Contacts of the helix formed by residues 183 - 193 (chain B) in PDB entry 4GJ0
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 GLN 183 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B LYS* 1.3 76.8 - - - +
184B TRP* 1.3 69.3 + - - +
185B VAL* 3.3 17.3 - - - +
186B HIS* 3.1 11.4 + - + +
187B ALA* 3.1 18.2 + - - +
220B TRP* 3.4 1.1 - - - -
273B CYS 3.7 7.1 + - - +
274B ASP* 3.6 36.2 - - - +
275B ARG 3.2 9.2 - - - +
276B LYS* 3.0 33.2 + - + +
189C TYR* 5.7 5.3 - - - -
193C ASP* 4.8 4.5 + - - +
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Residues in contact with TRP 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 4.7 7.4 - - + -
183B GLN* 1.3 75.7 - - - +
185B VAL* 1.3 65.5 + - + +
187B ALA* 3.0 5.7 + - - +
188B ARG* 2.9 53.5 + - + -
198B LEU* 3.7 15.5 - - + +
220B TRP* 3.3 45.6 - + + +
221B ILE 3.0 23.9 + - - -
222B GLY* 4.7 0.9 - - - -
223B LEU 4.2 6.3 + - - -
224B ARG* 3.1 41.5 - - + -
235B VAL* 3.6 34.5 - - + -
259B CYS* 3.4 25.4 - - + -
260B VAL 4.3 0.9 - - - -
273B CYS* 3.1 17.5 + - + +
301B GOL 5.6 0.4 - - - -
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Residues in contact with VAL 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B GLN* 4.5 15.5 - - - +
184B TRP* 1.3 87.8 - - + +
186B HIS* 1.3 64.1 + - + +
188B ARG* 3.3 14.4 + - - +
189B TYR* 3.2 41.8 + - + -
273B CYS 4.7 0.4 + - - +
301B GOL 3.6 37.3 + - - +
189C TYR* 3.7 38.4 - - + +
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Residues in contact with HIS 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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181B THR 5.1 0.2 - - - -
182B LYS* 3.5 23.2 - - + +
183B GLN* 3.1 16.4 + - + +
185B VAL* 1.3 79.6 - - + +
187B ALA* 1.3 60.0 + - - +
189B TYR* 3.3 2.6 + - + -
190B ALA* 2.9 21.1 + - - +
186C HIS* 3.7 13.3 - + - -
189C TYR* 3.7 40.0 - + + +
190C ALA* 3.9 3.8 + - - -
193C ASP* 2.7 33.1 + - + +
301C GOL 2.7 39.3 + - - -
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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
----------------------------------------------------------
182B LYS* 4.0 11.3 - - + +
183B GLN 3.1 10.8 + - - +
184B TRP 3.0 9.2 + - - +
186B HIS* 1.3 75.6 - - - +
188B ARG* 1.3 64.9 + - - +
190B ALA* 3.3 4.0 + - - +
191B CYS* 3.1 27.7 + - - -
198B LEU* 4.0 10.3 - - + -
220B TRP* 4.0 12.8 - - + -
280B TRP* 3.7 33.6 - - + -
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Residues in contact with ARG 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 3.8 45.0 + - - +
255A GLN* 3.6 13.5 - - - +
258A ASP* 5.3 4.2 + - - -
184B TRP* 2.9 37.5 + - + +
185B VAL* 3.4 17.9 - - - +
186B HIS 3.2 0.2 - - - -
187B ALA* 1.3 77.0 - - - +
189B TYR* 1.3 95.7 + - - +
191B CYS* 3.4 3.5 + - - +
192B ASP* 3.0 46.9 + - - +
198B LEU* 3.5 22.0 + - + +
235B VAL* 5.6 5.8 - - + -
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Residues in contact with TYR 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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255A GLN* 2.8 27.4 + - - +
256A GLY* 4.8 7.3 - - - -
258A ASP* 5.4 0.9 + - - -
185B VAL* 3.2 35.0 + - + +
186B HIS* 4.0 4.3 - - - +
188B ARG* 1.3 106.5 + - - +
190B ALA* 1.3 66.3 + - - +
192B ASP* 3.7 12.7 - - - +
193B ASP* 2.9 28.8 + - - +
183C GLN* 3.4 42.0 - - - -
185C VAL* 3.3 26.7 - - + +
186C HIS* 4.0 21.8 - - + -
189C TYR* 4.2 7.4 - + + -
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Residues in contact with ALA 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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182B LYS* 4.0 7.2 - - - -
186B HIS 2.9 17.8 + - - +
187B ALA* 3.6 6.3 - - - +
189B TYR* 1.3 76.0 - - - +
191B CYS* 1.3 63.3 + - - +
193B ASP* 3.7 1.7 + - - +
194B MET* 3.4 26.3 + - - +
280B TRP* 3.9 20.0 - - + -
186C HIS* 3.7 14.0 - - - +
301C GOL 3.5 26.0 - - - -
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Residues in contact with CYS 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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187B ALA 3.1 16.5 + - - -
188B ARG 3.6 7.6 - - - +
190B ALA* 1.3 74.1 - - - +
192B ASP* 1.3 67.0 + - - +
194B MET* 2.9 13.6 + - - +
195B GLU 3.4 0.2 + - - -
196B GLY* 2.9 18.7 + - - -
197B GLN* 3.7 18.8 - - - -
198B LEU* 3.7 21.8 - - - +
280B TRP* 4.1 4.0 - - - -
282B CYS* 2.0 56.3 - - + -
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Residues in contact with ASP 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A GLN* 5.4 0.5 + - - -
188B ARG* 3.0 40.1 + - - +
189B TYR* 3.2 20.5 + - - +
191B CYS* 1.3 74.1 - - - +
193B ASP* 1.3 59.9 + - - +
195B GLU* 2.8 25.1 + - - +
196B GLY 3.4 14.7 - - - +
197B GLN* 4.1 13.3 - - - +
183C GLN* 4.4 12.7 + - - +
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Residues in contact with ASP 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B TYR 2.9 15.3 + - - +
190B ALA 4.4 0.9 - - - +
192B ASP* 1.3 76.4 - - - +
194B MET* 1.3 59.2 + - - +
195B GLU* 3.4 3.3 - - - +
181C THR* 4.2 14.3 + - - +
182C LYS* 4.3 0.4 - - - -
183C GLN* 2.9 49.6 + - - +
186C HIS* 2.5 37.3 + - + +
276C LYS* 3.1 42.4 + - + +
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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