Contacts of the helix formed by residues 208 - 213 (chain F) in PDB entry 1FZB
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207F ASN* 1.3 75.5 - - - +
209F ILE* 1.3 67.5 + - + +
211F TYR* 3.0 5.0 + - - +
212F LYS* 2.8 37.5 + - + +
230F ASN* 4.9 1.3 - - - +
270F GLU* 2.8 33.4 + - + +
273F LYS* 4.1 24.2 - - + -
274F TYR* 3.7 35.5 - + - -
312F PHE* 3.6 41.3 - + + -
313F SER 4.5 0.7 - - - -
314F THR* 3.4 17.9 + - + +
316F ASP* 3.0 21.8 + - - +
317F ASN* 3.2 40.1 - - + +
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Residues in contact with ILE 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216E ARG 3.7 22.9 - - - +
217E LYS* 3.9 5.6 - - - -
218E GLY* 3.8 15.3 - - - +
207F ASN* 3.4 23.3 - - - +
208F TRP* 1.3 84.4 - - + +
210F GLN* 1.3 53.6 + - - +
212F LYS* 2.8 14.1 + - + +
213F GLU* 2.8 38.2 + - + +
316F ASP* 3.8 13.5 - - - +
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Residues in contact with GLN 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217E LYS 5.0 0.9 - - - -
218E GLY* 3.1 28.7 + - - +
220E GLU* 2.7 40.9 + - - +
206F LYS* 3.2 32.9 - - + +
207F ASN* 2.8 47.1 + - - +
209F ILE* 1.3 76.9 - - + +
211F TYR* 1.3 56.1 + - - +
213F GLU 4.7 0.2 - - - +
214F GLY 3.0 28.3 + - - +
215F PHE* 3.4 18.5 - - + +
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Residues in contact with TYR 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204F PHE* 2.5 49.2 + - - +
206F LYS* 3.1 38.1 - - + -
207F ASN 2.9 13.8 + - - +
208F TRP* 3.4 4.5 - - + +
210F GLN* 1.3 74.6 - - - +
212F LYS* 1.3 58.6 + - - +
214F GLY 4.3 0.7 - - - -
215F PHE* 3.4 16.6 - + - -
227F TRP* 3.3 22.6 + + - -
229F GLY* 3.6 0.5 - - - -
230F ASN* 2.9 32.3 + - - +
312F PHE* 3.5 30.3 - + + -
314F THR* 4.0 7.9 - - + -
333F GLY 3.4 21.2 + - - -
345F ASN* 3.1 27.1 + - - +
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Residues in contact with LYS 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208F TRP* 2.8 16.4 + - + +
209F ILE* 3.3 14.4 - - + +
211F TYR* 1.3 80.6 - - - +
213F GLU* 1.3 80.1 + - + +
214F GLY 3.5 0.2 - - - -
229F GLY 3.4 2.6 - - - -
230F ASN* 3.4 10.6 + - - +
231F GLU* 3.1 37.2 + - + +
232F LYS* 4.5 0.5 + - - +
270F GLU* 2.9 32.6 + - - +
274F TYR* 3.2 33.9 - - + +
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Residues in contact with GLU 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205E VAL* 4.1 0.7 - - - +
206E VAL* 4.3 10.2 - - + -
217E LYS* 3.2 69.7 + - + +
209F ILE* 2.8 21.9 + - + +
210F GLN 4.7 0.4 - - - +
212F LYS* 1.3 100.1 + - + +
214F GLY* 1.3 61.3 + - - +
229F GLY* 3.9 3.1 - - - -
231F GLU* 5.1 7.1 - - - +
232F LYS* 3.5 30.9 + - - +
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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