Contacts of the helix formed by residues 190 - 198 (chain B) in PDB entry 3FZ7
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 ASP 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180B ILE* 5.0 0.2 - - - +
183B ARG* 4.9 1.0 + - - -
186B GLN* 3.4 30.2 + - + +
188B PHE* 3.3 8.6 + - + +
189B MET* 1.3 73.4 - - - +
191B PRO* 1.4 68.7 - - + +
192B LYS* 3.7 11.3 + - - +
193B ARG* 2.7 61.9 + - - +
194B MET* 2.9 27.7 + - - +
223B LEU* 4.0 2.2 - - - -
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Residues in contact with PRO 191 (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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190B ASP* 1.4 85.4 - - + +
192B LYS* 1.3 68.2 + - - +
194B MET* 3.1 6.2 + - + +
195B ILE* 2.8 29.8 + - - +
222B PRO* 4.2 23.8 - - + +
223B LEU* 3.6 23.3 - - + -
226B ALA* 4.0 20.0 - - + -
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Residues in contact with LYS 192 (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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190B ASP* 3.4 10.8 + - - +
191B PRO* 1.3 81.5 - - - +
193B ARG* 1.3 60.7 + - + +
195B ILE* 3.2 4.9 + - - +
196B GLU* 3.0 53.6 + - - +
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Residues in contact with ARG 193 (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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180B ILE* 3.3 32.1 - - + +
181B PRO* 2.3 42.4 + - - +
183B ARG* 3.3 46.4 - - - +
186B GLN* 3.0 19.4 + - - +
188B PHE 3.3 16.4 + - - -
190B ASP* 2.7 44.5 + - - +
192B LYS* 1.3 76.7 - - + +
194B MET* 1.3 68.6 + - - +
196B GLU* 3.6 18.2 + - + +
197B ALA* 3.3 19.1 + - - +
414B GLU* 5.5 0.2 + - - -
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Residues in contact with MET 194 (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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158B VAL* 3.8 15.7 - - + +
180B ILE* 4.2 1.7 - - - +
189B MET* 3.8 24.0 - - + +
190B ASP 2.9 15.7 + - - +
191B PRO* 3.4 8.1 - - + +
193B ARG* 1.3 75.9 - - - +
195B ILE* 1.3 78.5 + - + +
197B ALA* 3.0 15.2 + - - +
198B CYS* 3.3 16.1 + - - -
205B VAL* 3.6 30.3 - - + -
223B LEU* 3.4 44.4 - - - +
226B ALA* 3.8 8.1 - - + -
227B LEU* 3.6 20.9 - - + -
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Residues in contact with ILE 195 (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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191B PRO 2.8 22.3 + - - +
192B LYS* 3.8 4.3 - - - +
194B MET* 1.3 76.3 - - + +
196B GLU* 1.3 56.5 + - - +
198B CYS* 2.8 32.9 + - - +
226B ALA* 3.4 36.8 - - + +
227B LEU* 3.6 26.7 - - + -
230B PHE* 3.6 35.4 - - + -
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Residues in contact with GLU 196 (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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192B LYS* 3.0 50.2 + - - +
193B ARG* 3.8 19.6 - - + +
195B ILE* 1.3 76.6 - - - +
197B ALA* 1.3 59.3 + - - +
198B CYS 4.6 2.1 - - - +
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Residues in contact with ALA 197 (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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158B VAL* 3.7 16.8 - - + +
178B ARG* 2.9 45.0 + - + +
180B ILE* 4.0 16.6 - - + -
193B ARG 3.3 10.7 + - - +
194B MET 3.0 11.7 + - - +
196B GLU* 1.3 75.9 - - - +
198B CYS* 1.3 59.3 + - - +
199B ASP 3.8 0.3 + - - -
202B THR* 4.0 0.3 + - - -
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Residues in contact with CYS 198 (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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158B VAL* 3.9 15.9 - - - -
178B ARG* 5.0 0.2 + - - -
194B MET* 3.3 20.2 + - - -
195B ILE* 2.8 24.5 + - - +
196B GLU 4.6 2.1 - - - +
197B ALA* 1.3 72.5 - - - +
199B ASP* 1.3 65.2 + - - +
202B THR* 3.4 4.0 - - - -
205B VAL* 4.0 21.8 - - - -
227B LEU* 4.3 10.1 - - - -
230B PHE* 3.8 20.7 - - + -
238B ILE* 3.8 21.5 - - + -
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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