Contacts of the helix formed by residues 221 - 226 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201G LEU* 3.4 37.8 - - + +
202G ASN* 5.8 1.6 + - - -
206G VAL* 4.2 17.3 - - + +
219G ASN* 3.0 9.8 + - + +
220G GLY* 1.3 79.4 - - - +
222G VAL* 1.3 70.3 + - + +
223G ALA 3.1 0.6 - - - +
224G GLU* 3.3 7.7 + - - +
225G PHE* 3.1 20.8 + - - +
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Residues in contact with VAL 222 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199G VAL* 4.0 26.2 - - + -
201G LEU* 4.7 2.7 - - + -
206G VAL* 3.3 38.4 - - + -
207G GLU* 4.1 17.3 - - + +
214G LEU* 4.6 15.9 - - + +
217G ALA 6.0 0.2 - - - +
219G ASN* 4.9 7.7 - - + +
221G GLU* 1.3 73.7 - - + +
223G ALA* 1.3 61.2 + - - +
225G PHE* 3.8 5.8 - - - +
226G LEU* 2.9 53.4 + - + +
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Residues in contact with ALA 223 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214G LEU 5.2 4.4 + - - -
215G PHE* 5.4 1.1 - - - +
218G LYS* 3.5 43.5 - - + +
219G ASN 4.5 1.2 - - - +
220G GLY* 3.4 26.9 - - - +
221G GLU 3.6 0.4 - - - +
222G VAL* 1.3 78.0 - - - +
224G GLU* 1.3 65.0 + - - +
226G LEU* 3.4 3.5 + - - +
227G SER* 3.0 23.4 + - - -
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Residues in contact with GLU 224 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160F LYS* 3.6 28.3 + - - +
220G GLY* 3.8 16.1 - - - +
221G GLU* 3.3 11.9 + - - +
222G VAL 3.3 0.2 - - - -
223G ALA* 1.3 78.3 - - - +
225G PHE* 1.3 61.8 + - - +
227G SER* 2.7 29.3 + - - -
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Residues in contact with PHE 225 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F ASP* 3.5 31.6 - - - +
160F LYS* 3.6 22.4 - - + +
30G LEU* 3.5 34.1 - - + -
31G GLY* 3.9 19.3 - - - -
32G PRO* 3.6 34.5 - - + -
185G HIS 4.0 13.2 - - - -
187G LEU* 4.2 7.5 - - + +
199G VAL* 4.3 13.0 - - + -
201G LEU* 4.9 8.3 - - + -
221G GLU 3.1 10.4 + - - +
222G VAL* 3.8 8.5 - - - +
224G GLU* 1.3 82.1 + - - +
226G LEU* 1.3 72.1 + - + +
227G SER 3.1 4.2 + - - -
228G ALA* 3.6 5.9 + - - +
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Residues in contact with LEU 226 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G LEU* 3.7 13.9 - - + -
187G LEU* 3.7 22.2 - - + -
199G VAL* 4.7 2.7 - - + -
211G LEU* 4.1 5.6 - - + -
214G LEU* 3.4 38.4 - - + +
215G PHE* 3.3 29.5 - - + -
222G VAL* 2.9 37.3 + - + +
223G ALA* 3.7 4.0 - - - +
225G PHE* 1.3 86.9 - - + +
227G SER* 1.3 56.0 + - - +
228G ALA* 3.0 6.3 - - - -
229G ARG* 3.1 31.6 + - - +
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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