Contacts of the helix formed by residues 110 - 115 (chain R) in PDB entry 2QJK
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 THR 110 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88R VAL 6.1 0.4 - - - -
90R LEU* 4.6 12.6 - - + -
108R GLU* 2.5 31.5 + - + +
109R ALA* 1.3 73.4 - - - +
111R ASP* 1.3 55.9 + - - +
112R GLN* 3.4 18.9 + - - +
113R ASN* 2.5 59.3 + - - +
114R ARG* 3.4 4.6 + - - +
161R ARG* 4.1 0.7 - - - +
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Residues in contact with ASP 111 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77R ARG* 2.9 38.0 + - - -
82R ILE 3.7 2.4 - - - +
85R GLY* 3.0 37.9 + - - +
86R ARG* 3.1 38.8 + - + +
110R THR* 1.3 70.9 - - - +
112R GLN* 1.3 63.6 + - - +
114R ARG* 3.4 18.1 + - - +
115R THR* 3.8 9.5 + - - +
159R ALA* 4.4 2.5 - - - +
161R ARG* 3.2 15.0 - - - +
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Residues in contact with GLN 112 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86R ARG* 3.5 47.9 + - - +
110R THR* 2.7 28.2 + - - +
111R ASP* 1.3 82.1 - - - +
113R ASN* 1.3 60.1 + - - +
114R ARG 3.2 1.4 + - - -
115R THR* 3.7 17.8 + - - +
117R ASP 4.9 0.2 - - - +
118R GLU* 4.9 9.5 - - - +
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Residues in contact with ASN 113 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98R ALA* 4.0 9.2 - - + +
100R ASN* 3.1 22.5 + - - +
103R ILE* 3.7 27.2 - - + +
107R ALA* 4.2 3.4 - - - +
108R GLU* 2.9 41.2 + - - +
110R THR* 2.5 27.3 + - - +
112R GLN* 1.3 74.5 - - - +
114R ARG* 1.3 58.0 + - - -
115R THR 3.6 1.6 - - - -
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Residues in contact with ARG 114 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98R ALA* 2.5 47.7 + - - +
99R ARG* 3.9 1.4 - - - +
100R ASN* 4.6 0.8 + - - -
109R ALA* 4.5 4.0 - - - +
110R THR 3.7 15.5 - - - +
111R ASP 3.8 7.9 - - - +
112R GLN 3.2 1.2 - - - -
113R ASN* 1.3 82.1 - - - +
115R THR* 1.3 63.5 + - + +
123R LEU* 3.5 16.1 - - + +
124R VAL 4.7 2.4 + - - +
125R MET* 4.7 3.8 - - - +
159R ALA* 3.0 30.4 + - + +
160R GLY* 2.8 30.3 + - - -
161R ARG* 3.9 18.6 - - - +
170R ASN* 3.7 14.8 - - - +
171R LEU* 3.0 28.2 + - - +
173R ILE* 3.3 33.2 - - - +
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Residues in contact with THR 115 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77R ARG* 2.9 38.8 - - - +
86R ARG* 4.9 0.3 + - - -
100R ASN* 4.5 8.6 + - - -
111R ASP 3.8 8.1 + - - +
112R GLN* 3.7 17.7 + - - +
113R ASN 4.5 0.9 - - - -
114R ARG* 1.3 86.3 + - + +
116R LEU* 1.3 64.0 - - - +
117R ASP* 2.9 24.2 + - - +
118R GLU* 5.8 0.2 - - - +
120R GLY* 3.3 20.3 - - - +
122R TRP 3.7 11.4 - - - +
123R LEU* 4.6 5.4 - - + -
124R VAL 6.0 0.2 - - - -
173R ILE* 6.4 0.4 - - - -
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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