Contacts of the strand formed by residues 196 - 201 (chain F) 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 196 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1F MET* 5.3 5.9 - - - +
23F GLY* 3.6 19.8 + - - -
25F ASP* 4.0 12.0 - - - +
26F TYR 3.6 1.6 + - - -
27F CYS* 3.7 8.6 - - + -
28F VAL 3.3 13.0 + - - -
194F ALA* 2.9 17.8 - - - +
195F ASP* 1.3 86.5 - - + +
197F VAL* 1.3 64.4 + - - +
208F LYS* 3.1 40.5 + - - +
209F GLY* 3.1 15.6 - - - +
210F LYS* 5.0 4.9 - - + +
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Residues in contact with VAL 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F VAL 3.2 9.9 - - - +
30F LEU* 4.0 22.7 - - + -
190F ALA* 4.2 7.9 - - + +
194F ALA* 3.3 21.3 - - + -
196F GLU* 1.3 80.1 - - - +
198F ALA* 1.3 74.4 + - - +
199F VAL* 4.3 0.4 - - + -
208F LYS* 3.1 5.7 - - - -
209F GLY 2.6 33.8 + - - +
211F LEU* 4.0 24.7 - - + +
214F LEU* 3.7 26.0 - - + +
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Residues in contact with ALA 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F PHE* 3.9 25.1 - - + -
27F CYS* 4.7 2.3 - - - -
28F VAL 3.0 6.2 + - - +
29F LEU* 3.4 22.4 - - + -
30F LEU 2.9 18.5 + - - -
197F VAL* 1.3 76.4 - - - +
199F VAL* 1.3 71.9 + - - +
205F ILE* 4.1 14.8 - - + -
207F GLU 3.4 5.4 - - - -
208F LYS* 3.9 7.8 - - + +
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Residues in contact with VAL 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F LEU* 3.2 14.6 - - + +
197F VAL* 4.3 3.8 - - + -
198F ALA* 1.3 85.3 - - - +
200F MET* 1.3 60.9 + - - +
201F LEU* 4.4 14.4 - - + -
205F ILE* 3.6 4.2 - - - +
206F VAL* 3.0 27.4 + - - +
207F GLU 2.9 15.9 + - - +
214F LEU* 4.1 16.6 - - + -
222F VAL* 4.0 40.4 - - + -
225F PHE* 4.3 17.3 - - + -
226F LEU* 4.7 5.4 - - + -
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Residues in contact with MET 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F LEU* 4.5 5.8 - - + -
18F VAL* 4.8 1.8 - - + -
29F LEU* 3.9 26.1 - - + +
30F LEU 2.7 12.7 + - - +
31F GLY* 3.4 15.9 - - - -
32F PRO* 3.6 1.4 - - - +
35F ALA* 2.9 33.3 - - + +
36F GLY* 3.2 23.1 - - - +
37F LYS* 3.8 17.7 - - + -
40F PHE* 4.3 9.6 - - + -
198F ALA 4.3 0.2 - - - -
199F VAL* 1.3 70.6 - - - +
201F LEU* 1.3 75.0 + - - +
203F GLY* 3.5 20.9 - - - +
204F ARG 3.4 14.1 - - - +
205F ILE* 3.5 19.7 - - + -
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Residues in contact with LEU 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F PRO* 3.5 26.5 - - + -
35F ALA* 4.3 1.8 - - - -
199F VAL* 4.1 13.9 + - + -
200F MET* 1.3 85.4 - - - +
202F ASN* 1.3 76.0 + - - +
203F GLY 3.5 0.2 - - - -
204F ARG* 2.8 21.7 + - - +
206F VAL* 3.9 15.7 - - + +
221F GLU* 3.4 57.1 - - + +
222F VAL* 4.5 2.5 - - - +
225F PHE* 4.8 10.1 - - + -
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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