA 170 (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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166B THR 2.9 18.3 + - - +
167B VAL 3.9 3.8 - - - +
168B GLN 3.3 0.2 - - - -
169B VAL* 1.3 77.0 - - - +
171B MET* 1.3 62.8 + - - +
174B ALA* 3.1 6.2 + - - +
192B LEU* 4.4 3.8 - - + -
205B TYR* 2.7 34.2 + - - -
208B LEU* 4.3 9.4 - - + -
209B CYS* 4.2 17.7 - - - -
212B VAL* 3.8 25.8 - - + -
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Residues in contact with MET 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A PHE* 6.2 3.1 - - + -
164A SER* 5.0 10.8 - - - +
168A GLN* 6.2 4.9 - - - +
98B LEU* 5.5 9.0 - - + -
167B VAL* 3.1 22.2 + - + +
168B GLN* 3.3 11.9 - - - +
170B ALA* 1.3 75.4 - - + +
172B ALA* 1.3 59.0 + - - +
174B ALA* 3.1 7.0 - - - +
175B MET* 3.0 41.2 + - + +
188B SER 5.6 1.6 - - - +
191B VAL* 3.7 28.3 - - + -
192B LEU* 3.7 27.1 - - + -
212B VAL* 5.8 0.4 - - + -
559B KAN 5.8 5.6 - - - +
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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
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138B LEU* 3.8 21.4 - - + +
142B GLU* 4.9 5.8 - - - +
143B LEU* 4.4 6.1 - - + -
146B TYR* 4.2 18.6 - - + +
168B GLN 3.4 10.1 - - - +
169B VAL* 3.2 8.7 - - - +
171B MET* 1.3 77.0 - - - +
173B GLY* 1.3 67.0 + - - +
174B ALA 2.9 1.6 - - - -
175B MET* 2.8 24.2 + - - +
176B LEU* 2.8 10.6 + - - +
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Residues in contact with GLY 173 (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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143B LEU* 4.4 5.2 - - - +
169B VAL 2.8 16.9 + - - -
170B ALA 4.1 1.6 - - - -
172B ALA* 1.3 72.6 - - - +
174B ALA* 1.3 57.3 + - - +
176B LEU* 2.8 30.6 + - - +
177B ILE* 3.0 12.2 + - - +
202B PRO* 5.8 0.9 - - - +
205B TYR* 4.1 9.2 - - - -
230B PHE* 3.9 25.4 - - - -
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Residues in contact with ALA 174 (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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170B ALA 3.1 7.0 + - - +
171B MET* 3.1 13.2 - - - +
172B ALA 2.9 0.6 - - - -
173B GLY* 1.3 71.4 - - - +
175B MET* 1.3 66.2 + - + +
176B LEU 3.0 1.6 - - - -
177B ILE* 3.3 2.6 + - - +
178B GLY 3.2 10.2 + - - -
185B TYR* 3.0 22.2 + - - +
191B VAL* 3.5 29.2 - - + -
192B LEU* 4.3 0.4 - - + -
195B ALA* 3.9 11.0 - - + -
205B TYR* 3.0 22.8 + - - +
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Residues in contact with MET 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B SER 3.1 28.0 - - - +
95B ASP* 3.7 22.9 - - + -
97B PRO* 3.7 9.1 - - - +
98B LEU* 3.8 34.5 - - + +
138B LEU* 3.9 8.5 - - + -
142B GLU* 6.1 0.9 - - - +
171B MET* 3.0 26.7 + - + +
172B ALA* 2.8 17.0 + - - +
174B ALA* 1.3 78.6 - - - +
176B LEU* 1.3 62.3 + - - +
179B LEU* 3.0 28.6 + - - +
185B TYR* 4.5 6.1 - - + -
191B VAL* 4.3 20.0 - - + -
559B KAN 5.1 7.2 - - - +
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Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ILE* 3.6 30.0 - - + +
138B LEU* 3.8 28.5 - - + -
139B ILE* 4.5 9.0 - - + -
143B LEU* 4.5 10.3 - - + -
172B ALA 2.8 6.4 + - - +
173B GLY* 2.8 20.6 + - - +
175B MET* 1.3 80.9 - - - +
177B ILE* 1.3 50.0 + - + +
179B LEU* 3.3 3.6 + - - +
180B HIS* 2.8 34.3 + - - +
202B PRO* 4.8 6.7 - - + -
234B ILE* 4.1 26.5 - - + -
237B TRP* 4.1 26.1 - - + -
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Residues in contact with ILE 177 (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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173B GLY 3.0 11.2 + - - +
174B ALA 3.3 4.9 + - - +
176B LEU* 1.3 73.3 - - + +
178B GLY* 1.3 54.4 + - - +
180B HIS* 2.8 9.1 + - + +
181B HIS* 2.5 70.2 + - + +
185B TYR* 4.5 2.9 - - - +
195B ALA* 3.7 12.6 - - + +
198B GLN* 3.4 18.6 - - + -
200B ASP 5.8 0.4 - - - -
201B LEU* 3.3 31.4 - - + +
202B PRO* 4.4 16.8 - - + -
205B TYR* 3.8 26.5 - - + -
237B TRP* 5.3 3.1 - - + -
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Residues in contact with GLY 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B PRO* 4.0 9.9 - - - -
174B ALA 3.2 10.7 + - - -
177B ILE* 1.3 74.4 - - - +
179B LEU* 1.3 66.5 + - - +
181B HIS 3.0 0.3 + - - -
182B ARG* 2.8 23.9 + - - -
183B ILE* 2.9 41.5 + - - +
185B TYR* 3.9 2.3 + - - -
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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
----------------------------------------------------------
92B VAL* 3.5 31.4 - - + -
93B GLU 3.6 16.6 - - - +
94B SER* 4.0 4.3 - - - +
96B TRP* 4.3 2.0 - - + -
97B PRO* 3.7 15.7 - - + +
131B PHE* 3.8 26.8 - - + +
134B ALA* 3.5 29.8 - - + -
135B ILE* 4.1 16.4 - - + +
138B LEU* 3.7 29.8 - - + -
175B MET 3.0 15.0 + - - +
176B LEU* 3.6 3.4 - - - +
178B GLY* 1.3 76.0 - - - +
180B HIS* 1.3 64.4 + - - +
182B ARG* 3.7 9.5 + - - -
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Residues in contact with HIS 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ILE* 4.1 6.7 - - + +
176B LEU 2.8 15.6 + - - +
177B ILE* 2.8 12.0 + - + +
179B LEU* 1.3 80.9 - - - +
181B HIS* 1.3 85.9 + + - -
182B ARG* 3.7 15.6 + - - -
200B ASP* 3.6 15.6 + - + +
237B TRP* 3.3 30.4 - + + -
241B HIS* 3.4 35.1 + + + -
243B TYR* 3.0 24.6 + - - -
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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