Contacts of the helix formed by residues 82 - 91 (chain F) in PDB entry 1AOU
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 LEU 82 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F ILE* 4.0 26.2 - - + -
7F TRP* 4.1 7.4 - - + -
33F ILE* 4.5 6.7 - - + -
43F TYR* 3.0 49.1 - - + +
63F ILE* 3.9 17.9 - - + -
71F TYR* 3.0 36.2 - - + +
81F THR* 1.3 82.3 + - - +
83F GLN* 1.3 54.1 + - - +
85F LEU* 3.1 17.7 - - + +
86F VAL* 2.6 40.7 + - - +
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Residues in contact with GLN 83 (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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2F ILE* 3.6 45.1 + - + +
3F GLN* 4.2 15.6 + - - +
7F TRP* 4.4 0.4 - - + -
81F THR* 3.0 4.9 + - - +
82F LEU* 1.3 80.3 - - - +
84F GLN* 1.3 81.9 + - - +
86F VAL* 2.8 24.7 - - + +
87F GLN* 3.0 11.6 + - - +
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Residues in contact with GLN 84 (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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79F PHE* 3.9 8.1 - - + -
80F GLU* 3.2 35.2 - - + +
81F THR* 2.6 42.6 + - + +
82F LEU 3.3 0.2 - - - -
83F GLN* 1.3 98.8 + - - +
85F LEU* 1.3 58.0 + - - +
87F GLN* 3.0 26.9 - - - +
88F HIS* 3.2 6.1 + - - +
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Residues in contact with LEU 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F ILE* 5.6 1.1 - - + -
45F LEU* 5.8 1.3 - - + -
63F ILE* 4.8 11.4 - - + -
71F TYR* 3.8 12.8 - - + -
72F TYR* 5.2 2.2 - - - +
73F ILE* 5.2 6.1 - - + +
79F PHE* 3.6 31.4 - - + +
81F THR 3.2 17.3 + - - +
82F LEU* 3.1 39.9 - - + +
84F GLN* 1.3 75.3 - - - +
86F VAL* 1.3 69.6 + - + +
87F GLN 2.9 4.7 - - - -
88F HIS 4.2 0.2 - - - +
89F TYR* 2.6 66.6 + - + +
100F LEU* 5.5 0.2 - - + -
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Residues in contact with VAL 86 (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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3F GLN* 4.8 3.1 - - - +
7F TRP* 3.2 58.6 - - + +
33F ILE* 4.2 5.8 - - + -
45F LEU* 6.2 0.4 - - + -
82F LEU 2.6 26.8 + - - +
83F GLN* 2.8 36.1 - - + +
85F LEU* 1.3 84.6 - - + +
87F GLN* 1.3 58.5 + - - +
89F TYR* 4.3 0.2 - - - -
90F SER* 3.0 14.9 + - - -
100F LEU* 2.6 33.6 - - + +
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Residues in contact with GLN 87 (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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83F GLN 3.0 13.7 + - - +
84F GLN* 3.0 23.3 - - - +
86F VAL* 1.3 81.9 - - - +
88F HIS* 1.3 59.9 + - - +
90F SER* 3.5 16.8 + - - -
91F GLU* 3.7 20.2 + - - +
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Residues in contact with HIS 88 (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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79F PHE* 3.0 47.7 - + + -
84F GLN 3.2 3.7 + - - +
85F LEU 3.2 2.2 + - - +
87F GLN* 1.3 78.5 - - - +
89F TYR* 1.3 63.2 + + + +
90F SER 3.1 0.4 - - - -
91F GLU* 3.4 2.6 + - - -
92F ARG* 2.9 73.1 + - + +
94F ALA* 5.3 5.6 - - - -
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Residues in contact with TYR 89 (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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45F LEU* 4.7 5.8 - - + -
72F TYR* 4.7 0.3 - - - -
73F ILE* 3.9 27.6 + - + +
74F THR* 4.8 3.4 - - + +
77F ALA* 3.3 24.4 + - - +
79F PHE* 3.3 25.3 - + - -
85F LEU* 2.6 45.8 + - + +
88F HIS* 1.3 78.8 - - + +
90F SER* 1.3 58.4 + - - +
92F ARG 2.3 25.8 - - - +
93F ALA 3.7 0.2 - - - -
94F ALA* 2.8 33.1 + - + +
96F LEU* 3.0 25.4 - - + -
98F SER 4.9 0.4 - - - -
99F ARG* 2.9 21.3 - - - +
100F LEU* 3.1 28.0 - - + +
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Residues in contact with SER 90 (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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86F VAL 3.0 19.9 + - - -
87F GLN* 3.6 13.9 - - - -
88F HIS 3.1 0.4 - - - -
89F TYR* 1.3 79.7 - - - +
91F GLU* 1.3 63.1 + - - +
99F ARG* 2.8 24.9 + - - +
100F LEU* 3.0 23.8 - - - +
101F VAL 4.6 2.3 + - - -
103F PRO* 5.0 17.8 - - - +
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Residues in contact with GLU 91 (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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87F GLN* 3.7 21.7 - - - +
88F HIS* 3.4 3.4 + - - +
89F TYR 3.3 0.2 - - - -
90F SER* 1.3 80.2 - - - +
92F ARG* 1.3 78.3 + - + +
99F ARG* 3.8 13.5 + - - +
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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