Contacts of the strand formed by residues 145 - 148 (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 PHE 145 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138J LEU* 4.0 44.4 - - + -
143J VAL 4.8 2.9 - - - -
144J ARG* 1.3 75.6 - - - +
146J GLY* 1.3 63.4 + - - +
147J PHE* 3.9 14.8 - + - -
163J ILE* 4.7 4.7 - - + -
179J LEU* 3.3 38.6 - - + -
180J VAL* 4.9 0.2 - - + -
211J LYS* 3.2 26.6 + - - +
212J ILE* 3.3 38.8 - - + -
213J MET 3.4 2.3 + - - -
230J LEU* 3.5 5.8 - - - +
232J TYR* 2.8 27.6 - - + +
234J PHE* 3.9 25.6 - + + -
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Residues in contact with GLY 146 (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* 1.3 76.9 - - - +
147J PHE* 1.3 68.2 + - - +
213J MET 2.9 17.3 - - - -
221J LEU* 4.0 6.1 - - - -
230J LEU* 3.8 11.7 - - - +
232J TYR 2.8 9.7 + - - -
233J PHE* 3.4 2.5 - - - +
234J PHE* 3.1 28.1 + - - -
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Residues in contact with PHE 147 (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* 3.9 15.0 - + - -
146J GLY* 1.3 78.6 - - - +
148J SER* 1.3 81.9 + - - +
150J PRO* 4.8 4.3 - - + -
156J GLY 4.7 1.1 - - - -
159J SER* 4.0 24.2 - - - +
160J LEU* 3.8 36.6 - - + -
163J ILE* 5.2 1.6 - - + -
180J VAL* 4.5 6.3 - - + -
186J LEU* 4.2 20.9 - - + -
207J ILE* 5.5 1.6 - - + -
212J ILE* 3.5 42.8 - - + -
213J MET 3.4 3.8 + - - -
214J ILE* 3.2 28.3 - - + +
221J LEU* 3.6 12.6 - - - +
234J PHE* 4.3 8.3 - + + -
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Residues in contact with SER 148 (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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147J PHE* 1.3 95.6 - - - +
149J ASN* 1.3 63.0 + - - +
150J PRO* 3.4 4.0 - - - +
153J ASP* 3.3 9.2 + - - +
155J CYS* 3.5 4.2 - - - +
156J GLY* 2.8 36.7 + - - -
159J SER* 5.0 1.0 + - - -
214J ILE* 4.9 0.7 - - - -
215J ARG 3.3 10.8 - - - +
216J SER 3.7 9.6 - - - -
218J GLU* 3.3 30.9 + - - +
221J LEU* 3.7 8.3 - - - +
234J PHE 5.1 0.8 + - - -
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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