Contacts of the helix formed by residues 174 - 180 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139J LYS* 4.0 8.1 + - - -
172J ASP* 2.4 37.7 + - - +
173J PRO* 1.3 84.5 - - + +
175J ILE* 1.3 50.2 + - - +
176J PHE 3.3 2.5 - - - -
177J ASP* 2.5 32.7 + - - +
178J GLU* 2.5 39.1 + - - +
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Residues in contact with ILE 175 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134J TRP* 4.9 0.9 - - + -
135J TYR* 3.8 50.9 - - + -
139J LYS* 5.5 2.7 - - + -
163J ILE* 4.1 15.0 - - + +
166J ALA* 3.7 35.7 - - + +
167J GLU* 3.9 6.5 + - + +
170J TYR* 4.0 6.7 - - + -
172J ASP* 3.4 26.4 + - + +
174J THR* 1.3 73.7 + - - +
176J PHE* 1.3 58.5 + - - +
178J GLU* 3.2 5.0 + - - +
179J LEU* 2.8 49.2 + - + +
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Residues in contact with PHE 176 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160J LEU* 3.8 29.4 - - + -
163J ILE* 3.5 30.5 - - + +
164J GLN* 3.4 34.3 - - - +
167J GLU* 3.3 10.6 + - - +
174J THR 3.0 0.8 + - - -
175J ILE* 1.3 79.0 - - - +
177J ASP* 1.3 64.6 + - - +
179J LEU 4.6 0.2 - - - +
180J VAL* 3.1 41.0 + - + +
181J ALA* 3.3 6.6 + - + -
186J LEU 4.4 0.9 - - - -
187J ARG* 4.2 6.1 - - - -
188J PHE* 3.4 46.0 - + + -
197J LEU* 3.7 16.4 - - + -
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Residues in contact with ASP 177 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167J GLU* 3.0 1.1 - - - +
173J PRO 2.4 31.0 - - - +
174J THR* 2.5 18.7 + - - +
176J PHE* 1.3 78.1 - - - +
178J GLU* 1.3 57.4 + - - +
179J LEU 3.4 0.3 + - - -
181J ALA* 3.5 14.3 + - + +
182J LYS* 3.1 45.1 + - + +
187J ARG* 5.7 4.5 + - - +
188J PHE 5.4 4.0 - - - +
706J MG 2.4 16.9 - - - -
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Residues in contact with GLU 178 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139J LYS* 3.4 46.0 + - + +
174J THR* 2.5 34.0 + - - +
175J ILE 3.8 2.9 - - - +
177J ASP* 1.3 73.6 - - - +
179J LEU* 1.3 62.2 + - - +
182J LYS* 3.0 39.5 + - - +
183J ASN* 3.7 10.4 - - - +
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Residues in contact with LEU 179 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134J TRP* 4.6 3.8 - - + -
135J TYR* 4.0 11.9 - - - +
138J LEU* 3.5 47.8 - - + +
139J LYS* 3.3 33.0 - - + -
145J PHE* 3.3 26.4 - - + -
163J ILE* 4.6 12.1 - - + -
175J ILE* 2.8 32.9 + - + +
178J GLU* 1.3 81.3 - - - +
180J VAL* 1.3 68.8 + - + +
183J ASN* 3.6 8.5 - - - +
211J LYS* 5.8 1.3 - - - -
212J ILE* 3.5 6.9 - - - +
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Residues in contact with VAL 180 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145J PHE* 4.8 0.9 - - + -
147J PHE* 4.5 12.6 - - + -
160J LEU* 4.1 11.4 - - + -
163J ILE* 4.0 22.4 - - + -
176J PHE* 3.1 46.9 + - + +
178J GLU 3.6 0.8 - - - -
179J LEU* 1.3 89.0 - - + +
181J ALA* 1.3 64.9 + - - +
182J LYS 3.2 0.9 - - - -
183J ASN* 2.8 20.1 + - - -
184J SER* 2.9 31.8 + - - +
186J LEU* 4.0 14.1 - - + +
212J ILE* 4.5 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