Contacts of the helix formed by residues 74 - 82 (chain B) in PDB entry 2OQH
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 ALA 74 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B THR* 5.4 4.9 - - - -
71B SER* 3.2 26.8 + - - +
72B PRO 4.6 0.9 - - - -
73B PHE* 1.3 73.7 - - - +
75B LEU* 1.3 58.1 + - - +
76B GLU 3.4 2.5 - - - +
77B ALA* 3.5 16.6 + - + +
78B PHE* 3.0 26.3 + - - +
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B PRO 3.9 8.1 - - - +
73B PHE 2.9 11.9 + - - +
74B ALA* 1.3 70.4 - - - +
76B GLU* 1.3 67.6 + - + +
78B PHE* 3.2 10.2 + - + +
79B HIS* 3.0 39.7 + - + +
101B ASP* 3.9 22.0 - - - +
104B CYS* 4.0 15.5 - - + -
105B TRP* 3.2 39.5 - - + +
108B MSE 3.3 31.6 - - + -
278B ALA* 5.6 6.1 - - + -
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Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ALA* 3.4 0.6 - - - -
75B LEU* 1.3 78.4 - - + +
77B ALA* 1.3 63.0 + - - +
79B HIS* 5.0 1.3 - - - -
80B ARG* 2.8 71.8 + - + +
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Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ALA* 3.5 22.3 + - + +
75B LEU 3.2 0.2 - - - -
76B GLU* 1.3 80.1 - - - +
78B PHE* 1.3 62.2 + - - +
80B ARG* 3.3 7.6 + - - +
81B LYS* 3.1 23.6 + - - +
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Residues in contact with PHE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B MSE 4.4 9.9 - - + -
66B ASP* 6.3 1.1 - - + -
67B LEU* 3.6 36.3 - - + -
74B ALA 3.0 15.1 + - - +
75B LEU* 3.2 17.2 + - + +
77B ALA* 1.3 75.9 - - - +
79B HIS* 1.3 79.4 + + - +
80B ARG 3.2 0.3 + - - -
81B LYS* 3.2 6.6 + - + +
82B GLN* 3.2 46.9 + - + +
97B ILE* 3.8 30.3 - - + -
100B VAL* 3.6 31.6 - - + -
101B ASP 4.5 2.9 - - - -
104B CYS* 6.0 1.3 - - - -
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Residues in contact with HIS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B LEU* 3.0 34.3 + - + +
76B GLU 4.1 2.9 - - - +
78B PHE* 1.3 88.6 - + - +
80B ARG* 1.3 73.0 + - - +
82B GLN* 3.4 5.4 + - - -
83B HIS* 3.2 24.6 + - - +
97B ILE* 3.4 22.9 - - + +
101B ASP* 2.7 26.1 + - + -
275B GLY* 3.1 29.8 - - - -
276B GLY* 4.7 1.5 - - - -
278B ALA* 6.0 4.3 - - + +
279B ALA* 6.4 1.1 - - + -
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Residues in contact with ARG 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B GLU* 2.8 55.3 + - + +
77B ALA* 3.6 7.0 - - - +
78B PHE 3.2 0.2 - - - -
79B HIS* 1.3 87.6 - - - +
81B LYS* 1.3 61.0 + - - +
82B GLN 3.2 1.0 + - - -
83B HIS* 3.3 25.7 + - - +
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Residues in contact with LYS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ASP* 3.7 38.4 - - + +
77B ALA 3.1 13.5 + - - +
78B PHE* 3.2 5.6 + - + +
80B ARG* 1.3 78.6 - - - +
82B GLN* 1.3 68.7 + - - +
83B HIS 3.4 0.4 + - - -
84B MSE 5.1 2.6 + - - +
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Residues in contact with GLN 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B MSE 3.6 23.1 + - - +
66B ASP* 3.4 37.2 + - - +
78B PHE* 3.2 39.4 + - + +
79B HIS* 3.4 5.1 + - - +
80B ARG 3.1 0.6 - - - -
81B LYS* 1.3 90.4 + - - +
83B HIS* 1.3 61.7 + - - +
84B MSE 3.0 6.3 - - - +
85B VAL* 3.0 35.1 + - + +
86B PRO* 3.3 10.0 - - - +
97B ILE* 3.8 18.3 - - + +
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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