Contacts of the helix formed by residues 110 - 115 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90F LEU* 4.6 10.5 - - + -
108F GLU* 2.4 41.0 + - + +
109F ALA 1.3 68.8 - - - -
111F ASP* 1.3 54.3 + - - +
112F GLN* 2.8 23.5 + - - +
113F ASN* 2.5 56.7 + - - +
114F ARG* 3.5 3.3 + - - +
161F ARG* 4.1 0.4 - - - +
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Residues in contact with ASP 111 (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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77F ARG* 2.7 43.6 + - - -
82F ILE 3.9 4.7 - - - +
85F GLY* 3.6 33.6 + - - +
86F ARG* 3.4 30.3 + - + +
110F THR* 1.3 68.8 - - - +
112F GLN* 1.3 67.0 + - - +
114F ARG* 3.1 19.4 + - - +
115F THR* 3.6 9.6 + - - +
159F ALA* 4.6 3.4 - - + -
161F ARG* 3.2 14.8 - - - +
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Residues in contact with GLN 112 (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 ARG* 3.6 43.8 + - - +
110F THR* 2.6 31.7 + - - +
111F ASP* 1.3 82.7 + - - +
113F ASN* 1.3 60.4 + - - +
114F ARG 3.2 1.1 + - - -
115F THR* 3.6 18.7 + - - +
118F GLU* 4.1 19.9 - - - +
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Residues in contact with ASN 113 (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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98F ALA* 4.0 7.3 - - + +
100F ASN* 3.0 26.2 + - - +
103F ILE* 3.7 26.8 - - + +
107F ALA* 4.0 3.2 - - - +
108F GLU* 2.7 43.6 + - - +
110F THR* 2.5 28.2 + - - +
112F GLN* 1.3 73.9 - - - +
114F ARG* 1.3 59.0 + - - -
115F THR 3.6 2.2 - - - -
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Residues in contact with ARG 114 (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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98F ALA* 2.7 44.0 + - - +
99F ARG* 4.0 0.8 - - - +
100F ASN* 4.6 0.2 + - - -
109F ALA* 4.6 4.5 - - - +
110F THR 3.7 11.7 - - - +
111F ASP* 3.1 12.4 + - - +
113F ASN* 1.3 81.9 - - - +
115F THR* 1.3 64.9 + - + +
123F LEU* 3.4 16.3 - - + +
124F VAL 4.7 2.9 + - - +
125F MET* 3.9 8.5 - - - -
159F ALA* 2.9 36.8 + - + +
160F GLY* 2.8 31.7 + - - -
161F ARG* 3.9 14.5 - - - +
170F ASN* 3.7 14.2 - - - +
171F LEU 2.9 27.1 + - - +
173F ILE* 3.3 32.1 - - - +
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Residues in contact with THR 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F ARG* 3.0 37.5 - - - +
86F ARG* 4.9 0.9 + - - -
100F ASN* 4.4 10.2 + - - -
111F ASP* 3.8 8.8 + - - +
112F GLN* 3.6 16.8 + - - +
113F ASN 3.6 0.9 - - - -
114F ARG* 1.3 86.2 + - + +
116F LEU* 1.3 65.3 + - - +
117F ASP* 2.9 30.0 + - - +
120F GLY* 3.5 13.9 - - - +
122F TRP 3.7 11.0 - - - +
123F LEU* 4.6 5.4 - - + -
124F VAL 5.6 0.4 - - - +
173F ILE* 6.4 0.9 - - - -
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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