Contacts of the helix formed by residues 227 - 235 (chain B) in PDB entry 1FBU
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 ASN 227 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213B PHE* 5.1 2.5 - - + +
225B VAL* 3.9 3.1 - - - -
226B PRO* 1.3 84.0 - - + +
228B ARG* 1.3 64.9 + - - +
229B GLU* 3.0 19.0 + - - +
230B ARG* 2.9 40.9 + - + +
231B PHE* 3.0 22.3 + - - +
272B ASN* 6.1 1.0 - - - +
274B SER* 3.3 11.2 - - - -
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Residues in contact with ARG 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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225B VAL* 3.9 11.8 - - - +
227B ASN* 1.3 71.3 + - - +
229B GLU* 1.3 89.7 + - - +
231B PHE* 3.2 3.8 + - - +
232B VAL* 3.0 27.2 + - + +
245B PHE* 3.6 41.3 - - + -
273B ASP* 3.0 45.8 + - - +
274B SER* 2.7 32.0 + - - +
276B TRP* 3.4 23.9 - - + +
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Residues in contact with GLU 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 ASN* 3.0 8.9 + - - +
228B ARG* 1.3 104.8 + - - +
230B ARG* 1.3 62.5 + - + +
232B VAL* 3.3 6.8 + - - +
233B GLN* 2.8 44.4 + - - +
274B SER* 2.6 28.7 + - - -
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Residues in contact with ARG 230 (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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213B PHE* 3.9 29.1 - - + -
227B ASN* 2.9 39.9 + - + +
229B GLU* 1.3 73.2 - - + +
231B PHE* 1.3 53.4 + - - +
233B GLN* 3.2 25.2 + - - -
234B GLU* 2.8 81.9 + - - +
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Residues in contact with PHE 231 (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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204B MET* 3.8 20.4 - - + -
213B PHE* 3.9 25.9 - - - +
214B ILE* 3.8 22.7 - - + -
225B VAL* 3.7 14.6 - - + -
227B ASN 3.0 13.8 + - - +
228B ARG 3.4 6.3 - - - +
230B ARG* 1.3 77.8 - - - +
232B VAL* 1.3 61.2 + - + +
235B VAL* 2.9 41.4 + - + +
236B LEU* 3.1 27.9 + - + -
245B PHE* 4.1 24.7 - + - -
248B PHE* 3.8 42.0 - + - -
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Residues in contact with VAL 232 (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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228B ARG* 3.0 23.7 + - + +
229B GLU* 3.7 6.7 - - - +
231B PHE* 1.3 77.2 - - + +
233B GLN* 1.3 59.8 + - + +
236B LEU* 3.8 22.1 - - + +
237B PRO* 3.2 24.8 - - - +
243B SER 5.4 2.0 - - - +
244B ASN* 5.3 4.3 - - + -
245B PHE* 3.8 40.4 - - + +
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Residues in contact with GLN 233 (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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229B GLU* 2.8 33.2 + - - +
230B ARG* 3.2 36.4 + - - +
232B VAL* 1.3 83.6 - - + +
234B GLU* 1.3 65.5 + - + +
237B PRO* 3.9 10.9 - - - +
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Residues in contact with GLU 234 (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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213B PHE* 3.8 27.6 - - + -
230B ARG* 2.8 60.2 + - - +
233B GLN* 1.3 80.7 - - - +
235B VAL* 1.3 59.8 + - - +
237B PRO* 4.2 2.5 - - - +
238B LYS* 2.6 40.2 + - - +
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Residues in contact with VAL 235 (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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204B MET* 3.6 38.6 - - + -
210B ASN* 4.0 17.5 - - + +
213B PHE* 3.5 41.3 - - + -
214B ILE* 4.6 1.6 - - + -
231B PHE* 2.9 24.1 + - + +
234B GLU* 1.3 75.7 - - - +
236B LEU* 1.3 66.8 + - - +
237B PRO* 3.3 2.9 - - - -
238B LYS* 3.0 21.9 + - + +
239B TYR* 3.4 13.4 - - + -
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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