Contacts of the helix formed by residues 185 - 192 (chain A) in PDB entry 2Z9O
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 ILE 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A LEU 3.7 1.4 + - - -
184A LYS* 1.3 68.5 - - - +
186A ASP* 1.3 67.3 + - - +
188A ILE* 2.8 25.0 + - + +
189A ILE* 2.9 17.6 + - + +
199A GLN* 4.8 7.6 - - - +
201A MET* 3.9 23.8 - - + -
204A PHE* 3.7 32.1 - - + -
235A THR* 4.1 10.5 - - + +
236A THR* 2.9 28.4 + - - +
237A HIS 4.5 0.2 - - - -
238A ILE* 3.4 39.0 - - + +
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Residues in contact with ASP 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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184A LYS* 3.3 16.8 - - + +
185A ILE* 1.3 83.2 - - - +
187A TRP* 1.3 58.6 + - - +
189A ILE* 3.9 10.2 - - - +
190A GLU* 3.6 16.6 + - - +
199A GLN* 2.8 32.1 + - - +
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Residues in contact with TRP 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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172A TYR* 6.0 0.6 + - - -
183A LEU* 4.2 26.7 - - + +
184A LYS* 2.6 38.6 + - + +
186A ASP* 1.3 73.9 - - - +
188A ILE* 1.3 64.7 + - + -
190A GLU* 3.2 7.6 - - + +
191A ARG* 3.1 77.2 + - + +
192A TYR* 6.2 1.6 - - - -
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Residues in contact with ILE 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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183A LEU* 3.7 44.2 - - + +
184A LYS 2.9 12.3 + - - +
185A ILE* 2.8 14.1 + - - +
187A TRP* 1.3 79.0 - - + +
189A ILE* 1.3 58.4 + - - +
190A GLU 2.5 16.2 + - - -
191A ARG 3.4 0.2 + - - -
192A TYR* 3.2 51.0 + - + +
194A LEU* 4.8 0.9 - - + -
204A PHE* 4.1 24.7 - - + -
208A PHE* 3.8 16.6 - - + -
238A ILE* 4.6 7.0 - - + -
240A PHE* 4.4 14.1 - - + -
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Residues in contact with ILE 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 ILE* 2.9 18.4 + - + +
186A ASP* 3.9 13.0 - - - +
188A ILE* 1.3 75.8 - - - +
190A GLU* 1.3 65.9 + - + +
193A GLN* 3.5 1.6 + - - -
194A LEU* 3.0 57.3 + - + +
195A PRO 4.9 3.4 - - - +
196A GLN* 5.9 0.4 - - - -
198A TYR* 3.6 11.2 - - + +
199A GLN* 3.3 61.9 - - + +
204A PHE* 4.7 7.2 - - + -
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Residues in contact with GLU 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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186A ASP 3.6 12.8 - - - +
187A TRP* 3.2 15.9 + - + +
188A ILE 2.5 5.7 + - - -
189A ILE* 1.3 79.5 - - + +
191A ARG* 1.3 85.4 + - - +
192A TYR 2.5 4.4 + - - -
193A GLN* 2.4 38.0 + - - +
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Residues in contact with ARG 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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164A ARG* 4.7 5.2 + - - +
187A TRP* 3.1 60.5 + - + +
188A ILE* 5.8 0.2 - - - -
190A GLU* 1.3 100.0 + - - +
192A TYR* 1.3 77.1 + - + +
193A GLN* 3.5 6.5 + - - +
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Residues in contact with TYR 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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161A TYR* 3.4 12.5 - - + -
164A ARG* 3.7 32.7 + - + +
165A LEU* 3.0 36.4 + - + +
168A SER* 2.7 42.5 - - - -
183A LEU* 4.5 10.1 - - + +
187A TRP* 6.2 1.6 - - - -
188A ILE* 3.2 33.4 + - + +
189A ILE 4.1 0.2 - - - -
190A GLU 2.5 5.9 + - - -
191A ARG* 1.3 104.7 - - + +
193A GLN* 1.3 71.1 + - - +
194A LEU* 2.9 22.6 + - + +
208A PHE* 3.5 26.7 - + + -
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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