Contacts of the helix formed by residues 190 - 207 (chain B) in PDB entry 5GJQ
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 190 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B CYS* 4.4 2.2 - - - -
188B ASP* 2.6 31.4 + - + +
189B TRP* 1.3 74.8 - - - +
191B PHE* 1.3 55.0 + - - +
192B GLU* 3.8 8.6 + - - +
193B GLN* 3.2 21.5 + - - +
194B THR* 2.5 42.0 + - - -
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Residues in contact with PHE 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B CYS* 3.9 24.3 - - + -
190B THR* 1.3 75.8 - - - +
192B GLU* 1.3 82.2 + - + +
194B THR* 3.2 2.4 + - - -
195B VAL* 2.9 44.2 + - + +
219B VAL* 3.3 43.3 - - + -
221B THR* 4.4 17.3 - - + -
230B LEU* 5.2 7.4 - - + -
238B HIS* 3.9 25.4 - + - -
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Residues in contact with GLU 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B THR* 4.1 6.6 + - - +
191B PHE* 1.3 95.3 + - - +
193B GLN* 1.3 61.3 + - - +
195B VAL* 3.9 5.7 - - - +
196B GLU* 2.9 34.0 + - - +
238B HIS* 4.1 21.6 + - + +
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Residues in contact with GLN 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LYS* 4.6 12.9 - - - +
187B PHE* 5.1 13.4 - - + +
188B ASP 3.5 16.5 - - - +
189B TRP* 4.0 18.9 - - + -
190B THR* 3.2 28.3 + - - +
192B GLU* 1.3 79.1 - - - +
194B THR* 1.3 52.7 + - - +
196B GLU* 3.9 4.4 - - - +
197B THR* 2.3 50.5 + - - -
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Residues in contact with THR 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 3.7 37.1 - - + +
43B ARG 4.3 0.7 - - - +
44B GLY* 3.8 17.9 - - - +
47B CYS* 3.5 11.8 - - - -
49B VAL* 3.5 22.7 - - + -
189B TRP* 4.1 9.7 - - + -
190B THR 2.5 25.5 + - - -
191B PHE 3.6 3.8 - - - -
193B GLN* 1.3 71.8 - - - +
195B VAL* 1.3 66.5 + - - +
197B THR* 3.1 6.4 + - - -
198B ALA* 3.0 22.7 + - - +
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Residues in contact with VAL 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B VAL* 3.9 24.2 - - + -
191B PHE* 2.9 46.1 + - + +
192B GLU 3.9 2.7 - - - +
194B THR* 1.3 75.5 - - - +
196B GLU* 1.3 57.7 + - - +
198B ALA* 3.3 1.2 + - - +
199B ILE* 2.9 54.8 + - + +
217B VAL* 4.7 13.5 - - + -
219B VAL* 5.0 0.9 - - + -
230B LEU* 5.1 3.1 - - + -
238B HIS* 3.5 28.5 - - + +
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Residues in contact with GLU 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LYS* 4.8 2.2 - - - +
192B GLU 2.9 19.5 + - - +
193B GLN* 4.0 5.4 - - - +
195B VAL* 1.3 78.0 - - - +
197B THR* 1.3 51.6 + - - +
199B ILE* 4.6 4.3 - - - -
200B THR* 2.6 44.0 + - + +
238B HIS* 5.3 2.4 - - + +
242B LEU* 3.8 27.4 - - + -
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Residues in contact with THR 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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42B VAL* 4.8 4.3 - - + -
178B PHE* 4.0 1.4 - - - -
179B LEU* 4.2 18.6 - - + -
182B LYS* 3.7 33.1 + - + +
189B TRP* 3.2 34.5 - - + -
193B GLN* 2.3 30.3 + - - -
194B THR 3.1 5.8 + - - -
196B GLU* 1.3 76.1 - - - +
198B ALA* 1.3 58.5 + - - +
200B THR* 2.9 18.2 + - - -
201B CYS* 3.0 17.9 + - - +
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Residues in contact with ALA 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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40B VAL* 4.2 9.3 - - + +
42B VAL* 3.8 22.2 - - + +
49B VAL* 4.3 15.7 - - + +
51B VAL* 3.7 23.5 - - + +
194B THR 3.0 15.3 + - - +
195B VAL 3.7 4.0 - - - +
197B THR* 1.3 74.2 - - - +
199B ILE* 1.3 65.6 + - - +
201B CYS* 3.1 4.7 + - - +
202B LEU* 3.1 22.7 + - - +
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Residues in contact with ILE 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B VAL* 6.2 0.2 - - + -
51B VAL* 4.2 22.2 - - + -
195B VAL* 2.9 39.7 + - + +
196B GLU* 4.0 4.9 - - - +
198B ALA* 1.3 76.4 - - + +
200B THR* 1.3 58.3 + - - +
202B LEU* 3.4 3.6 + - - +
203B SER* 2.9 28.1 + - - -
210B PHE* 4.3 8.3 - - + -
215B ILE* 4.2 20.9 - - + -
217B VAL* 4.2 11.4 - - + -
235B ILE* 5.2 3.1 - - + -
238B HIS* 4.8 10.1 - - + -
239B LEU* 4.1 27.1 - - + -
242B LEU* 4.1 13.5 - - + -
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Residues in contact with THR 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B PHE* 4.1 7.9 - - - -
182B LYS* 3.7 12.1 + - - +
196B GLU 2.6 25.4 + - - +
197B THR* 2.9 15.6 + - - -
199B ILE* 1.3 72.7 - - - +
201B CYS* 1.3 60.0 + - - +
203B SER* 4.1 7.6 - - - -
204B THR* 2.9 42.0 + - - +
242B LEU* 3.8 33.0 - - + -
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Residues in contact with CYS 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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40B VAL* 4.1 6.7 - - + -
175B SER* 2.6 38.1 - - - -
178B PHE* 3.5 34.2 - - + -
179B LEU* 3.7 17.5 - - + -
197B THR 3.0 15.8 + - - +
198B ALA 3.1 9.8 + - - +
200B THR* 1.3 76.3 + - - +
202B LEU* 1.3 59.4 + - - +
204B THR* 3.1 4.1 + - - -
205B VAL* 2.8 29.1 + - - +
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Residues in contact with LEU 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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38B THR* 3.6 39.0 - - + +
40B VAL* 3.8 13.0 - - + +
51B VAL* 4.3 11.4 - - + +
52B THR* 4.1 10.8 - - - +
53B GLN* 3.9 26.7 - - + +
198B ALA 3.1 9.3 + - - +
199B ILE* 3.7 7.4 - - - +
201B CYS* 1.3 78.0 - - - +
203B SER* 1.3 61.2 + - - +
205B VAL* 2.5 24.4 - - + +
206B LEU* 3.0 31.5 + - + +
210B PHE* 3.9 16.6 - - + -
215B ILE* 4.3 6.3 - - + -
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Residues in contact with SER 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ILE* 2.9 20.5 + - - -
200B THR* 3.8 8.3 - - - -
201B CYS 3.3 0.2 - - - -
202B LEU* 1.3 77.1 - - - +
204B THR* 1.3 51.3 + - - +
207B SER* 2.0 43.5 + - - -
208B ILE 3.7 1.4 + - - +
209B ASP* 3.1 30.8 + - - -
210B PHE* 3.5 23.3 - - - -
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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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178B PHE* 3.6 28.1 - - + +
200B THR* 2.9 36.0 + - + +
201B CYS 3.1 4.9 + - - -
203B SER* 1.3 73.4 - - - +
205B VAL* 1.3 65.6 + - - +
207B SER* 3.5 13.9 + - - +
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Residues in contact with VAL 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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171B LYS* 3.0 48.2 - - + +
174B GLU* 3.9 25.5 - - + +
175B SER* 4.5 8.1 - - - +
178B PHE* 6.4 0.9 - - + -
201B CYS* 2.8 17.7 - - - +
202B LEU* 2.5 48.0 - - + +
204B THR* 1.3 81.7 + - - +
206B LEU* 1.3 63.0 + - + +
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Residues in contact with LEU 206 (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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38B THR* 4.7 1.1 - - - +
53B GLN* 3.6 42.6 - - + +
171B LYS* 3.5 36.3 - - + +
202B LEU* 3.0 25.2 + - + +
205B VAL* 1.3 79.0 - - + +
207B SER* 1.3 80.5 + - - +
208B ILE* 3.4 16.5 - - + +
210B PHE* 3.7 21.5 - - + -
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Residues in contact with SER 207 (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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203B SER* 2.0 25.5 + - - -
204B THR* 3.5 12.6 + - - +
206B LEU* 1.3 84.2 + - - +
208B ILE* 1.3 72.9 + - - +
209B ASP* 4.6 1.8 - - - -
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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