Contacts of the helix formed by residues 191 - 197 (chain F) in PDB entry 4GTU
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 GLU 191 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22F TYR* 5.6 1.2 - - + -
189F GLY 3.2 6.6 + - - -
190F LEU* 1.3 70.4 - - - +
192F LYS* 1.3 75.5 + - + +
194F SER* 3.3 13.0 + - - -
195F ALA* 3.5 12.1 + - - +
22G TYR* 4.4 11.4 + - - -
189G GLY 3.4 15.8 + - - +
190G LEU* 3.4 30.0 - - + +
191G GLU* 3.6 29.9 + - + +
192G LYS 5.1 0.2 + - - -
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Residues in contact with LYS 192 (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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21F GLU* 4.1 9.7 - - - +
22F TYR* 2.9 61.6 - - + +
24F ASP* 3.4 34.0 + - - +
190F LEU 3.5 0.8 - - - -
191F GLU* 1.3 91.7 + - + +
193F ILE* 1.3 61.9 + - - +
195F ALA* 3.6 5.9 + - - +
196F TYR* 3.2 22.0 + - - +
191G GLU* 2.9 30.9 + - - +
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Residues in contact with ILE 193 (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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18F LEU* 4.0 20.9 - - + +
21F GLU* 5.3 0.2 - - + -
22F TYR* 3.6 39.3 - - + +
157F PHE* 4.5 1.6 - - + -
160F TYR* 5.1 0.9 - - + -
187F PHE* 3.7 48.7 - - + +
188F GLU* 4.6 0.7 - - - -
190F LEU* 2.9 15.5 + - + +
192F LYS* 1.3 75.8 - - - +
194F SER* 1.3 65.8 + - - +
196F TYR* 3.8 8.6 - - + +
197F MET* 3.0 49.2 + - + +
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Residues in contact with SER 194 (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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188F GLU 4.0 16.8 + - - -
189F GLY 4.6 4.5 - - - -
190F LEU 2.8 13.2 + - - -
191F GLU* 3.3 11.9 + - - -
193F ILE* 1.3 76.1 - - - +
195F ALA* 1.3 61.2 + - - +
197F MET* 4.2 5.7 - - - +
198F LYS* 3.3 25.6 + - - +
186G ARG* 4.5 16.1 + - - -
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Residues in contact with ALA 195 (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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191F GLU 3.5 7.8 + - - +
192F LYS* 3.9 9.0 - - - +
193F ILE 3.3 0.4 - - - -
194F SER* 1.3 77.9 - - - +
196F TYR* 1.3 65.0 + - - +
198F LYS* 3.1 6.4 + - - -
199F SER* 3.1 25.7 + - - -
201F ARG* 5.5 3.4 - - - +
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Residues in contact with TYR 196 (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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14F HIS* 5.2 3.2 - + - -
17F ARG* 3.8 35.7 + - + +
18F LEU* 4.4 23.3 - - + -
21F GLU* 3.2 53.1 - - + -
27F TYR* 4.1 5.6 - + - -
29F GLU* 4.8 2.3 + - - -
192F LYS 3.2 9.3 + - - +
193F ILE* 3.4 8.9 + - + +
195F ALA* 1.3 80.4 - - - +
197F MET* 1.3 64.7 + - + +
199F SER* 2.8 27.3 + - - -
201F ARG* 3.4 41.0 + - + +
202F PHE* 3.2 30.4 - + - +
203F LEU 4.3 2.9 + - - -
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Residues in contact with MET 197 (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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18F LEU* 5.8 2.5 - - + -
160F TYR* 3.9 22.7 - - - -
188F GLU* 3.7 46.7 - - + +
193F ILE* 3.0 33.8 + - + +
194F SER* 4.3 4.7 - - - +
196F TYR* 1.3 79.5 - - + +
198F LYS* 1.3 62.8 + - + +
199F SER 3.2 3.3 + - - +
202F PHE* 3.2 56.2 - - + +
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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