Contacts of the helix formed by residues 277 - 283 (chain B) in PDB entry 2OOR
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 277 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B ARG* 4.5 22.4 - - + +
274B VAL* 3.8 19.3 - - + +
275B LEU 5.8 0.4 - - - -
276B ILE* 1.3 77.1 - - - +
278B GLU* 1.3 65.0 + - - +
279B GLU* 3.6 13.5 + - - +
280B MET* 3.1 41.5 + - - +
281B VAL* 3.1 15.4 + - - +
301B CYS* 5.2 0.2 - - - -
302B PRO* 4.3 7.9 - - + -
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Residues in contact with GLU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B THR* 1.3 70.1 - - - +
279B GLU* 1.3 66.0 + - - +
281B VAL* 3.1 19.1 + - - +
282B THR* 3.2 15.2 + - + +
302B PRO* 4.8 8.7 - - + +
303B LEU* 3.6 30.3 - - + +
312B LYS* 3.4 22.8 + - - -
313B HIS* 3.0 31.4 + - + +
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Residues in contact with GLU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B LEU* 5.3 5.0 - - - +
277B THR* 3.6 13.5 + - - +
278B GLU* 1.3 78.5 - - - +
280B MET* 1.3 67.7 + - - +
282B THR* 2.5 29.3 + - - +
283B LYS* 3.6 29.9 + - - +
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Residues in contact with MET 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B PHE* 5.1 0.2 - - + -
248B ALA* 3.9 29.4 - - + -
251B VAL* 4.3 11.2 - - + -
252B LEU* 4.7 17.0 - - + +
255B LEU* 3.4 29.8 - - + +
275B LEU 3.3 24.5 - - - +
276B ILE* 3.8 10.3 - - + -
277B THR* 3.1 33.8 + - - +
279B GLU* 1.3 88.9 - - - +
281B VAL* 1.3 60.6 + - - +
283B LYS* 3.4 17.5 + - + +
284B MET* 3.6 15.9 + - - +
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Residues in contact with VAL 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ILE* 3.7 15.7 - - + -
277B THR 3.2 15.9 - - - +
278B GLU 3.1 6.7 + - - +
280B MET* 1.3 73.3 - - - +
282B THR* 1.3 64.7 + - - +
283B LYS 3.2 0.2 - - - -
284B MET* 3.3 29.2 + - + +
290B ILE* 3.9 16.6 - - + -
301B CYS* 4.1 5.4 - - - -
303B LEU* 3.6 23.8 - - + -
312B LYS 4.2 5.2 - - - +
313B HIS* 3.3 35.8 - - + +
315B VAL* 3.7 13.1 - - + +
317B ILE* 5.2 0.7 - - + -
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Residues in contact with THR 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B GLU* 3.2 16.5 + - + +
279B GLU* 2.5 25.4 + - - +
281B VAL* 1.3 76.1 - - - +
283B LYS* 1.3 65.4 + - - +
284B MET 3.2 9.6 + - - +
313B HIS* 3.4 40.2 - - + +
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Residues in contact with LYS 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B LEU* 3.9 31.6 - - + -
256B VAL* 3.5 35.8 - - + +
279B GLU* 3.6 41.5 + - - +
280B MET* 3.4 10.9 + - - +
281B VAL 3.2 1.0 - - - -
282B THR* 1.3 79.9 + - - +
284B MET* 1.3 59.1 + - - +
285B LYS 4.2 0.2 + - - -
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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
------------------------------------------------------------
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