Contacts of the strand formed by residues 212 - 215 (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 ILE 212 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145J PHE* 3.3 28.9 - - + +
147J PHE* 3.5 27.6 - - + -
179J LEU 3.5 24.2 - - - +
180J VAL* 4.5 5.6 - - + +
183J ASN* 4.1 16.6 - - + +
184J SER* 5.5 1.1 - - - -
207J ILE* 3.0 30.3 - - + +
208J ASN 3.1 9.9 + - - +
209J LYS* 4.2 10.5 - - - +
211J LYS* 1.3 85.6 - - + +
213J MET* 1.3 67.8 + - - +
214J ILE* 3.3 25.2 + - + -
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Residues in contact with MET 213 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H VAL* 4.7 6.3 - - + +
126H ASP* 3.0 44.9 - - + +
209H TYR* 6.0 0.9 - - - -
144J ARG* 3.5 29.8 - - + +
145J PHE 3.4 4.9 + - - -
146J GLY* 2.9 27.0 - - - -
147J PHE 3.4 1.2 + - - -
209J LYS* 6.1 2.0 - - + -
212J ILE* 1.3 71.9 - - - +
214J ILE* 1.3 63.4 + - - +
215J ARG* 4.4 0.4 - - - +
221J LEU* 4.3 2.4 - - - +
224J LEU* 4.0 30.5 - - + -
229J GLU* 3.5 30.7 - - + +
230J LEU* 3.7 20.4 - - + -
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Residues in contact with ILE 214 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209H TYR* 3.3 40.7 - - + +
147J PHE* 3.2 27.4 - - + +
149J ASN* 4.5 20.6 - - + +
150J PRO* 5.7 1.1 - - + -
186J LEU* 6.1 0.9 - - + -
205J ILE* 4.1 24.0 - - + -
207J ILE* 4.1 19.7 - - + -
212J ILE* 3.3 23.5 + - + -
213J MET* 1.3 80.0 - - - +
215J ARG* 1.3 87.3 + - - +
221J LEU* 4.6 1.8 - - - -
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Residues in contact with ARG 215 (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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126H ASP* 2.9 39.9 + - - -
204H VAL 5.3 1.6 + - - -
205H VAL 5.7 1.6 + - - -
206H ILE 4.9 4.9 + - - -
208H TYR* 3.8 34.0 - - - +
209H TYR* 4.5 10.1 - - - -
222I LEU* 6.3 0.2 - - - +
147J PHE 3.9 3.4 + - - -
148J SER* 3.3 3.5 - - - +
149J ASN* 2.7 29.0 + - - +
213J MET* 4.4 1.2 - - - +
214J ILE* 1.3 97.8 + - - +
216J SER* 1.3 62.5 + - - +
217J MET 3.4 2.2 - - - +
220J GLU* 3.4 38.8 - - + +
221J LEU* 4.4 9.5 - - + +
223J HIS* 3.9 15.0 + - - -
224J LEU* 3.5 41.5 - - + +
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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