Contacts of the strand formed by residues 223 - 228 (chain F) in PDB entry 2ORE
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 VAL 223 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F PRO* 5.9 0.2 - - - -
169F MET* 4.6 1.1 - - + -
178F VAL* 3.2 24.5 - - + +
180F CYS* 4.3 4.9 - - - -
213F ALA* 4.0 26.0 - - + +
216F LEU* 3.8 30.3 - - + -
221F ILE 3.5 12.1 - - - +
222F PRO* 1.3 81.4 - - - +
224F LEU* 1.3 61.0 + - - +
225F ILE* 4.1 15.0 - - + -
267F LEU* 3.7 3.0 - - - +
268F TYR* 2.7 50.5 + - + -
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Residues in contact with LEU 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F ILE* 3.7 39.7 - - + +
24F HIS* 4.0 9.4 - - + -
25F LEU* 4.0 24.9 - - + +
26F PRO* 4.8 2.4 - - + +
177F VAL* 5.7 0.2 - - - +
178F VAL 2.8 12.3 + - - +
179F TYR* 3.3 16.1 - - + -
180F CYS 2.8 31.2 + - - -
223F VAL* 1.3 73.6 - - - +
225F ILE* 1.3 66.5 + - - +
265F LEU* 4.4 13.9 - - + -
266F ALA 3.2 27.4 - - - +
267F LEU* 3.9 17.9 - - + -
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Residues in contact with ILE 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179F TYR* 5.0 0.4 - - - -
180F CYS* 3.2 20.4 - - + +
182F PRO* 4.2 7.6 - - + -
209F LEU* 4.4 17.7 - - + +
210F ALA* 4.9 0.4 - - - -
213F ALA* 4.1 13.9 - - + -
223F VAL* 4.1 8.5 - - + -
224F LEU* 1.3 84.0 - - - +
226F SER* 1.3 68.7 + - - +
237F TYR* 3.5 47.1 - - + +
264F LEU 3.8 0.2 - - - +
265F LEU* 3.4 4.9 - - - -
266F ALA* 2.9 39.5 + - + +
268F TYR* 3.9 21.8 - - + +
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Residues in contact with SER 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F LYS* 5.5 0.6 - - - +
17F LEU* 5.8 0.7 - - - -
21F ILE* 5.0 3.6 - - - -
179F TYR* 3.1 23.3 + - - -
180F CYS 3.0 5.1 + - - -
181F ASP* 3.0 29.3 + - - +
182F PRO* 3.6 19.8 - - - +
225F ILE* 1.3 75.6 - - - +
227F ASN* 1.3 66.5 + - - +
237F TYR* 5.3 0.2 - - - -
263F GLU* 4.7 8.1 - - - -
264F LEU 3.4 4.9 - - - -
265F LEU* 3.8 18.2 - - - -
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Residues in contact with ASN 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182F PRO* 4.1 9.8 - - - +
183F PRO 4.7 0.2 + - - -
184F TYR* 3.8 10.8 - - - -
185F ALA* 3.1 28.3 + - - +
206F GLN* 3.5 19.2 + - - +
226F SER* 1.3 75.1 - - - +
228F HIS* 1.3 76.1 + - - +
233F THR* 3.6 13.7 - - - +
236F TRP* 4.8 0.2 - - - -
237F TYR* 2.8 36.8 + - + +
263F GLU* 3.2 18.2 + - - +
264F LEU* 2.7 33.9 + - + +
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Residues in contact with HIS 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184F TYR* 3.3 50.3 - + + +
185F ALA 3.6 22.7 - - - +
187F LEU* 3.9 20.7 - - + +
227F ASN* 1.3 86.2 + - - +
229F ASP* 1.3 60.0 + - - +
230F THR* 3.7 14.8 - - + -
233F THR* 2.8 26.4 + - + +
261F VAL* 5.1 15.0 - - + +
262F ASP 3.8 5.9 + - - +
263F GLU* 3.6 12.1 + - - -
264F LEU* 3.8 2.5 - - - +
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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