Contacts of the helix formed by residues 188 - 206 (chain B) in PDB entry 3N9Z
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 188 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B GLN 4.7 10.4 + - - +
181B GLY 5.2 1.4 + - - -
182B MET* 4.2 7.3 - - - -
186B VAL 4.3 0.4 + - - -
187B VAL* 1.3 78.3 - - - +
189B PRO* 1.4 70.5 - - - +
190B GLU* 3.0 25.4 + - - +
191B ALA* 3.3 18.2 + - + +
192B GLN 3.2 17.3 + - - -
241B TYR* 5.8 1.2 + - - -
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Residues in contact with PRO 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B VAL* 3.3 11.4 - - + +
188B ASN* 1.4 90.1 - - - +
190B GLU* 1.3 66.2 + - + +
192B GLN* 3.5 8.8 + - + +
193B ARG* 3.1 30.4 + - - +
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Residues in contact with GLU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ASN* 3.0 13.3 + - - +
189B PRO* 1.3 84.8 - - + +
191B ALA* 1.3 63.0 + - - +
193B ARG* 3.4 22.2 + - - -
194B PHE* 3.3 12.3 + - - +
237B LYS* 2.8 57.7 + - - +
241B TYR* 5.2 0.9 - - - +
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Residues in contact with ALA 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B PHE* 3.9 18.0 - - + -
180B GLN* 5.5 2.7 - - + +
182B MET* 3.5 29.8 - - + -
188B ASN* 3.3 14.7 + - + +
190B GLU* 1.3 74.8 - - - +
192B GLN* 1.3 65.1 + - - +
194B PHE* 3.2 8.4 + - - +
195B ILE* 3.1 24.6 + - - +
241B TYR* 3.9 17.4 + - - +
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Residues in contact with GLN 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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161B ASP* 5.6 2.4 + - - +
164B PHE* 5.9 0.2 - - - +
165B ARG* 2.9 43.5 + - - +
182B MET* 3.6 7.9 - - + +
187B VAL* 4.3 7.5 - - + +
188B ASN 3.2 12.9 + - - +
189B PRO* 3.7 12.1 - - + +
190B GLU 3.3 0.2 - - - -
191B ALA* 1.3 74.7 - - - +
193B ARG* 1.3 65.1 - - - +
195B ILE* 3.2 22.6 + - - +
196B ASP* 3.0 58.0 + - - +
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Residues in contact with ARG 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B PRO 3.1 14.8 + - - +
190B GLU* 3.4 39.8 + - - +
191B ALA 3.3 0.2 - - - -
192B GLN* 1.3 76.9 - - - +
194B PHE* 1.3 55.9 + - - +
196B ASP* 3.5 8.9 + - - +
197B ALA* 3.0 29.3 + - - +
233B VAL* 3.5 38.2 - - + +
237B LYS* 3.7 8.4 - - - +
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Residues in contact with PHE 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B PHE* 3.5 32.5 - + + -
190B GLU 3.3 9.5 + - - +
191B ALA* 3.2 12.3 + - - +
193B ARG* 1.3 78.4 - - - +
195B ILE* 1.3 61.4 + - - +
197B ALA* 3.2 4.0 + - - +
198B ILE* 3.1 50.7 + - + +
233B VAL* 4.1 8.6 - - - +
234B ILE* 3.6 40.4 - - + -
237B LYS* 3.4 30.1 - - + -
238B ALA* 4.4 6.3 - - + -
241B TYR* 5.3 3.4 - + - +
282B THR 5.2 0.2 - - - -
285B LEU* 3.9 32.1 - - + -
286B ALA 4.4 2.0 - - - -
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Residues in contact with ILE 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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164B PHE* 3.9 27.6 - - + +
165B ARG* 3.8 30.5 - - + -
168B PHE* 3.8 37.0 - - + -
182B MET* 3.9 18.4 - - + -
191B ALA 3.1 8.5 + - - +
192B GLN* 3.5 21.5 - - - +
194B PHE* 1.3 78.6 - - - +
196B ASP* 1.3 63.7 + - - +
198B ILE* 3.3 18.1 + - - +
199B TYR* 3.4 11.1 + - + +
289B VAL* 4.2 8.7 - - + +
290B ASP* 4.7 2.7 - - - +
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Residues in contact with ASP 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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192B GLN* 3.0 43.4 + - - +
193B ARG* 3.8 7.8 - - - +
195B ILE* 1.3 75.5 - - - +
197B ALA* 1.3 59.4 + - - +
199B TYR* 3.5 8.0 + - - +
200B GLN* 3.0 34.4 + - + +
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Residues in contact with ALA 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 ARG 3.0 18.7 + - - +
194B PHE 3.2 6.3 + - - +
196B ASP* 1.3 73.4 - - - +
198B ILE* 1.3 60.9 + - - +
200B GLN* 3.4 5.3 + - - -
201B MET* 2.8 30.0 + - - +
230B ALA* 3.5 23.6 - - - +
233B VAL* 3.6 26.0 - - + -
234B ILE* 4.1 6.2 - - + +
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Residues in contact with ILE 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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194B PHE* 3.1 47.4 + - + +
195B ILE* 3.5 7.4 - - - +
196B ASP 3.3 0.4 - - - -
197B ALA* 1.3 73.6 - - - +
199B TYR* 1.3 65.4 + - - +
201B MET* 3.3 4.9 + - + +
202B PHE* 3.2 39.3 + - + -
234B ILE* 4.1 20.9 - - + -
286B ALA* 3.8 30.1 - - + +
289B VAL* 3.6 25.4 - - + -
290B ASP* 3.9 15.0 - - + +
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Residues in contact with TYR 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B PHE* 4.5 17.9 - + + -
195B ILE* 3.4 8.4 + - + +
196B ASP* 3.7 10.5 - - - +
197B ALA 3.4 0.2 - - - -
198B ILE* 1.3 78.5 - - - +
200B GLN* 1.3 77.1 + - - +
202B PHE* 3.3 4.8 + - + +
203B HIS* 3.0 49.6 + + + +
290B ASP* 3.3 25.7 + - - +
459B ASN* 4.4 6.2 + - + -
463B MET* 3.4 39.0 - - + +
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Residues in contact with GLN 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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196B ASP* 3.0 23.1 + - + +
197B ALA* 3.6 6.5 - - - +
199B TYR* 1.3 95.6 - - - +
201B MET* 1.3 62.4 + - - +
203B HIS* 4.4 10.7 - - - +
204B THR* 2.8 51.4 + - + +
226B ASP* 5.6 3.0 - - - +
230B ALA* 4.0 11.9 - - + -
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Residues in contact with MET 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B TRP* 3.3 42.0 - - + -
197B ALA 2.8 19.8 + - - +
198B ILE* 3.3 5.8 + - + +
200B GLN* 1.3 74.8 - - - +
202B PHE* 1.3 78.6 + - + +
204B THR* 4.0 2.7 - - - -
205B SER* 2.6 26.3 + - - -
227B HIS* 3.3 12.1 + - + -
230B ALA* 3.6 10.4 - - + +
231B TRP* 3.4 55.4 - - + +
234B ILE* 3.8 14.4 - - + -
286B ALA* 5.3 2.9 - - + -
602B HC9 4.2 8.5 - - + -
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Residues in contact with PHE 202 (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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87B TRP* 3.7 28.3 - + - -
198B ILE* 3.2 37.0 + - + -
199B TYR* 3.6 6.1 - - + +
200B GLN 3.3 0.2 - - - -
201B MET* 1.3 83.0 - - + +
203B HIS* 1.3 61.8 + - - +
205B SER* 3.1 22.6 + - - -
206B VAL* 3.9 2.1 + - - +
286B ALA 4.6 4.7 - - - -
287B GLY* 5.8 0.2 - - - -
290B ASP* 3.7 26.0 - - + +
291B THR* 5.6 2.5 - - + -
459B ASN* 3.6 15.3 - - + +
460B LEU* 3.5 31.1 - - + +
461B ILE* 4.1 23.6 - - + -
463B MET* 6.6 0.2 - - - -
602B HC9 3.9 31.9 - - + -
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Residues in contact with HIS 203 (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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33B HIS* 5.0 12.0 + + - -
199B TYR* 3.0 40.2 + + + +
200B GLN* 3.9 13.2 - - - +
202B PHE* 1.3 75.2 - - - +
204B THR* 1.3 69.5 + - + +
205B SER 3.3 1.2 + - - -
206B VAL* 3.4 14.7 + - - +
207B PRO* 3.6 9.9 - - + +
459B ASN* 3.4 39.7 + - + +
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Residues in contact with THR 204 (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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200B GLN* 2.8 42.7 + - + +
201B MET 3.4 0.2 + - - -
203B HIS* 1.3 80.2 - - + +
205B SER* 1.3 63.2 + - - +
206B VAL 3.3 0.2 - - - -
207B PRO* 3.5 2.8 - - - +
208B MET* 3.4 8.1 - - - +
223B THR* 3.0 39.8 - - + +
226B ASP* 4.0 25.8 - - + +
227B HIS* 2.9 31.2 + - - +
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Residues in contact with SER 205 (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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86B PRO* 4.1 8.5 - - - +
87B TRP* 2.9 24.4 + - - -
201B MET 2.6 23.0 + - - -
202B PHE* 3.1 13.7 + - - -
204B THR* 1.3 80.0 - - - +
206B VAL* 1.3 62.0 + - - +
208B MET* 3.1 19.5 + - - +
209B LEU* 3.4 12.4 + - - +
227B HIS* 3.3 7.7 - - - -
460B LEU* 3.7 22.0 - - - -
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Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B THR* 3.9 32.4 - - - +
33B HIS* 3.9 22.9 - - + +
202B PHE 4.0 2.7 - - - +
203B HIS 3.4 10.1 + - - +
204B THR 3.3 0.2 - - - -
205B SER* 1.3 70.7 - - - +
207B PRO* 1.4 66.6 - - + +
208B MET 2.9 10.5 + - - -
209B LEU* 3.1 22.6 + - + +
458B PHE* 4.0 18.4 - - + +
459B ASN* 3.6 12.6 - - - +
460B LEU* 3.1 35.2 - - + +
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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
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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