Contacts of the helix formed by residues 185 - 201 (chain B) in PDB entry 3N6J
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 185 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154B TYR* 4.3 4.7 - - - -
182B LYS* 5.0 5.9 + - - -
184B MSE 1.3 82.0 + - - +
186B THR* 1.3 64.9 + - - +
187B GLN* 3.1 31.5 + - - +
188B ALA* 3.4 16.6 + - - +
189B VAL* 3.3 22.9 + - - +
216B LYS* 3.4 12.6 - - - +
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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
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185B ASP* 1.3 73.8 - - - +
187B GLN* 1.3 59.4 + - - +
189B VAL* 2.9 7.3 + - - +
190B ILE* 2.8 49.0 + - + +
216B LYS* 3.9 13.0 + - - +
219B ASP* 4.5 5.9 - - + +
220B THR* 3.5 43.3 + - + +
223B GLU* 3.6 17.7 - - + -
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Residues in contact with GLN 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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185B ASP* 3.1 13.1 + - - +
186B THR* 1.3 78.1 - - - +
188B ALA* 1.3 63.9 + - - +
190B ILE* 3.1 17.0 + - + +
191B GLU* 2.9 31.1 + - - +
223B GLU* 5.5 0.7 - - - +
227B HIS* 4.2 21.4 + - - -
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Residues in contact with ALA 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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178B ILE* 5.2 0.2 - - - +
182B LYS* 4.5 3.6 - - - +
183B ALA* 3.4 33.4 - - + +
184B MSE 4.2 0.2 - - - +
185B ASP* 3.4 22.3 + - - +
186B THR 3.4 0.4 - - - -
187B GLN* 1.3 77.5 - - - +
189B VAL* 1.3 58.3 + - - +
191B GLU* 3.4 13.2 - - - +
192B LEU* 3.3 28.8 + - - +
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Residues in contact with VAL 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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152B LEU* 4.3 21.1 - - + +
153B PHE 3.4 27.1 - - - +
154B TYR* 3.5 28.3 - - + -
183B ALA* 4.1 8.1 - - + +
185B ASP 3.3 7.8 + - - +
186B THR 2.9 9.5 + - - +
188B ALA* 1.3 77.0 - - - +
190B ILE* 1.3 64.2 + - - +
191B GLU 3.1 1.3 - - - -
192B LEU* 3.3 7.9 + - + +
193B ALA* 3.1 20.6 + - - +
207B LEU* 4.4 10.1 - - + -
220B THR* 4.0 19.3 - - + -
224B LEU* 4.3 3.4 - - + -
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Residues in contact with ILE 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 55.0 + - + +
187B GLN* 3.1 20.2 + - - +
189B VAL* 1.3 72.7 - - - +
191B GLU* 1.3 63.1 + - - +
193B ALA* 3.3 8.5 + - - +
194B ALA* 3.2 22.2 + - + +
220B THR 4.8 1.8 - - - +
223B GLU* 3.5 21.5 - - + -
224B LEU* 4.6 11.9 - - + +
227B HIS* 3.6 50.7 - - + +
228B PHE* 4.3 3.4 - - + -
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Residues in contact with GLU 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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174B GLU* 4.1 8.0 - - - +
178B ILE* 3.5 31.9 - - + +
187B GLN* 2.9 19.8 + - - +
188B ALA* 3.4 15.9 - - - +
189B VAL 3.1 0.2 - - - -
190B ILE* 1.3 77.1 - - - +
192B LEU* 1.3 65.3 + - - +
194B ALA* 3.4 4.9 + - + +
195B ALA* 3.0 25.3 + - - +
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Residues in contact with LEU 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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152B LEU* 4.1 9.6 - - + -
153B PHE 3.6 26.7 - - - +
155B VAL* 4.4 3.6 - - + -
175B TRP* 3.4 26.6 - - + -
178B ILE* 3.7 36.8 - - + +
179B ARG* 4.6 2.9 - - - -
183B ALA* 4.0 17.0 - - + -
188B ALA 3.3 17.1 + - - +
189B VAL* 3.4 11.7 - - + +
191B GLU* 1.3 76.4 - - - +
193B ALA* 1.3 56.3 + - - +
196B SER* 2.7 36.6 + - - -
372B TRP* 4.3 14.1 - - + -
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Residues in contact with ALA 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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152B LEU* 3.7 17.7 - - + +
189B VAL 3.1 7.8 + - - +
190B ILE 3.4 10.8 - - - +
191B GLU 3.2 0.2 - - - -
192B LEU* 1.3 79.0 - - - +
194B ALA* 1.3 57.4 + - - +
196B SER* 3.3 1.5 + - - -
197B LYS* 2.8 33.2 + - - +
205B PHE* 3.5 9.3 - - + -
224B LEU* 3.6 19.1 - - + -
228B PHE* 3.5 22.4 - - + -
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Residues in contact with ALA 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 ILE* 3.2 11.3 + - + +
191B GLU* 4.0 7.0 - - - +
193B ALA* 1.3 74.5 - - - +
195B ALA* 1.3 60.8 + - - +
197B LYS* 3.2 16.7 + - - +
198B ASP* 2.8 28.8 + - - +
228B PHE* 3.7 18.3 - - + -
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Residues in contact with ALA 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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173B HIS* 3.4 13.9 - - - -
174B GLU* 4.5 8.5 - - + +
175B TRP* 3.7 35.4 - - + +
178B ILE* 3.8 13.2 - - + -
191B GLU* 3.0 18.0 + - + +
194B ALA* 1.3 75.9 - - - +
196B SER* 1.3 61.7 + - - +
198B ASP* 3.1 10.8 + - - -
199B ARG* 3.2 11.8 + - - +
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Residues in contact with SER 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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152B LEU* 4.1 8.7 - - - +
175B TRP* 3.5 27.2 - - - -
192B LEU 2.7 25.3 + - - -
193B ALA* 3.3 6.2 + - - -
195B ALA* 1.3 72.5 - - - +
197B LYS* 1.3 59.6 + - - +
200B TYR* 2.9 52.3 + - - +
202B PHE* 3.9 6.5 - - - -
205B PHE* 4.1 4.2 - - - -
371B ILE* 4.1 10.9 - - - +
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Residues in contact with LYS 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 ALA 2.8 24.6 + - - +
194B ALA* 3.2 25.5 + - - +
196B SER* 1.3 77.1 + - - +
198B ASP* 1.3 75.8 + - - +
201B GLY* 2.9 28.1 + - - -
202B PHE* 4.3 25.0 - - - +
205B PHE* 3.6 19.5 - - + -
228B PHE* 4.2 22.4 - - + -
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Residues in contact with ASP 198 (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 HIS* 2.7 26.4 + - + +
194B ALA 2.8 20.2 + - - +
195B ALA* 3.1 5.1 + - - +
197B LYS* 1.3 87.9 + - - +
199B ARG* 1.3 65.6 + - - +
201B GLY* 4.1 3.1 + - - -
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Residues in contact with ARG 199 (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 HIS* 3.7 34.2 + - + +
175B TRP* 4.8 4.0 - - + -
176B TYR* 2.7 41.1 + - + +
195B ALA 3.2 8.4 + - - +
198B ASP* 1.3 80.0 - - - +
200B TYR* 1.3 90.9 + - + +
374B GLU* 3.5 14.6 + - - -
375B GLY* 6.0 0.4 - - - -
386B ILE 4.6 3.1 - - - +
387B LYS* 5.6 3.5 - - - +
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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
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175B TRP* 3.4 41.1 + + - -
176B TYR* 3.8 2.4 + - - -
196B SER* 2.9 25.5 + - - +
199B ARG* 1.3 95.3 - - + +
201B GLY* 1.3 59.7 + - - +
202B PHE* 3.6 17.7 - + + -
370B TRP* 5.7 0.2 - + - -
371B ILE* 3.7 34.2 + - + -
374B GLU* 2.5 43.8 + - + +
386B ILE* 3.7 31.9 - - + +
387B LYS* 3.5 5.9 - - - -
388B ASP 2.8 22.4 + - - -
389B GLY 3.0 7.5 + - - -
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Residues in contact with GLY 201 (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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197B LYS* 2.9 20.8 + - - -
198B ASP 4.1 2.9 + - - -
199B ARG 3.8 0.8 - - - -
200B TYR* 1.3 74.1 - - - +
202B PHE* 1.3 68.7 + - - +
203B LYS* 3.9 6.4 + - - -
388B ASP* 2.9 29.5 - - - +
389B GLY 3.3 6.5 - - - -
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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
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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