Contacts of the helix formed by residues 73 - 82 (chain A) in PDB entry 2XJZ
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 CYS 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A CYS* 3.4 5.5 - - - +
53A CYS* 4.2 1.1 - - - -
55A CYS* 3.7 16.2 - - - -
57A LEU* 3.7 22.0 - - + -
60A VAL* 6.1 2.0 - - + -
63A ARG 5.8 0.9 - - - -
64A LEU* 5.5 0.9 - - - +
65A TYR* 4.1 1.6 - - - -
72A LEU* 1.3 76.6 - - - +
74A ARG* 1.3 59.0 + - - +
75A ARG* 3.8 11.0 - - - -
76A ASP* 3.4 16.4 - - - -
77A TYR* 2.9 27.2 + - - +
203A ZN 2.4 34.3 - - - -
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Residues in contact with ARG 74 (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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63A ARG 5.6 1.8 + - - +
65A TYR* 3.7 40.6 - - + +
73A CYS* 1.3 71.2 - - - +
75A ARG* 1.3 53.1 + - - +
77A TYR* 3.6 0.5 - - - +
78A LEU* 2.8 54.8 + - + +
97A TYR* 4.3 6.4 + - + +
66B TYR* 5.5 4.2 - - - -
68B LEU* 3.4 45.4 - - - +
69B GLY* 3.4 11.5 - - - +
345I LEU* 3.7 22.6 - - + +
348I GLY* 6.3 1.6 - - - -
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Residues in contact with ARG 75 (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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73A CYS* 3.4 8.8 - - - -
74A ARG* 1.3 78.1 - - - +
76A ASP* 1.3 60.7 + - - +
78A LEU* 3.8 1.6 - - - +
79A ARG* 2.9 53.1 + - + +
97A TYR* 3.4 58.2 + - + +
69B GLY 5.4 3.4 + - - -
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Residues in contact with ASP 76 (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 CYS* 3.6 6.4 - - - -
52A LEU* 3.8 18.2 - - + +
53A CYS* 3.3 13.3 - - - +
72A LEU* 4.5 6.1 - - + -
73A CYS* 3.4 6.5 - - - +
75A ARG* 1.3 78.6 - - - +
77A TYR* 1.3 64.5 + - - +
79A ARG* 2.8 35.7 + - - +
80A LEU* 3.2 32.1 + - + +
203A ZN 1.9 38.9 - - - -
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Residues in contact with TYR 77 (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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65A TYR* 3.6 41.5 - + + -
67A LYS* 4.1 12.0 - - + -
72A LEU* 4.3 12.9 - - + +
73A CYS 2.9 19.9 + - - +
74A ARG 3.6 3.4 - - - +
76A ASP* 1.3 77.5 - - - +
78A LEU* 1.4 76.4 + - + +
81A PHE* 2.7 73.3 + + + +
82A GLY* 5.1 0.4 - - - -
350I PHE 4.7 1.0 + - - -
351I GLY* 3.5 21.9 - - - -
354I ASP* 2.6 41.4 + - + -
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Residues in contact with LEU 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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65A TYR* 5.6 2.9 - - + +
74A ARG* 2.8 36.2 + - + +
75A ARG 3.9 2.5 - - - +
77A TYR* 1.4 97.0 - - + +
79A ARG* 1.4 61.5 - - - +
82A GLY* 3.0 30.1 + - - +
96A ALA* 3.5 28.7 - - + +
97A TYR* 3.6 33.2 - - + -
345I LEU* 3.8 15.5 - - + -
347I GLY 4.0 20.6 - - - +
348I GLY* 4.6 6.7 - - - +
351I GLY* 5.7 0.2 - - - -
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Residues in contact with ARG 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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52A LEU* 4.9 10.1 - - - +
75A ARG* 2.9 42.3 + - + +
76A ASP* 2.8 30.7 + - - +
78A LEU* 1.4 75.7 - - - +
80A LEU* 1.3 82.5 + - - +
97A TYR* 5.2 8.5 - - + +
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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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52A LEU* 4.5 25.8 - - + -
72A LEU* 4.6 4.3 - - + -
76A ASP 3.2 20.6 + - - +
78A LEU 3.2 0.2 - - - -
79A ARG* 1.3 113.4 - - - +
81A PHE* 1.3 92.2 + - + +
82A GLY 3.8 0.7 - - - -
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Residues in contact with PHE 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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67A LYS* 3.7 38.4 - - + -
68A LEU* 3.8 27.6 - - + -
72A LEU* 3.8 21.8 - - + -
77A TYR* 2.7 54.9 + + + +
80A LEU* 1.3 98.2 - - + +
82A GLY* 1.3 66.5 + - - +
83A GLN* 5.3 0.7 - - - +
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Residues in contact with GLY 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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77A TYR* 3.6 3.9 + - - -
78A LEU* 3.0 35.7 + - - +
80A LEU 3.8 0.7 - - - -
81A PHE* 1.3 81.8 - - - +
83A GLN* 1.4 60.5 + - - -
84A ASP* 4.1 4.7 + - - +
96A ALA* 3.5 12.7 - - - +
347I GLY* 4.9 1.6 - - - -
350I PHE* 6.1 0.4 - - - -
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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