Contacts of the helix formed by residues 183 - 193 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A LYS* 1.3 76.2 - - - +
184A TRP* 1.3 68.8 + - - +
185A VAL* 3.9 16.4 - - + +
186A HIS* 3.1 18.8 + - + +
187A ALA* 3.1 17.3 + - - +
220A TRP* 3.4 1.6 + - - -
273A CYS 3.4 10.9 - - - +
274A ASP* 3.9 30.5 + - - +
275A ARG 3.3 16.2 - - - +
276A LYS* 4.5 19.0 - - + +
303A SO4 4.8 5.5 + - - -
189D TYR* 5.1 8.3 - - + -
193D ASP* 5.3 6.5 + - - +
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Residues in contact with TRP 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A GLN* 1.3 74.9 - - - +
185A VAL* 1.3 64.8 + - + +
187A ALA* 3.0 5.0 + - - +
188A ARG* 2.8 54.8 + - + -
198A LEU* 3.7 13.8 - - + +
220A TRP* 3.3 48.1 - + + +
221A ILE 3.0 24.5 + - - -
222A GLY 4.7 1.1 - - - -
223A LEU 4.1 6.6 + - - -
224A ARG* 3.2 44.4 - - + -
235A VAL* 3.4 34.5 - - + -
259A CYS* 3.4 27.6 - - + +
260A VAL 4.3 0.7 - - - -
273A CYS* 3.1 12.6 + - + +
228B LEU* 5.0 4.9 - - + -
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Residues in contact with VAL 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A GLN* 3.9 19.3 - - + +
184A TRP* 1.3 89.1 - - + +
186A HIS* 1.3 65.8 + - - +
188A ARG* 3.4 17.0 + - - +
189A TYR* 3.2 41.3 + - + -
273A CYS 4.7 0.4 + - - -
303A SO4 3.4 37.8 + - - +
189D TYR* 3.6 33.0 - - + +
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Residues in contact with HIS 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A LYS* 3.4 27.3 + - + +
183A GLN* 3.1 19.5 + - + +
185A VAL* 1.3 83.4 - - - +
187A ALA* 1.3 62.5 + - - +
189A TYR* 3.2 3.5 + - - -
190A ALA* 3.0 14.7 + - - +
186D HIS* 3.7 17.1 - + - -
189D TYR* 3.6 38.9 - + + +
190D ALA* 3.9 1.5 + - - -
193D ASP* 2.5 31.9 + - + -
301D GOL 2.6 35.8 + - - -
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Residues in contact with ALA 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A LYS* 4.0 10.9 - - + +
183A GLN 3.1 10.7 + - - +
184A TRP 3.0 9.0 + - - +
186A HIS* 1.3 73.3 - - - +
188A ARG* 1.3 67.6 + - - +
190A ALA* 3.2 3.6 + - - +
191A CYS* 3.0 27.0 + - - -
198A LEU* 4.1 9.6 - - + -
220A TRP* 4.1 10.8 - - + -
280A TRP* 3.6 36.1 - - + -
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Residues in contact with ARG 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A TRP* 2.8 36.3 + - + +
185A VAL* 3.4 21.2 - - - +
187A ALA* 1.3 76.9 - - - +
189A TYR* 1.3 98.7 + - + +
191A CYS* 3.4 3.5 + - - +
192A ASP* 3.1 41.1 + - - +
198A LEU* 3.4 21.9 + - + +
235A VAL* 5.2 8.5 - - + -
228B LEU* 3.8 45.3 + - - +
255B GLN* 4.4 6.5 - - - +
258B ASP* 5.0 3.8 + - - -
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Residues in contact with TYR 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A VAL* 3.2 28.6 + - + +
186A HIS* 3.2 9.1 + - - +
188A ARG* 1.3 111.0 + - + +
190A ALA* 1.3 61.1 + - - +
192A ASP* 3.6 14.6 - - - +
193A ASP* 2.9 33.8 + - - +
255B GLN* 3.0 27.3 + - - +
256B GLY* 4.9 7.4 - - - -
258B ASP* 5.5 0.9 + - - -
183D GLN* 3.4 33.7 - - - -
185D VAL* 3.3 33.1 - - + +
186D HIS* 4.0 21.1 - - + -
189D TYR* 4.1 10.1 - + + -
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Residues in contact with ALA 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A LYS* 4.1 7.9 - - - -
186A HIS 3.0 13.5 + - - +
187A ALA 3.2 8.3 + - - +
189A TYR* 1.3 76.3 - - - +
191A CYS* 1.3 64.5 + - - +
193A ASP* 3.5 2.4 + - - +
194A MET* 3.5 27.1 + - + +
280A TRP* 3.9 24.0 - - + -
186D HIS* 3.6 14.3 - - - +
301D GOL 3.6 19.1 - - - +
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Residues in contact with CYS 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ALA 3.0 16.0 + - - -
188A ARG 3.6 8.3 - - - +
190A ALA* 1.3 75.4 - - - +
192A ASP* 1.3 66.1 + - - +
194A MET* 3.0 10.5 + - - +
196A GLY* 3.0 21.5 + - - -
197A GLN* 3.6 20.0 - - - -
198A LEU* 3.6 22.0 - - - +
280A TRP* 4.3 4.0 - - - -
281A VAL 4.2 0.4 - - - -
282A CYS* 2.0 56.5 - - + -
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Residues in contact with ASP 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ARG* 3.1 42.8 + - - +
189A TYR* 3.2 21.0 + - - +
191A CYS* 1.3 76.0 - - - +
193A ASP* 1.3 64.0 + - - +
195A GLU* 3.0 22.0 + - - +
196A GLY 3.3 15.2 - - - +
197A GLN* 4.1 15.9 + - - +
255B GLN* 5.4 0.7 + - - -
183D GLN* 4.5 8.0 + - - +
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Residues in contact with ASP 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A TYR 2.9 14.0 + - - +
190A ALA 4.3 1.1 - - - +
191A CYS 3.2 0.2 - - - -
192A ASP* 1.3 76.5 - - - +
194A MET* 1.3 60.2 + - - +
195A GLU* 3.4 4.4 - - - +
181D THR* 4.1 10.5 + - - +
182D LYS* 3.5 0.9 - - - -
183D GLN* 2.9 56.2 + - - +
186D HIS* 2.7 33.2 + - + +
276D LYS* 2.9 44.0 + - + +
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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