Contacts of the strand formed by residues 243 - 245 (chain B) in PDB entry 2OT7
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 243 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B PHE 3.7 3.1 - - - -
83B THR* 5.6 1.0 + - - -
186B ALA* 3.3 2.8 - - - +
187B TRP* 3.0 32.0 + - + +
223B ALA* 5.1 0.4 - - + -
227B PHE* 3.6 34.3 - - + -
237B PHE* 3.5 24.1 + - - -
238B LEU* 3.6 28.1 + - + +
241B LYS* 4.7 0.2 - - - +
242B MET* 1.3 79.5 + - - +
244B LEU* 1.3 62.0 + - - +
245B ILE* 3.9 19.7 - - + -
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Residues in contact with LEU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B VAL* 4.1 16.8 - - + -
80B GLY 3.8 0.6 - - - +
81B LEU* 3.8 1.7 - - - -
82B PHE* 3.0 47.4 + - + +
84B GLN* 4.1 32.5 - - + +
121B TYR* 4.0 9.9 - - - +
122B TRP* 4.6 9.2 - - + -
125B LEU* 3.6 26.0 - - + -
184B SER* 4.4 4.3 - - - +
185B PHE 4.3 4.0 - - - +
186B ALA* 3.3 41.7 - - + +
187B TRP* 4.1 2.9 - - - -
243B THR* 1.3 72.0 - - - +
245B ILE* 1.3 65.4 + - - +
277B ALA* 6.0 0.9 - - + -
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Residues in contact with ILE 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B GLY 3.3 5.2 - - - +
81B LEU* 4.2 12.3 - - + -
122B TRP* 3.6 10.7 - - - -
187B TRP* 3.0 38.0 + - + +
219B LEU* 4.3 20.2 - - + -
222B LEU* 4.7 6.1 - - + -
223B ALA* 4.4 21.5 - - + -
226B PHE* 4.5 9.9 - - + -
227B PHE* 5.0 0.4 - - + -
238B LEU* 5.7 1.1 - - + -
243B THR* 3.9 21.3 - - + -
244B LEU* 1.3 78.8 - - - +
246B SER* 1.3 70.1 + - - +
247B PRO* 3.8 0.9 - - - +
249B MET* 3.8 15.7 - - + -
250B LEU* 3.5 23.3 - - + -
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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