Contacts of the strand formed by residues 225 - 230 (chain F) in PDB entry 2W8B
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 ALA 225 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216F TYR 3.9 0.5 - - - +
217F VAL* 3.4 3.6 - - - -
218F THR* 2.9 47.0 + - + +
221F SER* 4.9 8.5 - - - +
223F ARG 4.7 2.0 - - - +
224F SER* 1.3 75.2 - - - +
226F LEU* 1.3 60.5 + - - +
227F VAL* 4.5 2.7 - - + -
238F GLN* 4.6 13.7 - - - +
240F ALA 3.6 6.7 - - - +
241F SER* 3.6 16.4 - - - +
246F ASN* 4.3 4.9 - - - -
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Residues in contact with LEU 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215F ALA* 4.4 1.6 - - + -
216F TYR 3.5 21.8 - - - +
217F VAL* 4.2 4.0 - - + +
225F ALA* 1.3 71.4 - - - +
227F VAL* 1.3 61.2 + - - +
238F GLN* 4.2 1.2 - - - +
239F VAL* 2.8 49.8 + - + -
240F ALA* 2.8 19.4 + - + +
246F ASN* 4.0 15.7 - - + +
247F GLY* 4.6 4.7 - - - +
249F PRO* 3.6 36.1 - - + -
258F LEU* 4.1 5.8 - - + -
260F PHE* 3.6 41.7 - - + -
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Residues in contact with VAL 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215F ALA* 3.1 5.7 - - - +
216F TYR* 2.9 76.0 + - + +
218F THR* 4.5 12.3 - - + -
225F ALA* 4.4 6.7 - - + +
226F LEU* 1.3 85.2 - - - +
228F ILE* 1.3 66.5 + - - +
229F GLN 4.8 0.2 - - - +
236F VAL* 3.9 13.2 - - + -
237F ARG 3.2 9.9 - - - +
238F GLN* 3.8 30.5 - - - +
239F VAL* 4.1 2.2 - - - -
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Residues in contact with ILE 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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213F LYS* 3.8 38.1 - - + -
214F LEU 3.5 4.7 - - - +
215F ALA* 4.0 7.9 - - + -
227F VAL* 1.3 80.3 - - - +
229F GLN* 1.3 61.4 + - - +
230F THR* 4.0 0.9 + - - +
235F ALA 3.6 1.6 - - - +
236F VAL* 3.6 2.0 - - - -
237F ARG* 2.8 53.7 + - + +
239F VAL* 3.7 21.3 - - + -
251F PHE* 3.8 26.2 - - + -
258F LEU* 4.1 7.4 - - + -
275F LEU* 3.9 24.5 - - + -
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Residues in contact with GLN 229 (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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195F VAL* 3.0 42.2 + - + +
196F HIS* 4.1 4.2 + - - +
213F LYS* 3.4 3.8 - - - -
214F LEU* 2.8 36.7 + - + +
216F TYR* 2.7 41.0 + - + -
227F VAL 4.2 0.6 - - - -
228F ILE* 1.3 74.0 - - - +
230F THR* 1.3 74.0 + - - +
231F LEU* 3.5 4.7 + - - +
234F GLY* 3.7 23.2 - - - +
235F ALA 3.2 8.7 - - - +
236F VAL* 3.7 11.6 - - + +
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Residues in contact with THR 230 (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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212F SER* 3.8 12.6 - - - +
213F LYS* 3.3 31.1 - - + +
228F ILE* 4.0 1.3 + - - +
229F GLN* 1.3 71.5 - - - +
231F LEU* 1.3 60.5 + - - +
232F ALA* 4.1 10.1 - - + +
233F ASN* 3.2 26.9 - - - +
234F GLY* 2.9 29.6 + - - -
235F ALA* 2.7 20.9 + - - +
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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