Contacts of the helix formed by residues 230 - 237 (chain B) in PDB entry 1FIC
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 230 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B TRP* 5.0 3.6 + - - -
211B TYR* 2.9 24.8 + - - +
212B LYS* 3.1 3.8 + - - +
227B TRP* 3.2 27.3 + - - -
229B GLY* 1.3 71.4 - - - -
231B GLU* 1.3 64.6 + - - +
233B ILE* 3.8 7.1 - - - +
234B HIS* 3.0 25.3 + - - +
267B VAL* 4.4 3.5 - - + +
274B TYR* 3.4 46.0 - - + -
312B PHE* 3.4 32.2 - - - -
335B TRP* 5.1 2.4 - - - -
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Residues in contact with GLU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B LYS* 3.1 28.6 + - + +
213B GLU* 5.2 3.8 - - - +
230B ASN* 1.3 78.6 - - - +
232B LYS* 1.3 62.0 + - + +
234B HIS* 3.4 10.8 + - - +
235B LEU* 3.0 55.2 + - + +
270B GLU* 4.6 5.9 + - - +
274B TYR* 2.7 37.2 + - - +
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Residues in contact with LYS 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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402A LEU* 5.3 10.5 - - - +
178B PHE* 3.9 52.8 - - + +
179B LEU 5.3 2.0 + - - -
212B LYS 5.4 0.7 - - - +
213B GLU* 4.0 17.5 + - - +
228B LEU* 3.5 35.7 + - + +
229B GLY 3.2 8.1 + - - +
231B GLU* 1.3 81.2 - - + +
233B ILE* 1.3 62.0 + - - +
235B LEU* 3.4 8.3 + - + +
236B ILE* 2.9 34.7 + - - +
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Residues in contact with ILE 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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194B PHE* 3.3 61.0 - - + +
227B TRP* 3.8 28.3 - - + -
228B LEU* 4.4 4.9 - - + -
229B GLY 3.0 22.1 + - - +
230B ASN* 3.2 7.2 + - - +
232B LYS* 1.3 77.2 - - - +
234B HIS* 1.3 58.7 + - - +
236B ILE* 4.3 6.1 - - - +
237B SER* 2.8 28.8 + - - -
265B PHE* 4.2 4.7 - - + -
267B VAL* 3.5 26.9 - - + -
335B TRP* 5.7 1.1 - - + -
386B ILE* 5.2 2.4 - - + +
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Residues in contact with HIS 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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230B ASN 3.0 16.9 + - - +
231B GLU* 3.6 15.7 - - - +
233B ILE* 1.3 78.0 - - - +
235B LEU* 1.3 79.7 + - + +
237B SER* 3.3 4.6 + - - -
238B THR* 2.8 54.1 + - + -
267B VAL* 2.6 28.0 + - + +
268B GLY 3.3 12.1 - - - +
269B PRO* 3.4 39.0 - - + +
274B TYR* 4.3 3.6 - - + -
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Residues in contact with LEU 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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171B PRO* 3.8 16.5 - - + +
173B LYS* 4.3 27.0 + - + +
174B ALA* 4.2 22.4 - - + -
175B ASN* 5.4 2.9 - - - +
178B PHE* 4.8 9.2 - - + -
231B GLU* 3.0 42.3 + - + +
232B LYS* 3.4 7.4 + - + +
234B HIS* 1.3 87.1 - - + +
236B ILE* 1.3 62.1 + - - +
238B THR* 4.2 2.8 - - - +
239B GLN* 3.4 24.3 + - - +
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Residues in contact with ILE 236 (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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151B LYS 4.7 1.1 - - - +
152B ASP* 4.3 12.3 - - + -
169B ILE* 4.1 12.6 - - + -
171B PRO* 4.2 3.8 - - + -
178B PHE* 4.1 15.3 - - + -
192B THR* 4.0 17.9 - - + -
194B PHE* 6.0 1.6 - - + -
228B LEU* 3.9 26.2 - - + -
232B LYS 2.9 18.8 + - - +
233B ILE* 4.3 4.0 - - - +
235B LEU* 1.3 77.7 - - - +
237B SER* 1.3 60.2 + - - +
238B THR 3.3 1.0 + - - -
239B GLN* 3.3 18.9 - - - +
244B TYR* 3.1 39.1 + - + +
386B ILE* 3.8 21.8 - - + -
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Residues in contact with SER 237 (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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233B ILE 2.8 20.6 + - - -
234B HIS* 3.3 6.1 + - - -
236B ILE* 1.3 78.7 - - - +
238B THR* 1.3 61.7 + - - +
239B GLN 3.7 0.2 - - - -
242B ILE 5.0 1.9 - - - +
243B PRO* 5.7 0.9 - - - +
244B TYR* 3.6 23.3 + - - -
265B PHE* 4.0 19.6 - - - +
266B LYS* 3.9 25.0 - - - +
267B VAL 3.2 20.2 + - - -
386B ILE* 4.7 4.9 - - - -
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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