Contacts of the helix formed by residues 83 - 91 (chain F) in PDB entry 1O9R
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 SER 83 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34E LEU* 4.6 6.3 - - - -
35E VAL* 5.6 3.1 - - - +
38E GLN* 3.3 23.0 - - - +
96E TYR* 4.5 15.5 + - - -
98E THR* 4.2 13.0 - - - +
81F LEU 3.8 1.2 - - - -
82F GLY* 1.3 80.5 - - - +
84F LEU* 1.3 65.0 + - - +
85F GLN* 3.6 15.5 + - - +
86F ALA* 3.1 20.1 + - - +
87F VAL* 2.9 21.8 + - - +
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Residues in contact with LEU 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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31E ASP* 3.7 32.3 + - - +
34E LEU* 4.0 22.9 - - + +
35E VAL* 6.1 0.2 - - - +
84E LEU* 3.7 26.2 - - + +
87E VAL* 3.7 29.4 - - + -
88E SER* 3.8 21.8 - - - +
91E THR* 3.8 18.4 - - + -
34F LEU* 5.5 0.9 - - + -
82F GLY 3.9 0.2 + - - -
83F SER* 1.3 72.2 - - - +
85F GLN* 1.3 75.7 + - - +
87F VAL* 3.4 3.4 + - - +
88F SER* 2.9 32.9 + - - -
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Residues in contact with GLN 85 (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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31E ASP* 5.1 4.0 + - - +
91E THR* 5.5 1.4 - - - +
93E LEU 5.1 2.1 - - - +
94E LYS 5.0 0.3 - - - -
95E ALA* 3.4 43.6 + - + +
96E TYR* 3.9 6.9 + - - +
83F SER* 3.9 11.7 + - - +
84F LEU* 1.3 99.0 - - + +
86F ALA* 1.3 66.6 + - - +
88F SER* 3.3 6.0 + - - -
89F SER* 3.0 25.3 + - - -
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Residues in contact with ALA 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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98E THR* 5.4 2.0 - - + -
27F ALA* 4.9 1.3 - - - -
81F LEU* 3.8 42.6 - - + +
83F SER* 3.1 19.2 + - - +
85F GLN* 1.3 78.7 - - - +
87F VAL* 1.3 63.5 + - - +
89F SER* 3.3 6.8 + - - -
90F THR* 3.0 31.6 + - - +
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Residues in contact with VAL 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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34E LEU* 5.4 1.3 - - + -
84E LEU* 3.8 26.0 - - + -
27F ALA* 3.5 31.0 - - + +
30F ILE* 3.9 28.9 - - + -
31F ASP* 4.0 13.7 - - + +
34F LEU* 5.4 0.2 - - + -
81F LEU 4.9 0.4 - - - +
82F GLY* 3.8 17.0 - - - +
83F SER 2.9 20.2 + - - +
84F LEU* 3.8 5.4 - - - +
86F ALA* 1.3 77.0 - - - +
88F SER* 1.4 59.1 + - - +
91F THR* 2.9 31.5 + - - -
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Residues in contact with SER 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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84E LEU* 3.5 21.4 - - - +
88E SER* 3.4 20.8 + - - -
84F LEU 2.9 19.6 + - - -
85F GLN* 3.7 7.2 - - - -
86F ALA 3.3 0.2 - - - -
87F VAL* 1.4 79.4 - - - +
89F SER* 1.3 60.9 + - - +
91F THR* 4.1 9.5 - - - +
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Residues in contact with SER 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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85F GLN 3.0 14.2 + - - -
86F ALA* 3.3 14.2 + - - -
88F SER* 1.3 78.2 - - - +
90F THR* 1.4 63.9 + - - +
91F THR 5.1 0.6 - - - +
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Residues in contact with THR 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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23F ASN* 4.1 4.3 - - + +
24F GLU* 3.9 28.0 - - + +
27F ALA* 3.6 19.1 - - + +
28F SER* 4.6 1.0 + - - -
86F ALA* 3.0 18.5 + - - +
89F SER* 1.4 84.0 + - - +
91F THR* 1.3 68.7 + - - +
92F LYS* 3.5 14.7 + - - +
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Residues in contact with THR 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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84E LEU* 3.8 12.3 - - + -
85E GLN* 5.5 1.3 - - - +
27F ALA* 3.8 8.6 - - - +
28F SER* 3.7 9.2 + - - -
31F ASP* 2.6 42.2 + - - +
87F VAL 2.9 19.7 + - - +
88F SER 4.1 9.2 - - - +
89F SER 5.1 0.5 - - - +
90F THR* 1.3 80.9 - - - +
92F LYS* 1.3 64.5 + - - +
93F LEU* 3.1 17.3 + - - +
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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