Contacts of the strand formed by residues 251 - 256 (chain C) in PDB entry 2OZL
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 251 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C LEU* 4.3 11.2 - - + -
189C CYS 3.2 2.0 + - - -
190C ILE* 3.5 8.4 - - + +
191C PHE* 2.9 26.3 + - - +
220C ILE* 3.9 3.4 - - - -
221C PRO* 3.5 18.2 - - + +
223C LEU* 3.9 19.5 - - + -
239C PHE* 4.0 22.7 - - + -
240C ALA* 4.1 21.3 - - + +
243C TYR* 4.0 24.0 - - + -
244C CYS* 4.0 19.5 - - - -
250C PRO* 1.3 79.4 - - - +
252C LEU* 1.3 69.7 + - - +
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Residues in contact with LEU 252 (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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165C TYR* 3.6 17.0 - - - +
179C TYR* 3.7 23.6 - - + +
191C PHE* 3.3 20.4 - - + +
193C CYS* 4.4 7.0 - - + +
213C TYR 3.5 24.9 - - - +
214C TYR* 3.9 16.4 - - - +
217C GLY* 3.7 21.5 - - - +
220C ILE* 4.0 7.1 - - + +
221C PRO 2.8 14.6 + - - +
222C GLY* 2.8 23.2 - - - -
223C LEU* 2.9 10.2 + - - +
251C ILE* 1.3 73.8 - - - +
253C MET* 1.3 80.9 + - - +
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Residues in contact with MET 253 (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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75C LEU* 3.5 32.1 - - + -
190C ILE* 4.6 8.3 - - + -
191C PHE 2.8 12.9 + - - +
192C ILE* 3.3 25.9 - - + +
193C CYS 3.0 23.4 + - - -
223C LEU* 3.4 13.5 - - + +
225C VAL* 3.8 11.4 - - + -
233C VAL* 5.2 0.9 - - + +
236C ALA* 3.9 35.2 - - + +
237C THR* 3.7 10.8 - - + +
240C ALA* 4.4 9.0 - - + -
251C ILE* 5.9 0.2 - - + -
252C LEU* 1.3 77.6 - - - +
254C GLU* 1.3 60.4 + - - +
255C LEU* 3.7 22.4 - - + -
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Residues in contact with GLU 254 (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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193C CYS* 3.6 12.3 - - + +
195C ASN* 3.0 32.3 + - + -
211C THR 4.6 2.0 - - - +
212C ASP* 4.2 0.3 - - - -
213C TYR* 3.4 25.2 + - + -
214C TYR* 3.1 36.7 + - + +
223C LEU 2.8 10.8 + - - +
224C ARG* 3.4 28.2 + - + +
225C VAL* 2.7 33.8 + - - +
252C LEU* 4.3 0.6 - - + -
253C MET* 1.3 73.0 - - - +
255C LEU* 1.3 62.8 + - - +
256C GLN* 3.7 11.1 + - - +
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Residues in contact with LEU 255 (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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71C CYS* 3.8 37.7 - - + -
75C LEU* 4.3 19.7 - - + -
192C ILE* 3.8 20.9 - - + -
193C CYS 2.9 12.3 + - - +
194C GLU* 3.7 8.6 - - + -
195C ASN* 2.8 30.0 + - - -
225C VAL* 3.8 16.4 - - + -
227C GLY* 4.5 6.7 - - - -
233C VAL* 4.6 8.5 - - + -
253C MET* 3.7 30.7 + - + -
254C GLU* 1.3 78.1 - - - +
256C GLN* 1.3 62.8 + - - +
257C THR* 3.4 2.3 + - - +
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Residues in contact with GLN 256 (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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10C LYS* 5.6 3.5 + - - -
13C ASP* 5.6 0.7 - - - +
195C ASN* 3.7 11.9 - - - +
224C ARG* 3.4 40.4 + - + +
225C VAL 3.0 19.7 + - - +
226C ASP* 4.3 4.9 - - - +
227C GLY* 2.8 26.2 + - - +
228C MET* 3.8 5.4 + - - +
254C GLU* 3.7 19.2 + - - +
255C LEU* 1.3 70.0 - - - +
257C THR* 1.3 60.6 + - - +
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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