Contacts of the helix formed by residues 169 - 177 (chain F) in PDB entry 5O6I
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 169 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146F GLY 3.4 12.7 - - - +
147F VAL* 3.9 17.3 - - + -
148F ARG* 2.8 67.4 + - - +
165F ILE* 5.3 0.7 - - + -
166F SER* 2.9 12.9 + - - +
168F ARG* 1.3 82.9 - - - +
170F ARG* 1.3 62.4 + - - +
171F ILE 3.3 2.9 - - - -
172F LYS* 3.2 9.4 + - + +
173F PHE* 3.0 23.0 + - - +
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Residues in contact with ARG 170 (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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122F LEU* 2.7 28.9 + - - +
123F LYS* 3.0 29.1 + - - +
125F LEU* 4.0 21.1 - - + +
167F LEU* 3.1 45.0 + - - +
168F ARG 3.4 1.8 + - - -
169F ASP* 1.3 75.7 - - - +
171F ILE* 1.3 72.8 + - + +
173F PHE* 3.3 1.2 + - - +
174F VAL* 3.0 34.2 + - + +
4G T 5.3 3.8 + - - -
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Residues in contact with ILE 171 (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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169F ASP 3.3 0.2 - - - -
170F ARG* 1.3 85.4 - - + +
172F LYS* 1.3 64.5 + - - +
174F VAL* 5.0 2.2 - - - -
175F HIS* 3.0 34.7 + - + +
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Residues in contact with LYS 172 (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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145F LEU* 3.2 28.8 + - + +
146F GLY* 4.4 6.1 - - - +
147F VAL* 3.5 18.5 - - + +
169F ASP* 3.2 17.4 + - + +
171F ILE* 1.3 79.9 - - - +
173F PHE* 1.3 59.1 + - - +
175F HIS* 5.2 0.4 - - - -
176F THR* 2.9 62.3 + - - +
177F ILE* 5.2 0.2 - - - +
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Residues in contact with PHE 173 (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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110F ILE* 4.1 24.7 - - + -
114F TYR* 3.6 35.0 - + + -
125F LEU* 3.8 20.9 - - + -
127F ILE* 5.0 0.2 - - + -
142F LEU* 4.2 12.3 - - + -
147F VAL* 3.6 13.2 - - + +
165F ILE* 4.0 30.5 - - + -
169F ASP 3.0 15.6 + - - +
170F ARG 3.9 2.0 - - - +
172F LYS* 1.3 76.7 - - - +
174F VAL* 1.3 68.1 + - + +
176F THR* 5.1 0.2 - - - -
177F ILE* 3.1 40.1 + - + +
178F LEU* 3.4 36.9 + - + -
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Residues in contact with VAL 174 (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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122F LEU* 4.5 18.8 - - + -
125F LEU* 4.4 12.8 - - + -
170F ARG* 3.0 27.9 + - + +
171F ILE* 4.4 2.2 - - - +
173F PHE* 1.3 85.9 - - + +
175F HIS* 1.3 59.7 + - - +
178F LEU* 3.1 23.2 + - + -
179F SER* 2.4 50.4 + - - +
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Residues in contact with HIS 175 (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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16C T 4.8 0.8 + - - -
17C T 3.2 36.6 + - - -
18C C 5.8 0.4 + - - -
171F ILE* 3.0 26.3 + - + +
172F LYS* 5.2 0.4 - - - -
174F VAL* 1.3 79.5 - - + +
176F THR* 1.3 66.2 + - - +
179F SER* 3.5 32.0 + - - +
180F SER* 3.9 2.8 + - - -
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Residues in contact with THR 176 (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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107F ILE* 3.7 27.6 - - + +
145F LEU* 5.0 11.0 - - + -
172F LYS* 2.9 50.5 + - - +
175F HIS* 1.3 82.0 + - - +
177F ILE* 1.3 64.4 + - + +
180F SER* 3.2 17.4 - - - -
182F LEU* 5.1 1.2 - - - +
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Residues in contact with ILE 177 (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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107F ILE* 3.6 34.5 - - + +
110F ILE* 3.8 26.2 - - + +
111F LYS* 3.2 29.6 - - - +
142F LEU* 3.7 30.5 - - + -
145F LEU* 3.9 17.7 - - + -
147F VAL* 5.3 1.6 - - + -
173F PHE* 3.1 24.3 + - + +
176F THR* 1.3 91.9 - - + +
178F LEU* 1.3 67.0 + - + +
179F SER 3.7 0.2 - - - -
180F SER* 3.3 8.2 + - - -
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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