Contacts of the helix formed by residues 200 - 205 (chain C) 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 200 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199C GLU* 1.3 78.6 - - - +
201C GLY* 1.3 73.2 + - - +
202C ALA 3.5 1.1 - - - -
203C VAL* 2.9 6.8 + - - +
204C VAL* 2.9 53.7 + - + +
208C TYR* 6.2 0.2 - + - -
214C PRO* 4.1 15.0 - - + -
215C THR* 4.0 21.1 - - + -
218C TYR* 3.4 42.8 - + + -
99D HIS* 3.4 17.8 - - + -
100D THR* 3.6 19.3 - - - +
200D PHE* 4.0 19.5 - + - -
201D GLY* 3.7 24.7 - - - -
204D VAL* 4.9 3.6 - - + -
218D TYR* 5.6 2.9 - + - -
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Residues in contact with GLY 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C HIS* 3.9 14.5 - - - +
100C THR* 4.3 2.0 - - - -
199C GLU* 3.6 2.7 + - - -
200C PHE* 1.3 82.0 - - - +
202C ALA* 1.3 65.3 + - - +
203C VAL 2.9 1.0 + - - -
204C VAL* 3.1 8.4 - - - +
205C VAL* 3.0 23.0 - - - +
99D HIS* 4.7 1.8 - - - -
200D PHE* 3.7 25.9 - - - +
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Residues in contact with ALA 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C HIS* 3.4 24.3 + - - +
102C ALA* 4.2 5.8 - - + -
103C GLY* 3.4 15.8 - - - +
106C LEU* 5.1 1.1 - - + -
134C ALA* 4.1 9.6 - - + +
138C VAL* 3.9 17.5 - - + -
199C GLU* 2.6 28.7 + - + +
201C GLY* 1.3 72.5 - - - +
203C VAL* 1.3 60.2 + - - +
205C VAL 3.9 1.6 + - - -
206C ILE* 3.1 22.0 - - - +
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Residues in contact with VAL 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C ILE* 4.2 13.0 - - + +
134C ALA* 3.5 22.0 - - + -
135C MET* 4.2 10.8 - - + -
199C GLU* 3.6 27.8 - - + +
200C PHE* 2.9 8.4 + - - +
202C ALA* 1.3 74.5 - - - +
204C VAL* 1.3 57.7 + - + +
206C ILE* 2.6 30.8 + - - +
207C ALA 3.3 22.1 + - - +
212C ILE* 3.1 35.9 - - + -
215C THR* 5.7 1.8 - - - +
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Residues in contact with VAL 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C PHE* 2.9 57.7 + - + +
201C GLY* 3.1 20.0 - - - +
203C VAL* 1.3 73.3 - - + +
205C VAL* 1.3 79.6 + - + +
206C ILE 3.2 1.6 + - - -
207C ALA 4.2 5.8 - - - -
208C TYR* 3.7 32.8 + - + +
215C THR* 3.9 15.5 - - + +
200D PHE* 5.0 1.6 - - + -
218D TYR* 3.8 29.8 + - + +
215E ARG* 5.2 1.6 + - - -
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Residues in contact with VAL 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C THR* 4.4 16.6 - - + +
103C GLY* 3.4 34.3 - - - +
104C ILE* 3.5 11.2 - - + +
107C LEU* 3.6 8.8 - - + +
201C GLY 3.0 22.0 - - - +
202C ALA 4.1 0.4 - - - +
203C VAL 2.8 3.6 + - - -
204C VAL* 1.3 79.4 - - + +
206C ILE* 1.3 58.5 + - + +
218D TYR* 4.2 14.8 - - + -
221D TYR* 3.0 45.0 + - + -
215E ARG* 5.7 1.4 + - - -
223E HIS* 5.0 0.4 + - - -
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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