Contacts of the helix formed by residues 81 - 92 (chain A) in PDB entry 2OQ1
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 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A TYR* 3.6 13.7 - - - -
79A HIS* 3.2 5.4 + - - +
80A CYS* 1.3 78.9 - - - +
82A PRO* 1.3 76.0 - - - +
83A ALA 3.3 2.5 - - - -
84A GLU* 3.4 15.6 + - - +
85A LEU* 3.2 21.9 + - - +
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Residues in contact with PRO 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PRO* 4.2 22.7 - - + +
7A ALA* 3.9 20.6 - - + -
10A LEU* 5.0 1.6 - - + -
12A PHE* 6.3 0.2 - - - -
38A LEU* 3.8 24.6 - - + +
48A TYR* 4.0 19.5 - - + -
63A ILE* 6.1 2.9 - - + -
71A TYR* 4.0 21.7 - - + -
81A GLY* 1.3 83.1 - - - +
83A ALA* 1.3 63.1 + - + +
84A GLU* 5.1 0.2 - - - +
85A LEU* 3.3 10.0 + - + +
86A CYS* 3.1 27.9 + - - -
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Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PRO 5.9 0.2 - - - +
9A HIS* 5.2 5.4 - - + +
10A LEU* 4.1 32.7 - - + +
12A PHE* 5.4 2.1 - - - -
81A GLY 3.3 1.0 - - - -
82A PRO* 1.3 81.3 - - + +
84A GLU* 1.3 66.7 + - - +
86A CYS* 3.4 6.9 + - - +
87A GLU* 3.0 42.1 + - + +
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Residues in contact with GLU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A HIS* 4.2 10.2 - - + -
80A CYS* 3.7 32.8 - - - +
81A GLY* 3.5 23.3 - - - +
82A PRO 3.3 0.2 - - - -
83A ALA* 1.3 80.5 + - - +
85A LEU* 1.3 60.6 + - - +
87A GLU* 3.4 15.6 + - - +
88A PHE* 3.0 29.8 + - - +
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 4.3 9.0 - - + -
63A ILE* 3.9 47.3 - - + -
71A TYR* 4.1 13.9 - - + +
72A ALA* 4.3 6.7 - - - -
73A ILE* 4.5 3.8 - - + -
79A HIS* 3.8 31.8 - - + +
81A GLY 3.2 11.8 + - - +
82A PRO* 3.5 9.9 - - + +
83A ALA 3.2 0.2 - - - -
84A GLU* 1.3 78.2 - - - +
86A CYS* 1.3 74.2 + - - +
88A PHE* 3.4 1.9 + - - +
89A TYR* 3.0 51.0 + - + -
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Residues in contact with CYS 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PHE* 3.8 31.2 - - + -
36A PHE* 4.0 18.4 - - + -
38A LEU* 4.5 18.2 - - - -
50A LEU* 4.8 2.7 - - - -
82A PRO 3.1 19.8 + - - +
83A ALA 3.8 4.3 - - - +
84A GLU 3.4 0.2 - - - -
85A LEU* 1.3 84.2 - - - +
87A GLU* 1.3 63.8 + - + +
89A TYR 3.4 0.7 + - - -
90A SER* 2.8 28.1 + - - -
100A LEU* 3.6 19.3 - - + +
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Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ALA* 3.0 38.4 + - + +
84A GLU* 3.7 16.7 - - - +
85A LEU 3.3 0.2 - - - -
86A CYS* 1.3 77.0 - - + +
88A PHE* 1.3 63.2 + - - +
90A SER* 3.2 22.0 + - - -
91A ARG* 3.5 14.2 + - - +
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Residues in contact with PHE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LYS* 4.7 17.5 - - + -
79A HIS* 3.3 33.9 - + + +
84A GLU 3.0 17.4 + - - +
85A LEU 3.6 3.1 - - - +
86A CYS 3.3 0.2 - - - -
87A GLU* 1.3 76.7 - - - +
89A TYR* 1.3 80.8 + + - +
91A ARG* 3.1 10.5 + - + +
92A ASP* 2.9 40.7 + - + +
94A ASP* 3.6 35.2 - - + -
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Residues in contact with TYR 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 5.0 1.8 - - + -
73A ILE* 3.9 23.9 + - + +
76A GLY* 4.3 10.4 - - - -
77A LYS 4.3 2.9 + - - -
79A HIS* 3.9 16.3 - + - -
85A LEU* 3.0 49.0 + - + +
86A CYS 3.4 0.4 + - - -
87A GLU 3.3 0.2 - - - -
88A PHE* 1.3 96.4 - + - +
90A SER* 1.3 62.0 + - - +
91A ARG 3.3 0.2 - - - -
92A ASP 3.3 11.2 - - - +
93A PRO 3.2 28.0 - - - -
94A ASP* 3.9 11.0 + - + -
96A LEU* 3.6 18.4 - - + -
99A ASN* 3.3 11.1 - - - +
100A LEU* 3.0 37.6 + - + -
318B LEU* 4.2 14.9 - - + +
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Residues in contact with SER 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PHE* 5.1 4.5 - - - -
86A CYS 2.8 20.2 + - - -
87A GLU* 3.3 13.2 + - - -
88A PHE 3.1 0.4 - - - -
89A TYR* 1.3 78.6 - - - +
91A ARG* 1.3 79.1 + - - +
99A ASN* 3.0 24.8 + - - -
100A LEU* 3.5 26.6 + - - +
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Residues in contact with ARG 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A GLU* 3.8 11.1 + - - +
88A PHE* 3.1 10.9 + - + +
90A SER* 1.3 98.8 - - - +
92A ASP* 1.3 61.5 + - + +
93A PRO* 4.0 6.3 - - - +
99A ASN* 4.8 1.9 - - - +
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Residues in contact with ASP 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LYS* 5.7 0.3 + - - -
88A PHE* 2.9 27.3 + - + +
89A TYR* 3.3 24.6 - - - -
91A ARG* 1.3 80.4 - - + +
93A PRO* 1.3 76.9 - - - +
94A ASP* 3.2 27.6 + - - +
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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