Contacts of the helix formed by residues 174 - 180 (chain E) in PDB entry 2ONK
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 174 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139E LYS* 4.0 8.7 + - - -
172E ASP* 2.4 38.3 + - - +
173E PRO* 1.3 84.5 - - + +
175E ILE* 1.3 50.1 + - - +
176E PHE 3.3 2.7 - - - -
177E ASP* 2.5 34.1 + - - +
178E GLU* 2.5 38.1 + - - +
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Residues in contact with ILE 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E TRP* 4.9 1.1 - - + -
135E TYR* 3.8 53.2 - - + -
139E LYS* 5.5 3.4 - - + -
163E ILE* 4.1 14.8 - - + +
166E ALA* 3.7 35.7 - - + +
167E GLU* 4.0 5.8 - - + +
170E TYR* 4.1 6.1 - - + -
172E ASP* 3.4 25.5 + - + +
174E THR* 1.3 75.2 + - - +
176E PHE* 1.3 59.1 + - - +
178E GLU* 3.2 3.9 + - - +
179E LEU* 2.8 47.5 + - + +
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Residues in contact with PHE 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E LEU* 3.8 29.4 - - + -
163E ILE* 3.6 28.7 - - + -
164E GLN* 3.4 34.5 - - - +
167E GLU* 3.3 10.8 + - - +
174E THR 3.1 0.8 + - - -
175E ILE* 1.3 79.2 - - - +
177E ASP* 1.3 63.6 + - - +
179E LEU 4.6 0.4 - - - +
180E VAL* 3.1 42.4 + - + +
181E ALA* 3.3 6.6 + - + -
186E LEU 4.4 1.1 - - - -
187E ARG* 4.2 5.8 - - - -
188E PHE* 3.4 46.4 - + + -
197E LEU* 3.6 16.4 - - + -
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Residues in contact with ASP 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E GLU* 3.0 0.9 - - - +
173E PRO 2.4 31.2 - - - +
174E THR* 2.5 17.8 + - - +
176E PHE* 1.3 77.6 - - - +
178E GLU* 1.3 56.8 + - - +
179E LEU 3.4 0.7 + - - -
181E ALA* 3.5 16.2 + - + +
182E LYS* 3.1 45.3 + - - +
187E ARG* 5.7 4.3 + - - +
188E PHE 5.4 3.1 - - - +
705E MG 2.7 18.3 - - - -
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Residues in contact with GLU 178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E LYS* 3.4 46.5 + - + +
174E THR* 2.5 35.0 + - - +
175E ILE 3.8 2.5 - - - +
177E ASP* 1.3 73.9 - - + +
179E LEU* 1.3 63.7 + - - +
182E LYS* 3.0 39.3 - - - +
183E ASN* 3.7 10.9 - - - +
211E LYS* 6.1 0.3 - - - -
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Residues in contact with LEU 179 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E TRP* 4.6 3.6 - - + -
135E TYR* 4.0 12.1 - - - +
138E LEU* 3.5 48.0 - - + +
139E LYS* 3.3 33.2 - - + -
145E PHE* 3.3 24.9 - - + -
163E ILE* 4.6 12.1 - - + -
175E ILE* 2.8 36.6 + - + +
178E GLU* 1.3 77.3 - - - +
180E VAL* 1.3 69.5 + - + +
183E ASN* 3.6 9.6 - - - +
211E LYS* 5.6 1.6 - - - +
212E ILE* 3.5 6.6 - - - +
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Residues in contact with VAL 180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E PHE* 4.8 0.4 - - + -
147E PHE* 4.5 12.8 - - + -
160E LEU* 4.1 12.1 - - + -
163E ILE* 4.0 26.7 - - + -
176E PHE* 3.1 42.2 + - + +
178E GLU 3.6 0.8 - - - -
179E LEU* 1.3 86.9 - - + +
181E ALA* 1.3 62.1 + - - +
182E LYS 3.2 1.6 - - - -
183E ASN 2.8 18.9 + - - +
184E SER* 2.9 31.5 + - - +
186E LEU* 4.0 13.9 - - + +
212E ILE* 4.5 2.7 - - + -
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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