Contacts of the helix formed by residues 221 - 226 (chain B) 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 GLU 221 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201B LEU* 3.4 37.8 - - + +
202B ASN* 5.8 1.4 + - - -
206B VAL* 4.2 17.2 - - + +
219B ASN* 3.0 9.3 + - + +
220B GLY* 1.3 78.5 - - - +
222B VAL* 1.3 70.3 + - + +
223B ALA 3.1 0.6 - - - +
224B GLU* 3.3 7.6 + - - +
225B PHE* 3.1 21.0 + - - +
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Residues in contact with VAL 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B VAL* 4.0 26.2 - - + -
201B LEU* 4.7 2.7 - - + -
206B VAL* 3.4 39.3 - - + -
207B GLU* 4.1 16.8 - - + +
214B LEU* 4.6 15.9 - - + +
217B ALA 6.0 0.2 - - - +
219B ASN* 4.9 9.2 - - + +
221B GLU* 1.3 73.5 - - - +
223B ALA* 1.3 61.0 + - - +
225B PHE* 3.8 4.7 - - - -
226B LEU* 2.9 53.2 + - + +
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Residues in contact with ALA 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B LEU 5.2 4.5 + - - -
215B PHE* 5.4 0.9 - - - +
218B LYS* 3.5 44.0 - - + +
219B ASN 4.5 1.4 - - - +
220B GLY* 3.4 26.2 - - - +
222B VAL* 1.3 77.6 - - - +
224B GLU* 1.3 66.5 + - - +
226B LEU* 3.4 3.8 + - - +
227B SER* 3.0 22.9 + - - -
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Residues in contact with GLU 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A LYS* 3.5 25.5 - - + +
220B GLY* 3.8 16.5 - - - +
221B GLU* 3.3 10.5 + - - +
222B VAL 3.3 0.4 - - - -
223B ALA* 1.3 79.4 - - - +
225B PHE* 1.3 61.2 + - - +
227B SER* 2.7 29.7 + - - -
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Residues in contact with PHE 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A ASP* 3.3 38.4 - - + +
160A LYS* 3.4 22.2 - - + +
30B LEU* 3.5 35.2 - - + -
31B GLY* 3.8 18.2 - - - -
32B PRO* 3.6 29.4 - - + -
185B HIS 4.0 12.8 - - - -
187B LEU* 4.2 5.9 - - + +
199B VAL* 4.3 12.6 - - + -
201B LEU* 4.9 9.9 - - + -
221B GLU 3.1 10.6 + - - +
222B VAL* 3.8 8.3 - - - +
224B GLU* 1.3 81.3 + - - +
226B LEU* 1.3 72.1 + - + +
227B SER 3.1 4.0 + - - -
228B ALA* 3.6 5.0 + - - +
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Residues in contact with LEU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LEU* 3.7 24.0 - - + -
187B LEU* 3.7 11.0 - - + -
199B VAL* 4.7 2.9 - - + -
211B LEU* 4.1 5.8 - - + -
214B LEU* 3.4 37.2 - - + +
215B PHE* 3.3 29.6 - - + -
222B VAL* 2.9 36.8 + - + +
223B ALA* 3.7 4.3 - - - +
225B PHE* 1.3 88.2 - - + +
227B SER* 1.3 55.4 + - - +
228B ALA 3.0 6.2 + - - -
229B ARG* 3.1 32.5 - - - +
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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