Contacts of the helix formed by residues 166 - 190 (chain B) in PDB entry 3NA0
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 166 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B GLU 3.8 10.5 + - - -
163B ALA 3.3 16.0 + - - +
164B THR 3.0 0.6 - - - -
165B LYS* 1.3 89.6 - - - +
167B PHE* 1.3 64.4 + - - +
168B LEU 3.2 1.3 - - - -
169B PRO* 3.3 14.4 - - - +
170B LEU* 4.0 14.6 - - - +
298B TYR* 3.4 38.9 - - + +
304B ARG* 3.2 28.9 - - - +
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Residues in contact with PHE 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B GLU 3.6 21.8 - - - -
158B VAL* 3.8 3.6 - - - -
163B ALA 4.1 6.3 - - - -
164B THR* 2.9 44.9 + - + +
166B ASN* 1.3 78.7 - - - +
168B LEU* 1.3 57.0 + - - +
169B PRO 3.5 0.4 - - - -
170B LEU* 3.1 4.9 + - + +
171B LEU* 2.9 47.8 + - + +
213B VAL* 3.7 19.7 - - + -
298B TYR* 3.5 26.5 - + - -
301B ILE* 3.8 23.3 - - + -
467B ILE* 3.5 30.3 - - + -
470B LEU* 4.1 11.4 - - + -
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Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B THR 4.1 10.8 - - - +
165B LYS* 3.3 20.6 - - + +
166B ASN 3.2 0.2 - - - -
167B PHE* 1.3 76.1 - - - +
169B PRO* 1.4 65.1 - - + +
171B LEU* 4.1 0.2 - - - -
172B ASP* 2.9 33.9 + - - +
367B MET* 4.4 11.0 - - + -
368B ALA* 3.6 39.9 - - + +
371B LEU* 3.6 17.5 - - + -
470B LEU* 3.9 30.7 - - + -
474B ILE* 4.2 12.6 - - + +
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Residues in contact with PRO 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LYS 4.3 2.9 - - - +
166B ASN* 3.3 19.5 - - - +
168B LEU* 1.4 94.4 - - + +
170B LEU* 1.3 59.3 + - + +
172B ASP* 4.0 5.5 - - + +
173B ALA* 3.0 30.0 + - - +
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Residues in contact with LEU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ASN 4.0 10.8 - - - +
167B PHE* 3.1 7.0 + - - +
169B PRO* 1.3 80.3 - - + +
171B LEU* 1.3 63.7 + - - +
173B ALA* 3.8 1.6 + - - +
174B VAL* 3.5 14.4 + - - +
212B ASN* 2.7 57.3 + - - +
213B VAL* 4.2 18.4 - - + +
216B GLY* 4.9 12.1 - - - +
298B TYR* 3.8 35.2 - - + +
299B ARG 5.6 0.2 - - - -
300B GLY* 5.0 0.7 - - - +
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Residues in contact with LEU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B PHE* 2.9 31.0 + - + +
170B LEU* 1.3 73.9 - - - +
172B ASP* 1.3 61.7 + - - +
174B VAL* 3.1 8.6 + - - +
175B SER* 3.0 28.8 + - - +
205B PHE* 5.0 1.2 - - - -
209B SER* 4.0 29.2 - - - +
213B VAL* 3.8 23.3 - - + -
467B ILE* 4.2 8.5 - - + +
470B LEU* 3.8 18.4 - - + -
471B GLU* 3.7 39.7 - - + +
474B ILE* 4.2 14.4 - - + -
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Residues in contact with ASP 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LEU 2.9 21.0 + - - +
169B PRO* 4.0 6.0 - - + +
171B LEU* 1.3 77.1 - - - +
173B ALA* 1.3 56.3 + - - +
175B SER* 3.3 0.5 + - - -
176B ARG* 2.9 50.9 + - - +
360B ARG* 5.2 3.1 + - - -
367B MET* 3.8 27.3 - - + +
474B ILE* 3.5 14.9 - - + +
478B ASN* 3.1 26.2 + - - +
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Residues in contact with ALA 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B PRO 3.0 20.7 + - - +
170B LEU* 3.9 7.2 - - - +
171B LEU 3.3 0.2 - - - -
172B ASP* 1.3 75.3 - - - +
174B VAL* 1.3 63.0 + - - +
176B ARG* 3.6 8.9 + - - +
177B ASP* 3.2 28.2 + - - -
212B ASN* 4.9 2.9 - - - +
218B ARG* 3.9 13.9 - - - +
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Residues in contact with VAL 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU 3.5 15.0 + - - +
171B LEU 3.1 8.5 + - - +
173B ALA* 1.3 76.8 - - - +
175B SER* 1.3 64.5 + - - +
177B ASP* 3.1 6.1 + - - +
178B PHE* 3.0 18.7 + - - +
205B PHE* 3.5 25.8 - - + -
208B GLU* 3.5 36.6 - - + +
209B SER* 3.6 10.3 - - - +
212B ASN* 3.8 13.9 - - + +
218B ARG* 3.9 20.9 - - - +
222B LEU* 3.6 8.5 - - + +
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Residues in contact with SER 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B LEU* 3.0 12.7 + - - +
172B ASP 3.7 3.8 - - - -
174B VAL* 1.3 75.8 - - - +
176B ARG* 1.3 60.6 + - - +
178B PHE* 3.1 5.5 + - - +
179B VAL* 3.0 25.5 + - - +
205B PHE* 3.4 21.3 - - - -
471B GLU 4.4 1.2 + - - -
474B ILE* 3.9 4.4 - - - +
475B PHE* 3.3 31.0 + - - -
478B ASN* 3.6 26.0 - - - -
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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
----------------------------------------------------------
172B ASP* 2.9 46.4 + - - +
173B ALA* 3.9 7.0 - - - +
174B VAL 3.3 0.2 - - - -
175B SER* 1.3 71.2 - - - +
177B ASP* 1.3 58.4 + - - +
179B VAL* 3.3 10.6 + - - +
180B SER* 3.0 27.8 + - - -
360B ARG* 5.3 10.9 - - - +
478B ASN* 3.5 25.3 + - - +
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Residues in contact with ASP 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ALA 3.2 6.6 + - - +
174B VAL 3.1 9.7 + - - +
176B ARG* 1.3 76.7 - - - +
178B PHE* 1.3 64.6 + - - +
180B SER* 3.2 12.1 + - - -
181B VAL* 3.1 24.6 + - - +
218B ARG* 2.8 40.7 + - - +
222B LEU* 4.1 11.2 - - + -
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Residues in contact with PHE 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B VAL 3.0 11.7 + - - +
175B SER* 3.4 9.6 - - - +
177B ASP* 1.3 75.1 - - - +
179B VAL* 1.3 65.5 + - + +
181B VAL* 3.2 19.4 + - + +
182B LEU* 3.3 37.3 + - + +
198B ILE* 4.3 12.1 - - + -
201B ASP* 3.7 37.2 - - + -
202B LEU* 3.8 17.5 - - + -
205B PHE* 3.9 26.2 - - + -
222B LEU* 3.6 19.0 - - + +
475B PHE* 3.4 30.1 - + + -
479B MET* 4.0 9.2 - - + -
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Residues in contact with VAL 179 (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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175B SER 3.0 15.1 + - - +
176B ARG* 3.3 12.5 + - - +
178B PHE* 1.3 77.4 - - + +
180B SER* 1.3 57.2 + - - +
182B LEU 3.3 2.8 + - - -
183B HIS* 3.0 37.8 + - + -
478B ASN* 3.7 35.9 - - + +
479B MET* 4.2 7.9 - - + +
482B ASN* 3.4 29.2 - - + +
483B PHE* 3.5 21.6 - - + -
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Residues in contact with SER 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ARG 3.0 13.9 + - - -
177B ASP* 3.2 16.5 + - - -
179B VAL* 1.3 75.6 - - - +
181B VAL* 1.3 59.7 + - - +
183B HIS* 3.2 10.4 + - - +
184B ARG* 2.8 39.8 + - - +
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Residues in contact with VAL 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ASP 3.1 15.8 + - - +
178B PHE* 3.4 14.4 - - + +
180B SER* 1.3 73.7 - - - +
182B LEU* 1.3 68.1 + - + +
184B ARG* 3.0 26.9 + - - +
185B ARG* 2.9 54.7 + - + +
201B ASP* 5.1 2.9 - - - +
222B LEU* 3.2 38.8 - - + +
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Residues in contact with LEU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B PHE* 3.3 37.8 + - + +
179B VAL 3.3 2.0 + - - +
181B VAL* 1.3 79.7 - - + +
183B HIS* 1.3 57.7 - - - +
185B ARG* 3.0 12.8 + - - +
186B ILE* 2.9 36.9 + - + +
194B TYR* 3.8 31.2 - - + -
198B ILE* 4.6 8.3 - - + -
479B MET* 3.8 27.4 - - + -
483B PHE* 3.7 21.3 - - + -
511B PHE* 4.1 21.5 - - + -
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Residues in contact with HIS 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B VAL* 3.0 34.5 + - + +
180B SER* 3.5 11.4 - - - +
182B LEU* 1.3 75.5 - - - +
184B ARG* 1.3 61.0 + - + +
186B ILE* 3.5 11.4 + - - +
187B LYS* 3.1 23.0 + - - +
482B ASN* 3.3 29.6 + - - -
483B PHE* 3.6 21.0 - + - -
513B PRO* 4.6 14.6 - - + +
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Residues in contact with ARG 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 SER* 2.8 25.0 + - - +
181B VAL* 3.0 31.4 + - - +
183B HIS* 1.3 72.7 - - + +
185B ARG* 1.3 60.3 + - + +
187B LYS* 3.3 6.4 + - - +
188B LYS* 2.9 31.0 + - - +
222B LEU 3.5 22.4 + - - -
223B GLU* 4.6 3.8 - - - +
224B GLU* 3.4 44.5 + - - +
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Residues in contact with ARG 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B VAL* 2.9 36.8 + - + +
182B LEU* 3.0 12.2 + - - +
184B ARG* 1.3 77.7 - - + +
186B ILE* 1.3 59.4 + - - +
188B LYS* 4.0 6.5 - - + +
189B ALA* 3.0 31.5 + - - +
194B TYR* 3.1 59.9 + - + -
197B ASP 5.6 0.2 + - - -
198B ILE* 4.5 3.4 - - - +
201B ASP* 2.8 44.3 + - - -
204B ARG* 4.8 1.0 - - - +
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Residues in contact with ILE 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LEU* 2.9 17.9 + - - +
183B HIS* 3.7 9.2 - - - +
185B ARG* 1.3 75.5 - - - +
187B LYS* 1.3 62.3 + - - +
189B ALA* 3.6 2.3 + - - +
190B GLY* 3.2 17.3 + - - -
192B GLY* 3.7 11.7 + - - -
193B ASN 3.4 29.2 + - - +
194B TYR* 3.7 20.9 - - + +
483B PHE* 3.6 37.5 - - + -
511B PHE* 4.2 13.2 - - + +
513B PRO* 3.9 23.1 - - + -
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Residues in contact with LYS 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 HIS 3.1 14.3 + - - +
184B ARG* 3.6 10.3 - - - +
185B ARG 3.3 0.2 - - - -
186B ILE* 1.3 77.8 - - - +
188B LYS* 1.3 61.5 + - - +
190B GLY* 3.1 15.6 + - - -
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Residues in contact with LYS 188 (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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506A PRO* 3.4 19.3 - - + +
184B ARG* 2.9 17.4 + - - +
185B ARG* 4.1 7.0 - - + +
186B ILE 3.5 0.2 - - - -
187B LYS* 1.3 76.4 - - - +
189B ALA* 1.3 62.0 + - - +
190B GLY* 3.5 0.5 + - - -
224B GLU* 5.3 10.5 + - - -
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Residues in contact with ALA 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A PRO* 3.8 25.5 - - - +
508A SER* 6.4 2.2 - - - -
185B ARG 3.0 19.4 + - - +
186B ILE 3.9 0.4 - - - +
187B LYS 3.3 0.2 - - - -
188B LYS* 1.3 75.8 - - - +
190B GLY* 1.3 59.7 + - - +
191B SER* 3.2 8.4 + - - +
193B ASN 3.3 23.3 - - - +
194B TYR* 4.9 8.5 - - + -
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Residues in contact with GLY 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A LYS* 3.6 21.4 + - - +
506A PRO* 4.3 9.6 - - - -
186B ILE 3.2 5.9 + - - -
187B LYS* 3.1 17.4 + - - -
188B LYS 4.3 1.3 - - - -
189B ALA* 1.3 75.6 - - - +
191B SER* 1.3 60.0 + - - +
192B GLY 3.6 2.6 + - - -
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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