Contacts of the helix formed by residues 77 - 83 (chain A) in PDB entry 2OUX
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 LYS 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A GLU* 4.9 14.0 - - - +
76A MSE 1.3 81.9 - - + +
78A ASP* 1.3 60.7 + - - +
79A TYR 3.4 0.9 - - - +
80A LEU* 3.5 4.7 + - - +
81A ALA* 2.8 23.0 + - - +
106A MSE 3.8 16.8 - - - +
107A LEU* 3.4 20.0 - - + +
108A ASP* 3.0 35.1 + - - +
111A GLN* 3.1 33.2 + - - +
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Residues in contact with ASP 78 (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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74A GLU 5.3 0.9 - - - +
75A ASN* 2.4 52.3 + - - +
76A MSE 2.3 21.1 + - - +
77A LYS* 1.3 68.5 - - - +
79A TYR* 1.3 63.9 + - - +
80A LEU 3.1 1.3 - - - -
81A ALA* 3.5 11.4 - - + -
82A GLU* 2.9 32.3 + - + +
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Residues in contact with TYR 79 (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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42A TYR* 3.2 39.3 - + - +
43A GLN* 3.7 29.5 + - + +
50A ARG* 3.6 29.0 + - - -
54A TYR* 3.7 1.6 + - - -
66A PHE* 4.2 11.9 - + + -
69A ILE* 5.0 0.4 - - + -
73A ASN* 3.4 26.1 + - - -
75A ASN* 3.0 40.9 + - - +
76A MSE 3.6 28.9 - - + -
77A LYS 3.4 0.8 - - - -
78A ASP* 1.3 73.9 + - - +
80A LEU* 1.3 65.8 + - + +
82A GLU* 2.9 25.9 - - - +
83A MSE 3.6 11.4 + - - +
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Residues in contact with LEU 80 (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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66A PHE* 4.1 25.4 - - + -
76A MSE 5.4 1.1 - - + -
77A LYS 3.5 9.8 + - - +
78A ASP 3.1 0.2 - - - -
79A TYR* 1.3 84.3 - - + +
81A ALA* 1.3 65.1 + - - +
83A MSE 3.1 30.0 + - + +
88A ALA* 4.2 8.3 - - + +
91A MSE 4.1 14.8 - - + -
92A LEU* 4.5 13.5 - - + -
103A LEU* 3.5 31.9 - - + -
107A LEU* 3.5 25.8 - - + -
111A GLN* 4.4 0.4 - - - +
115A TYR* 3.4 26.8 + - + +
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Residues in contact with ALA 81 (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 2.8 21.7 + - - +
78A ASP* 3.2 13.4 + - + +
80A LEU* 1.3 73.1 - - - +
82A GLU* 1.3 61.9 + - - +
83A MSE 3.0 10.9 + - - +
85A PRO* 5.4 1.0 - - - +
111A GLN* 4.0 7.0 - - - +
115A TYR* 3.5 8.0 + - - -
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Residues in contact with GLU 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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47A GLU* 4.3 17.0 - - - +
50A ARG* 2.8 42.7 + - - +
51A GLN* 3.2 31.7 + - - +
54A TYR* 2.7 29.3 + - + +
78A ASP* 2.9 21.1 + - - +
79A TYR* 2.9 26.2 - - - +
81A ALA* 1.3 75.3 - - - +
83A MSE 1.3 60.1 + - - +
84A ARG* 4.0 0.9 + - - +
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Residues in contact with MSE 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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54A TYR* 3.9 25.6 - - + -
62A LEU* 4.1 10.5 - - + -
66A PHE* 5.2 2.0 - - - -
79A TYR 3.7 16.4 - - - +
80A LEU* 3.1 25.0 + - - +
81A ALA 3.0 13.7 - - - +
82A GLU* 1.3 80.4 - - - +
84A ARG* 1.3 65.3 + - - +
85A PRO* 3.2 8.0 - - - +
87A TYR* 3.0 36.3 - - + +
88A ALA* 3.0 37.7 - - + -
91A MSE 3.9 28.3 - - + -
115A TYR* 5.8 0.2 - - - -
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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