Contacts of the strand formed by residues 252 - 257 (chain C) in PDB entry 2O2C
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 THR 252 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197C ILE* 4.1 5.4 - - - +
199C HIS* 3.3 19.1 - - + +
201C VAL* 3.7 30.7 - - + -
247C ILE* 3.6 8.9 - - + +
248C ASP 3.0 20.3 + - - -
249C ILE* 3.3 16.2 + - - -
250C GLU 3.4 1.0 - - - -
251C ALA* 1.3 77.5 - - - +
253C LEU* 1.3 64.8 + - - +
254C PHE* 3.8 23.0 + - + -
295C HIS* 2.8 32.4 + - - +
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Residues in contact with LEU 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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180C PHE* 3.5 31.6 - - + -
184C VAL* 4.0 17.3 - - + -
189C TRP* 4.8 3.1 - - + +
197C ILE* 3.9 21.9 - - + +
199C HIS 2.9 7.1 + - - +
200C VAL* 3.5 4.8 - - + +
201C VAL 2.8 26.5 + - - +
252C THR* 1.3 75.0 - - - +
254C PHE* 1.3 69.5 + - - +
255C ILE* 4.2 10.8 - - + -
294C LYS 4.4 8.1 - - - +
295C HIS* 3.6 21.1 - - - +
297C VAL* 4.1 18.2 - - + -
339C ILE* 4.2 13.7 - - + -
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Residues in contact with PHE 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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201C VAL* 3.4 29.4 - - + +
203C ILE* 4.0 7.6 - - + -
240C ILE* 5.6 2.0 - - + -
243C VAL* 5.5 1.6 - - + -
244C LEU* 4.8 6.7 - - + -
247C ILE* 4.0 8.7 - - + -
249C ILE* 3.9 33.2 - - + -
252C THR* 3.8 26.7 - - + -
253C LEU* 1.3 77.6 - - - +
255C ILE* 1.3 60.9 + - - +
256C VAL 4.0 0.2 - - - -
273C ALA* 3.9 30.7 - - + -
277C LEU* 5.0 3.6 - - + -
295C HIS* 2.7 24.4 + - + +
296C PHE* 3.4 34.6 - + + +
297C VAL 3.1 24.3 + - - +
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Residues in contact with ILE 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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200C VAL* 3.6 27.6 - - + -
201C VAL 2.7 15.0 + - - +
202C ASN* 3.5 10.8 - - - +
203C ILE* 2.7 33.8 + - - +
253C LEU* 4.2 8.7 - - + -
254C PHE* 1.3 75.6 - - - +
256C VAL* 1.3 58.3 + - - +
257C ALA 3.5 1.6 + - - -
297C VAL* 3.7 21.1 - - + -
299C LEU* 3.6 36.6 - - + -
335C LEU* 4.4 5.2 - - + -
336C PRO* 4.2 18.6 - - + -
339C ILE* 3.9 20.2 - - + -
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Residues in contact with VAL 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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203C ILE* 3.6 9.6 - - + +
255C ILE* 1.3 72.7 - - - +
257C ALA* 1.3 60.6 + - - +
261C PHE* 3.6 32.5 - - + -
266C THR* 4.0 17.5 - - + -
267C ILE* 5.2 2.7 - - + -
270C ALA* 3.8 30.5 - - + -
296C PHE* 3.9 29.2 - - + -
297C VAL 2.9 13.2 + - - +
298C ALA* 3.4 2.8 - - - -
299C LEU 2.9 26.0 + - - +
309C PHE* 4.7 1.8 - - + -
311C ILE* 4.4 7.2 - - + -
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Residues in contact with ALA 257 (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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202C ASN* 3.9 11.0 - - - +
203C ILE 2.8 21.6 + - - +
204C GLY* 3.4 6.4 - - - -
208C SER* 3.3 32.5 - - - +
212C PRO* 6.4 0.4 - - + -
255C ILE 3.5 0.4 + - - -
256C VAL* 1.3 70.6 - - - +
258C SER* 1.3 64.5 + - - +
266C THR* 3.6 2.0 + - - +
299C LEU* 3.7 20.0 - - + -
333C ILE* 3.8 18.2 - - + +
5003C G6Q 4.5 0.3 + - - -
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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