Contacts of the helix formed by residues 208 - 213 (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 TRP 208 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B ASN* 1.3 73.5 - - - +
209B ILE* 1.3 71.0 + - + +
211B TYR* 3.3 3.6 + - - +
212B LYS* 3.0 24.8 + - + +
230B ASN* 5.1 1.2 + - - -
270B GLU* 3.1 28.4 + - + +
273B LYS* 3.7 42.4 - - + -
274B TYR* 3.7 30.2 - + - -
312B PHE* 3.2 37.9 - + + -
313B SER* 4.4 0.2 - - - -
314B THR* 3.4 26.7 + - + +
316B ASP* 2.9 19.1 + - - +
317B ASN* 3.2 34.6 - - + +
319B ASN* 3.9 5.6 - - - -
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Residues in contact with ILE 209 (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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207B ASN* 3.2 12.3 + - - +
208B TRP* 1.3 84.6 - - + +
210B GLN* 1.3 59.7 + - + +
212B LYS* 3.1 11.6 + - + +
213B GLU* 2.9 56.6 + - + +
316B ASP* 5.9 0.7 - - - +
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Residues in contact with GLN 210 (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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294A ASP* 2.8 39.1 + - - +
296A GLY* 3.3 19.0 - - - -
206B LYS* 3.1 34.8 - - + +
207B ASN* 2.8 41.8 + - - +
209B ILE* 1.3 79.1 - - + +
211B TYR* 1.3 55.5 + - - +
213B GLU* 4.9 2.2 - - - -
214B GLY* 2.7 40.4 + - - +
215B PHE* 3.9 7.8 - - + -
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Residues in contact with TYR 211 (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 PHE* 2.7 45.9 + - - +
206B LYS* 3.6 32.8 - - + -
207B ASN 3.0 14.1 + - - +
208B TRP 3.7 4.9 - - - +
210B GLN* 1.3 76.6 - - - +
212B LYS* 1.3 57.6 + - - +
214B GLY 4.3 0.2 - - - -
215B PHE* 3.6 16.2 - + - -
227B TRP* 3.0 36.1 + + - -
230B ASN* 2.9 25.5 + - - +
312B PHE* 3.5 27.8 - + + -
314B THR* 3.8 10.3 - - + -
333B GLY* 3.3 25.2 + - - -
345B ASN* 3.5 22.7 + - - -
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Residues in contact with LYS 212 (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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208B TRP* 3.0 15.1 + - + +
209B ILE* 3.2 18.4 - - + +
210B GLN 3.0 0.2 - - - -
211B TYR* 1.3 78.5 - - - +
213B GLU* 1.3 75.7 + - - +
229B GLY* 3.4 3.5 - - - -
230B ASN* 3.1 12.9 + - - +
231B GLU* 3.1 40.8 + - + +
232B LYS* 4.5 1.2 + - - +
270B GLU* 3.3 29.9 + - - +
274B TYR* 3.3 31.6 - - + +
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Residues in contact with GLU 213 (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* 5.5 3.7 - - - +
209B ILE* 2.9 37.8 + - + +
210B GLN* 4.2 2.2 - - - +
212B LYS* 1.3 96.8 - - + +
214B GLY* 1.3 62.9 + - - +
228B LEU 3.3 10.9 - - - +
229B GLY* 3.9 1.5 - - - -
231B GLU* 5.2 3.5 - - - +
232B LYS* 4.0 17.0 + - - +
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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