Contacts of the helix formed by residues 80 - 92 (chain E) in PDB entry 3O2Q
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 80 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77E THR 3.4 14.7 + - - -
78E GLN 3.4 1.2 + - - -
79E ASN* 1.3 76.4 + - - +
81E ILE* 1.3 59.8 + - - +
82E LEU 3.6 1.8 - - - -
83E HIS* 3.5 14.5 + - - +
84E MET* 3.0 27.0 + - - +
145E HIS* 4.1 12.4 + - - -
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Residues in contact with ILE 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E LEU* 4.4 11.4 - - + -
45E PRO* 3.3 39.5 - - + +
68E LEU* 3.6 30.3 - - + -
76E TYR* 3.2 7.1 + - + +
79E ASN* 3.5 35.7 - - + +
80E GLY* 1.3 77.2 - - - +
82E LEU* 1.3 61.4 + - - +
84E MET* 3.1 11.0 + - - +
85E LEU* 2.9 38.0 + - + +
145E HIS* 4.7 1.1 - - - +
6F PRO* 4.5 18.8 - - + -
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Residues in contact with LEU 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E TYR* 3.3 59.1 - - + +
68E LEU* 4.0 12.6 - - + -
69E LEU* 4.1 12.1 - - + +
73E LYS* 4.0 20.6 - - + +
76E TYR* 3.0 31.6 + - + +
77E THR* 3.5 30.3 - - + +
81E ILE* 1.3 77.2 - - - +
83E HIS* 1.3 61.5 + - - +
85E LEU* 3.4 1.2 + - + -
86E ASP* 3.0 19.2 + - - +
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Residues in contact with HIS 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E TYR 4.7 0.4 + - - -
77E THR* 6.0 0.2 - - - +
80E GLY* 3.5 16.3 + - - +
81E ILE 3.3 0.4 - - - -
82E LEU* 1.3 77.9 - - - +
84E MET* 1.3 61.3 + - - +
86E ASP* 3.3 6.2 + - + +
87E ARG* 3.0 36.9 + - + +
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Residues in contact with MET 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E GLN* 3.6 34.1 - - - +
17E ASN* 3.4 25.8 - - + +
44E LEU* 5.3 2.7 - - - -
80E GLY 3.0 17.0 + - - +
81E ILE* 3.1 13.0 + - - +
83E HIS* 1.3 79.3 - - - +
85E LEU* 1.3 58.1 + - - +
87E ARG* 3.4 17.9 + - - +
88E ASN* 2.9 34.8 + - - +
145E HIS* 2.9 44.0 - - + +
5F SEP 4.6 0.2 - - - +
6F PRO* 3.6 19.1 - - + -
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Residues in contact with LEU 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E GLN* 3.3 28.7 - - - +
44E LEU* 4.2 7.0 - - + -
61E TYR* 3.9 20.7 - - + +
64E MET* 3.9 20.2 - - + -
65E TYR* 3.7 41.1 - - + +
68E LEU* 4.0 21.3 - - + -
81E ILE* 2.9 25.3 + - + +
82E LEU* 3.8 5.6 - - - +
84E MET* 1.3 75.6 - - + +
86E ASP* 1.3 60.1 + - - +
88E ASN* 3.3 4.7 + - - +
89E LYS* 2.9 30.2 + - - +
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Residues in contact with ASP 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E TYR* 4.1 20.1 + - + -
82E LEU 3.0 17.6 + - - +
83E HIS* 3.7 7.0 - - + +
85E LEU* 1.3 76.6 - - - +
87E ARG* 1.3 62.2 + - - +
89E LYS* 3.5 19.0 + - - +
90E ARG* 2.6 65.1 + - - +
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Residues in contact with ARG 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E GLN 3.3 16.8 + - - -
17E ASN* 4.0 5.1 + - - +
20E MET* 3.6 7.1 - - - +
21E GLU* 2.7 46.7 + - - +
24E ASN* 4.3 18.2 + - - +
83E HIS* 3.0 26.6 + - + +
84E MET* 3.5 22.2 - - - +
85E LEU 3.2 0.2 - - - -
86E ASP* 1.3 77.2 + - - +
88E ASN* 1.3 88.2 + - - +
90E ARG* 3.2 25.0 + - - +
91E ILE* 3.5 25.3 + - - +
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Residues in contact with ASN 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E GLN* 3.0 44.2 + - - +
20E MET* 3.2 25.1 - - + +
61E TYR* 3.6 25.2 - - + -
84E MET* 2.9 21.7 + - - +
85E LEU* 3.5 6.0 - - - +
87E ARG* 1.3 102.4 + - - +
89E LYS* 1.3 63.8 + - - +
91E ILE* 3.0 15.0 + - - +
92E LYS 3.2 12.6 + - - +
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Residues in contact with LYS 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E TYR* 4.0 9.5 - - + -
62E ASP* 3.8 40.6 + - + +
85E LEU 2.9 19.5 + - - +
86E ASP* 3.5 22.1 + - - +
88E ASN* 1.3 72.3 - - - +
90E ARG* 1.3 67.6 + - + +
92E LYS 3.2 21.7 + - - +
93E PRO* 5.1 1.9 - - + +
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Residues in contact with ARG 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E ASP* 2.6 43.6 + - - +
87E ARG* 3.2 13.1 + - - +
88E ASN 3.1 0.6 - - - -
89E LYS* 1.3 85.9 - - + +
91E ILE* 1.3 61.8 + - + +
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Residues in contact with ILE 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E MET* 3.7 46.0 - - + +
23E HIS* 3.5 37.0 - - + +
24E ASN* 3.8 29.8 - - + +
27E SER* 6.2 0.2 - - - -
87E ARG* 3.7 23.3 - - - +
88E ASN 3.0 6.0 + - - +
90E ARG* 1.3 81.1 - - + +
92E LYS* 1.3 60.7 + - + +
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Residues in contact with LYS 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E ASN* 2.9 24.2 - - - +
20E MET* 4.2 3.1 - - + -
23E HIS* 4.2 20.0 - - + -
35E SER* 3.1 20.0 + - - +
61E TYR* 3.4 24.4 - - + -
88E ASN 3.2 8.6 + - - +
89E LYS* 3.2 17.0 + - - +
91E ILE* 1.3 82.8 - - + +
93E PRO* 1.3 79.4 - - + +
94E ARG 3.1 22.0 - - - +
96E GLU* 2.7 30.1 + - - +
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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