Contacts of the helix formed by residues 81 - 87 (chain A) in PDB entry 1ZET
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 VAL 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A GLN* 3.3 37.9 - - + +
61A TYR* 3.5 33.3 + - + +
62A LEU 4.3 0.7 - - - +
63A VAL* 4.6 11.8 - - + +
80A ASN* 1.3 73.0 + - - +
82A ARG* 1.3 59.4 + - - +
83A ASP 3.5 0.2 + - - -
84A ALA* 4.2 1.7 + - - +
85A LYS* 3.0 34.5 + - + +
91A LEU* 4.6 1.2 - - - +
93A LEU* 3.2 28.7 - - + +
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Residues in contact with ARG 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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80A ASN* 3.0 13.8 + - - +
81A VAL* 1.3 78.1 - - - +
83A ASP* 1.3 67.7 + - - +
85A LYS* 3.1 32.6 - - - +
86A GLU* 3.0 41.5 + - + +
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Residues in contact with ASP 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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78A LEU* 3.4 29.6 - - + +
79A MET* 3.6 1.6 - - - +
80A ASN* 2.9 52.5 + - - +
82A ARG* 1.3 79.3 - - - +
84A ALA* 1.3 63.8 + - - +
86A GLU* 3.4 9.2 + - - +
87A LYS* 2.9 27.4 + - - +
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Residues in contact with ALA 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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63A VAL* 6.0 4.3 - - + -
75A VAL* 3.6 33.9 - - + -
78A LEU* 5.0 3.5 - - + +
80A ASN 4.5 0.8 + - - +
81A VAL 4.2 2.1 + - - +
82A ARG 3.6 0.2 - - - -
83A ASP* 1.3 79.1 - - + +
85A LYS* 1.3 65.1 + - - +
87A LYS* 3.0 17.7 + - - +
88A CYS* 2.8 23.7 + - + +
91A LEU* 3.4 26.5 - - + -
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Residues in contact with LYS 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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81A VAL* 3.0 28.1 + - + +
82A ARG* 3.1 34.5 - - - +
83A ASP 3.1 0.2 - - - -
84A ALA* 1.3 76.9 - - - +
86A GLU* 1.3 57.9 + - - +
88A CYS 2.7 32.8 - - - +
89A PRO* 3.1 20.9 + - + +
91A LEU* 3.6 12.6 - - + +
92A VAL* 4.6 12.7 - - - +
93A LEU* 4.0 24.8 - - - +
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Residues in contact with GLU 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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82A ARG* 3.0 47.8 + - + +
83A ASP 3.9 5.2 - - - +
85A LYS* 1.3 72.3 - - - +
87A LYS* 1.3 55.7 + - - +
88A CYS 2.7 15.1 + - - -
89A PRO* 3.6 13.6 - - - +
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Residues in contact with LYS 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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73A LEU* 3.4 39.9 - - + +
74A GLY* 5.5 1.8 - - - -
75A VAL* 4.7 3.1 - - + +
83A ASP* 2.9 35.0 + - - +
84A ALA* 3.1 25.3 - - + +
86A GLU* 1.3 78.2 - - - +
88A CYS* 1.3 63.1 + - + +
89A PRO* 4.2 1.6 - - - -
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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