Contacts of the helix formed by residues 227 - 235 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A PHE* 5.1 2.0 + - - +
225A VAL* 3.3 3.5 - - - +
226A PRO* 1.3 83.8 - - + +
228A ARG* 1.3 64.1 + - - +
229A GLU* 3.1 19.4 + - - +
230A ARG* 3.0 40.9 + - + +
231A PHE* 3.0 22.3 + - - +
274A SER* 3.4 9.9 - - - -
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Residues in contact with ARG 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A VAL* 4.0 11.6 - - - +
227A ASN* 1.3 71.3 + - - +
229A GLU* 1.3 85.0 + - + +
231A PHE* 3.2 2.8 + - - +
232A VAL* 3.0 36.5 + - + +
245A PHE* 3.6 40.8 - - + -
273A ASP* 2.9 49.2 + - - +
274A SER* 2.7 29.6 + - - +
276A TRP* 3.4 23.8 - - + +
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Residues in contact with GLU 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ASN* 3.1 8.2 + - - +
228A ARG* 1.3 106.4 + - + +
230A ARG* 1.3 63.7 + - + +
232A VAL* 3.4 6.6 + - - +
233A GLN* 3.0 43.7 + - - +
274A SER* 2.6 28.9 + - - -
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Residues in contact with ARG 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A LYS* 5.3 10.0 - - - +
213A PHE* 4.1 27.0 - - + -
227A ASN* 3.0 37.0 + - + +
229A GLU* 1.3 76.7 - - + +
231A PHE* 1.3 58.2 + - - +
233A GLN* 3.0 30.1 + - - +
234A GLU* 2.8 77.1 + - - +
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Residues in contact with PHE 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A MET* 3.8 25.1 - - + -
213A PHE* 3.9 25.7 - - + +
214A ILE* 3.9 16.6 - - + -
225A VAL* 3.6 15.9 - - + -
227A ASN 3.0 13.3 + - - +
228A ARG 3.2 6.7 + - - +
230A ARG* 1.3 77.1 - - - +
232A VAL* 1.3 64.0 + - + +
235A VAL* 3.0 36.7 + - + +
236A LEU* 3.1 28.2 + - + -
245A PHE* 4.0 25.1 - + - -
248A PHE* 3.7 43.3 - + - -
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Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ARG* 3.0 24.8 + - + +
229A GLU* 3.8 6.5 - - - +
231A PHE* 1.3 76.7 - - + +
233A GLN* 1.3 58.9 + - + +
236A LEU* 3.8 21.5 - - + +
237A PRO* 3.1 26.2 - - - +
243A SER 5.5 1.8 - - - +
244A ASN* 5.2 4.5 - - + -
245A PHE* 3.8 41.3 - - + +
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Residues in contact with GLN 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A GLU* 3.0 42.6 + - - +
230A ARG* 3.0 29.9 + - - +
232A VAL* 1.3 81.3 - - + +
234A GLU* 1.3 70.3 + - - +
237A PRO* 3.6 12.7 - - - +
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Residues in contact with GLU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A PHE* 3.9 25.5 - - + -
230A ARG* 2.8 59.1 + - - +
233A GLN* 1.3 81.9 - - - +
235A VAL* 1.3 59.8 + - + +
237A PRO* 4.2 1.9 - - - +
238A LYS* 3.2 35.2 + - - +
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Residues in contact with VAL 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A MET* 3.6 37.5 - - + -
210A ASN* 4.1 15.3 - - + +
213A PHE* 3.5 45.1 - - + -
214A ILE* 4.9 1.1 - - + -
231A PHE* 3.0 17.6 + - + +
234A GLU* 1.3 76.0 - - - +
236A LEU* 1.3 69.0 + - - +
237A PRO* 3.3 2.9 - - - -
238A LYS* 2.9 23.4 + - + +
239A TYR* 3.5 16.7 - - + -
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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