Contacts of the strand formed by residues 223 - 229 (chain B) in PDB entry 3F7F
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164B HIS* 2.9 28.1 + - - -
165B PHE* 3.9 16.5 - - + -
177B PHE* 3.6 33.3 - - + +
178B LEU 5.1 0.4 + - - -
181B GLY* 5.6 0.8 + - - -
183B LEU* 4.9 5.2 - - + -
221B ASP 4.0 0.4 + - - -
222B SER* 1.3 73.8 - - - +
224B ILE* 1.3 63.1 + - - +
225B SER 3.0 29.2 - - - +
226B CYS* 4.3 1.1 - - + -
236B VAL* 3.5 31.0 - - + -
237B LEU 3.2 8.3 - - - +
238B THR* 4.2 6.5 - - + +
276B VAL* 4.4 3.3 - - - +
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Residues in contact with ILE 224 (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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164B HIS* 5.6 0.7 - - - +
165B PHE* 4.8 0.2 - - - -
223B VAL* 1.3 75.7 - - - +
225B SER* 1.3 63.0 + - - +
237B LEU* 2.6 44.6 + - + +
238B THR 3.6 5.6 - - - +
239B GLN* 3.6 33.0 - - + +
273B VAL* 3.4 46.9 - - + +
275B ALA 4.0 12.8 - - - +
276B VAL* 3.2 21.8 - - + +
277B GLY 2.9 22.0 + - - +
279B TYR* 3.5 13.5 - - + -
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Residues in contact with SER 225 (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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165B PHE* 4.1 5.6 - - - -
223B VAL* 3.0 10.8 - - - +
224B ILE* 1.3 78.2 + - - +
226B CYS* 1.3 62.5 + - - +
236B VAL* 3.5 0.6 - - - -
237B LEU* 3.0 34.0 + - - -
277B GLY 2.7 24.3 + - - -
278B GLU* 4.3 0.3 - - - -
279B TYR* 3.1 18.6 + - - +
280B LEU* 3.8 26.7 - - - -
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Residues in contact with CYS 226 (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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165B PHE* 3.6 25.5 - - + -
167B PHE* 3.1 32.1 - - + -
177B PHE* 3.7 17.5 - - + -
223B VAL* 4.3 0.4 - - + -
225B SER* 1.3 79.0 - - - +
227B LYS* 1.3 74.2 + - - +
234B LEU* 3.3 40.6 - - - -
235B ILE 3.3 9.4 - - - +
236B VAL* 4.1 1.3 - - + -
280B LEU* 4.5 2.5 - - - +
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Residues in contact with LYS 227 (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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167B PHE* 4.0 6.5 - - + -
226B CYS* 1.3 80.0 + - - +
228B LEU* 1.3 61.1 + - - +
234B LEU* 4.3 1.6 - - - -
235B ILE* 2.9 49.6 + - + +
278B GLU* 5.6 5.4 + - - -
280B LEU* 3.5 39.2 - - + +
281B SER* 4.3 12.2 - - - +
282B LEU* 3.4 32.1 - - + +
287B LEU* 5.1 1.1 - - + -
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Residues in contact with LEU 228 (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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167B PHE* 3.4 21.4 - - + -
168B TYR 4.9 0.4 - - - +
169B VAL* 3.2 43.1 - - + +
227B LYS* 1.3 74.8 - - - +
229B PHE* 1.3 59.6 + - - +
230B HIS 4.3 0.3 + - - -
231B GLU* 3.2 47.7 + - - +
232B ARG 4.1 4.5 - - - +
233B TYR 3.3 20.6 - - - +
234B LEU* 4.1 10.5 - - + -
248B LEU* 4.3 2.7 - - + -
282B LEU* 4.8 8.8 - - - +
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Residues in contact with PHE 229 (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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227B LYS 3.5 0.6 + - - -
228B LEU* 1.3 72.1 - - - +
230B HIS* 1.3 108.7 + + - +
231B GLU* 2.7 5.2 + - - -
232B ARG 2.8 11.8 + - - -
233B TYR* 2.7 42.2 + + + +
235B ILE* 3.1 23.1 - - + -
282B LEU* 3.5 19.5 - - + -
284B ASN 3.5 20.4 - - - -
285B ASN* 4.3 9.9 - - + -
303B LEU* 3.6 35.7 - - + -
304B LEU* 5.6 0.4 - - - -
311B LEU* 4.1 12.6 - - + -
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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