Contacts of the helix formed by residues 82 - 88 (chain C) in PDB entry 2QJ9
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 GLY 82 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A ASN* 3.4 20.7 + - - -
62A ILE* 3.8 15.1 - - - +
103B TYR* 6.2 1.4 - - - -
80C TYR 3.3 1.0 + - - -
81C GLU* 1.3 72.4 - - - +
83C SER* 1.3 64.8 + - - +
84C ASP* 3.2 9.0 + - - -
85C PHE* 3.3 25.1 + - - +
86C GLN* 3.4 14.4 + - - +
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Residues in contact with SER 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C HIS* 2.9 40.7 + - - -
78C MET* 3.6 16.2 - - - -
79C LYS 3.4 11.7 - - - -
80C TYR* 2.9 23.3 + - - -
81C GLU 3.2 1.8 + - - -
82C GLY* 1.3 77.6 - - - +
84C ASP* 1.3 61.4 + - - +
86C GLN* 2.9 3.3 + - - -
87C CYS* 2.8 33.1 + - - +
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Residues in contact with ASP 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B TRP* 3.9 23.3 - - + -
91B TYR* 4.6 6.9 - - - -
101B LYS* 3.8 15.6 + - - -
103B TYR* 3.6 25.2 + - - -
80C TYR 4.8 1.4 - - - +
82C GLY* 3.8 7.3 + - - -
83C SER* 1.3 82.6 + - - +
85C PHE* 1.3 63.0 + - - +
86C GLN 3.3 0.3 + - - -
87C CYS* 4.6 2.7 - - - +
88C ARG* 2.9 50.5 + - - +
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Residues in contact with PHE 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ASN* 4.0 17.5 - - - -
62A ILE* 3.9 21.5 - - + -
63A VAL* 4.2 11.4 - - + -
66A LEU* 3.6 23.8 - - + +
23B PHE* 5.4 0.4 - + - -
28B TRP* 3.4 44.7 + + - +
31B TRP* 3.8 21.3 - + - -
32B ILE* 4.7 0.2 - - + -
89B MET* 4.4 8.7 - - + -
103B TYR* 4.0 26.2 - + - -
106B MET* 3.7 28.3 - - + -
82C GLY* 3.3 21.2 + - - +
84C ASP* 1.3 78.0 - - - +
86C GLN* 1.3 60.5 + - - +
88C ARG* 3.7 11.1 - - - +
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Residues in contact with GLN 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A PHE* 3.6 23.2 - - + -
50A PRO* 3.2 13.3 - - + +
51A LEU* 2.7 48.2 + - - +
62A ILE* 3.7 36.8 - - + +
65A THR* 5.9 0.5 - - - +
66A LEU* 5.1 0.9 - - + -
78C MET* 3.5 29.1 - - + +
79C LYS 5.4 1.0 + - - +
81C GLU 5.5 0.2 + - - -
82C GLY 3.4 10.2 + - - +
83C SER 2.9 6.8 + - - +
85C PHE* 1.3 78.3 - - - +
87C CYS* 1.3 61.7 + - - +
88C ARG 3.3 3.6 + - - +
99C ILE* 3.5 23.3 - - - +
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Residues in contact with CYS 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C HIS* 4.4 12.8 - - + -
78C MET* 3.3 20.9 - - - -
83C SER* 2.8 18.4 + - - +
84C ASP* 4.7 2.7 - - - +
86C GLN* 1.3 71.4 - - - +
88C ARG* 1.3 66.6 + - + +
89C ASP* 3.6 13.0 - - - +
99C ILE* 3.9 8.1 - - - +
100C GLU* 5.3 1.0 - - - -
101C CYS* 2.0 54.6 + - + -
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Residues in contact with ARG 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A PHE* 5.5 1.9 - - - -
66A LEU* 6.1 0.3 - - - +
28B TRP* 5.1 4.9 + - + -
31B TRP* 3.3 60.8 - - + +
91B TYR* 4.8 3.2 - - - -
92B LEU* 3.4 24.0 + - - +
93B ASP* 3.9 19.0 + - - +
94B GLU* 4.2 3.0 - - - +
84C ASP* 2.9 35.1 + - - +
85C PHE 3.7 10.2 - - - +
86C GLN 3.3 9.3 - - - +
87C CYS* 1.3 82.5 - - + +
89C ASP* 1.3 60.1 + - - +
90C THR* 3.6 8.5 + - - +
99C ILE* 4.6 1.4 - - - +
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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