Contacts of the helix formed by residues 178 - 199 (chain B) in PDB entry 3NAY
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 ASP 178 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177B PHE* 1.4 72.9 - - - +
179B GLU* 1.4 54.5 + - - +
180B THR* 3.3 11.9 + - - -
181B CYS* 2.9 37.6 + - - +
182B THR* 2.8 33.4 + - - -
306B PHE* 3.7 6.1 - - - -
359B THR* 3.0 43.8 + - + +
360B ALA 4.1 10.5 - - - +
361B TYR* 4.0 13.2 - - + +
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Residues in contact with GLU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ASP* 1.4 72.5 - - - +
180B THR* 1.4 53.1 + - - +
182B THR* 3.8 2.0 - - - -
183B ARG* 2.9 51.4 + - - +
306B PHE* 3.3 53.5 - - + +
307B PRO* 5.2 3.3 - - - +
308B LYS* 4.1 16.8 + - - +
341B PHE* 3.8 26.0 - - + -
361B TYR* 5.1 0.4 - - - -
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Residues in contact with THR 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ASP* 3.3 12.6 + - - +
179B GLU* 1.4 74.5 - - - +
181B CYS* 1.3 59.8 + - - +
183B ARG* 3.5 31.8 + - - +
184B PHE* 3.1 28.2 + - - +
356B PRO* 3.8 25.1 - - + -
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Residues in contact with CYS 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 PHE* 4.0 20.0 - - + -
178B ASP* 2.9 29.7 + - - +
180B THR* 1.3 69.4 - - - +
182B THR* 1.4 66.4 + - - +
184B PHE* 3.4 1.7 + - - -
185B TYR* 3.1 30.2 + - - +
356B PRO* 4.3 15.7 - - - -
357B LYS 3.2 27.1 - - - -
358B LEU* 3.7 15.0 - - + -
359B THR 3.4 16.4 - - - -
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Residues in contact with THR 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B PHE* 3.4 24.0 + - - +
178B ASP 2.8 22.6 + - - -
179B GLU* 3.8 5.8 - - - -
181B CYS* 1.4 72.2 - - - +
183B ARG* 1.4 54.3 + - - +
185B TYR* 4.0 0.5 - - - +
186B THR* 2.7 43.0 + - - +
272B ILE* 4.5 6.1 - - + -
275B LEU* 4.2 17.8 - - + +
276B VAL* 3.6 29.3 - - + +
306B PHE* 4.2 1.1 - - - -
341B PHE* 3.6 18.8 - - + -
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Residues in contact with ARG 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 GLU* 2.9 33.3 + - - +
180B THR* 3.5 47.4 + - - +
181B CYS 3.3 0.2 - - - -
182B THR* 1.4 70.1 - - - +
184B PHE* 1.4 64.7 + - - +
186B THR* 3.9 1.0 - - - -
187B ALA* 3.1 26.0 + - - +
341B PHE* 3.4 42.8 + - + +
342B PHE* 4.5 7.8 - - + -
344B SER* 3.9 47.5 + - - +
345B VAL* 4.6 9.4 - - + -
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Residues in contact with PHE 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 THR 3.1 14.3 + - - +
181B CYS 3.4 2.4 + - - +
183B ARG* 1.4 79.2 - - - +
185B TYR* 1.3 75.1 + + - +
187B ALA* 3.4 6.8 + - - +
188B GLU* 3.0 63.6 + - + +
218B HIS* 3.8 14.1 - + - -
345B VAL* 5.0 7.4 - - + -
350B LEU* 3.6 28.9 - - + +
353B GLN* 4.3 14.6 - - + -
354B THR 4.5 1.8 - - - -
355B PRO* 3.4 35.0 - - + -
356B PRO* 3.5 26.9 - - + -
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Residues in contact with TYR 185 (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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167B LEU* 5.2 12.3 - - + -
177B PHE* 4.7 5.4 - + + -
181B CYS* 3.1 24.7 + - - +
182B THR 4.4 1.1 - - - +
184B PHE* 1.3 95.8 - + + +
186B THR* 1.3 63.9 + - - +
188B GLU* 3.2 7.2 + - - +
189B ILE* 3.1 32.4 + - + +
213B LEU* 3.6 16.6 - - + -
217B MET* 2.7 45.6 + - + +
219B ILE* 3.6 22.2 - - + -
275B LEU* 4.7 13.0 - - + -
355B PRO* 3.6 10.2 - - - +
356B PRO* 4.6 9.7 + - + -
358B LEU* 3.6 29.7 - - + +
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Residues in contact with THR 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B THR* 2.7 31.7 + - - +
183B ARG 3.9 3.6 - - - -
185B TYR* 1.3 73.0 - - - +
187B ALA* 1.4 51.7 + - - +
189B ILE* 3.1 14.9 + - - +
190B VAL* 2.8 40.6 + - + +
268B LEU* 4.3 2.2 - - + -
272B ILE* 3.6 38.8 - - + +
275B LEU* 4.1 6.8 - - - +
312B LEU* 4.4 0.4 - - + -
341B PHE* 4.2 8.7 - - + -
342B PHE* 3.6 26.7 - - + -
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Residues in contact with ALA 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 ARG 3.1 18.3 + - - +
184B PHE 3.4 5.4 - - - +
185B TYR 3.3 0.2 - - - -
186B THR* 1.4 76.1 - - - +
188B GLU* 1.3 56.0 + - - +
190B VAL 3.3 0.2 + - - -
191B SER* 3.0 27.5 + - - -
342B PHE* 3.8 9.8 - - + -
345B VAL* 4.1 15.7 - - + -
347B TRP* 3.3 31.7 - - + -
350B LEU* 4.0 15.3 - - + -
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Residues in contact with GLU 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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141B PHE* 3.2 40.6 - - + -
184B PHE* 3.0 44.3 + - + +
185B TYR* 3.2 10.4 + - - +
187B ALA* 1.3 74.6 - - - +
189B ILE* 1.4 58.0 + - - +
192B ALA 3.2 20.3 + - - -
218B HIS* 2.7 31.7 + - - -
219B ILE* 2.9 50.0 + - + +
350B LEU* 3.9 8.3 - - + +
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Residues in contact with ILE 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B LEU* 4.8 7.9 - - + -
185B TYR* 3.1 22.9 + - + +
186B THR* 3.1 10.9 + - - +
188B GLU* 1.4 74.2 - - - +
190B VAL* 1.4 57.9 + - - +
192B ALA* 3.4 2.7 + - - +
193B LEU* 3.0 41.7 + - + +
206B LEU* 4.2 14.1 - - + -
211B ILE* 4.1 20.4 - - + -
219B ILE* 4.0 17.7 - - + -
221B ILE* 4.8 5.6 - - + -
268B LEU* 3.7 23.3 - - + -
271B ILE* 4.0 26.0 - - + -
272B ILE* 6.4 0.4 - - + -
275B LEU* 5.0 4.5 - - + -
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Residues in contact with VAL 190 (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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186B THR* 2.8 22.2 + - + +
187B ALA 3.3 5.4 + - - +
189B ILE* 1.4 74.6 - - - +
191B SER* 1.3 55.9 + - - +
193B LEU* 3.3 5.1 + - - -
194B GLU* 3.0 24.9 + - - +
268B LEU* 3.7 24.5 - - + -
333B TYR* 3.4 13.9 - - + -
336B LEU* 3.8 31.2 - - + -
337B LYS* 4.7 5.8 - - + -
342B PHE* 3.9 23.1 - - + -
347B TRP* 3.8 20.6 - - + -
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Residues in contact with SER 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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139B HIS* 3.9 15.8 + - - -
141B PHE* 4.0 18.4 - - - -
187B ALA 3.0 17.6 + - - -
190B VAL* 1.3 75.4 - - - +
192B ALA* 1.4 60.4 + - - +
194B GLU* 3.6 13.3 + - - +
195B TYR* 3.5 14.6 + - - +
337B LYS* 4.4 6.3 + - - +
347B TRP* 4.0 25.2 + - - -
350B LEU* 4.7 5.2 - - - +
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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
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139B HIS* 4.3 2.0 - - - -
141B PHE* 3.7 22.6 - - + -
142B PHE* 3.2 23.9 - - + -
188B GLU 3.2 18.3 + - - +
189B ILE 3.6 4.9 - - - +
190B VAL 3.2 0.2 - - - -
191B SER* 1.4 73.2 - - - +
193B LEU* 1.4 59.6 + - - +
194B GLU 3.2 1.3 - - - -
195B TYR 3.2 2.9 + - - -
196B LEU 3.0 22.3 + - - -
221B ILE* 3.7 25.1 - - + -
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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 ILE* 3.0 25.2 + - + +
190B VAL 3.3 3.8 + - - +
192B ALA* 1.4 71.5 - - + +
194B GLU* 1.4 55.7 + - - +
196B LEU* 3.6 13.9 - - + +
197B HIS* 2.8 38.2 + - + +
203B HIS* 5.3 0.2 - - + -
206B LEU* 3.8 30.7 - - + -
221B ILE* 5.5 3.1 - - + -
264B ASP* 3.8 38.4 - - + +
265B LEU* 4.9 3.1 - - + -
268B LEU* 3.8 31.9 - - + -
333B TYR* 3.1 23.6 + - + +
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Residues in contact with GLU 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 VAL 3.0 16.2 + - - +
191B SER* 3.6 12.9 + - - +
193B LEU* 1.4 74.2 - - - +
195B TYR* 1.4 56.2 + - - +
197B HIS* 3.8 0.3 - - - +
198B GLY* 2.8 33.8 + - - -
333B TYR* 3.4 38.5 - - + +
337B LYS* 3.2 38.8 + - - -
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Residues in contact with TYR 195 (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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136B ARG 3.9 1.7 + - - -
137B LEU* 3.7 25.8 - - + -
138B ASP* 2.9 48.1 + - - +
139B HIS* 3.5 44.4 - + + +
142B PHE* 4.0 5.4 - + - -
191B SER 3.5 3.3 + - - +
192B ALA 3.2 8.6 + - - +
194B GLU* 1.4 79.0 - - - +
196B LEU* 1.4 56.4 + - - +
198B GLY* 3.5 1.1 + - - -
199B LYS* 3.0 68.6 + - + +
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Residues in contact with LEU 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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137B LEU* 3.9 18.2 - - + -
142B PHE* 3.7 24.9 - - + -
192B ALA 3.0 16.8 + - - +
193B LEU* 3.6 15.3 - - + +
195B TYR* 1.4 78.1 - - - +
197B HIS* 1.3 60.5 + - + +
199B LYS* 3.2 12.3 + - - +
200B GLY 3.4 0.2 + - - -
201B ILE* 3.1 51.3 + - + +
202B ILE 4.4 0.2 - - - -
203B HIS* 3.9 35.9 - - + +
221B ILE* 6.1 0.4 - - + -
224B PHE* 3.8 15.0 - - + -
264B ASP* 4.0 7.0 - - - +
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Residues in contact with HIS 197 (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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193B LEU* 2.8 26.3 + - + +
196B LEU* 1.3 71.1 - - + +
198B GLY* 1.3 62.2 + - - +
200B GLY 3.1 6.8 + - - -
201B ILE 3.2 21.3 - - - -
202B ILE* 4.4 0.6 - - - -
261B LYS* 2.8 83.7 + - + +
264B ASP* 2.8 34.7 + - + +
265B LEU* 4.9 7.4 - - + +
333B TYR* 2.7 35.4 + - + +
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Residues in contact with GLY 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B GLU 2.8 21.8 + - - -
195B TYR* 3.8 2.2 - - - -
197B HIS* 1.3 72.0 - - - +
199B LYS* 1.4 58.4 + - - +
200B GLY* 3.1 4.6 + - - -
261B LYS* 5.0 2.6 + - - -
333B TYR* 5.8 0.2 - - - -
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Residues in contact with LYS 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ARG* 4.0 27.5 - - + +
137B LEU* 4.7 1.8 - - + -
195B TYR* 3.0 61.1 + - + +
196B LEU* 3.2 6.0 + - - +
198B GLY* 1.4 73.7 - - - +
200B GLY* 1.3 61.0 + - - +
201B ILE* 3.4 24.0 - - + +
229B VAL* 5.5 1.7 - - - +
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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
------------------------------------------------------------
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