Contacts of the helix formed by residues 81 - 91 (chain S) in PDB entry 1TQE
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 ASN 81 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33R TYR* 2.7 43.5 - - + +
36R SER* 2.9 26.9 + - - -
37R VAL* 4.6 7.5 - - + +
57R TYR* 2.4 22.0 + - - -
58R ALA 3.8 0.8 + - - -
59R SER* 3.1 25.7 + - - +
60R THR* 5.4 0.6 - - - +
80S THR* 1.3 75.2 - - - +
82S THR* 1.3 63.1 + - - +
84S ILE* 4.3 1.3 - - - -
85S LEU* 2.9 32.7 + - - +
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Residues in contact with THR 82 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59R SER 5.1 1.0 + - - -
60R THR* 6.2 0.3 - - - +
80S THR* 3.1 15.0 - - - +
81S ASN* 1.3 82.4 - - - +
83S ASP* 1.3 60.3 + - - +
85S LEU* 4.0 7.8 - - - +
86S GLU* 3.9 22.0 - - - +
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Residues in contact with ASP 83 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79S ARG* 2.8 42.2 + - - +
80S THR* 3.0 23.1 + - - +
82S THR* 1.3 77.5 - - - +
84S ILE* 1.3 65.4 + - - +
85S LEU 3.1 1.1 - - - -
86S GLU* 2.9 17.8 + - - +
87S THR* 3.2 13.9 + - - -
103Y SER* 4.5 1.9 - - - -
104Y PRO* 2.9 36.3 - - + +
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Residues in contact with ILE 84 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26R PHE* 3.9 22.2 - - + -
29R MET* 4.2 17.3 - - + +
30R LYS* 4.4 7.2 - - - -
33R TYR* 4.1 34.1 - - + -
57R TYR* 4.4 4.7 - - + -
79S ARG* 3.7 31.9 - - + +
80S THR 2.7 28.2 + - - +
81S ASN* 4.1 4.3 - - - +
83S ASP* 1.3 73.1 - - - +
85S LEU* 1.3 62.1 + - - +
86S GLU 3.2 0.5 + - - -
87S THR* 4.0 5.5 - - - -
88S LEU* 3.3 35.8 + - + +
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Residues in contact with LEU 85 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33R TYR* 3.8 30.7 - - + +
81S ASN* 2.9 20.8 + - + +
82S THR* 4.0 9.2 - - - +
83S ASP 3.1 0.4 + - - -
84S ILE* 1.3 77.7 - - - +
86S GLU* 1.3 59.1 + - + +
88S LEU* 3.8 5.5 - - + +
89S LYS* 2.9 42.9 + - + +
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Residues in contact with GLU 86 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82S THR* 3.9 18.6 - - - +
83S ASP* 2.9 7.4 + - - +
85S LEU* 1.3 73.9 - - + +
87S THR* 1.3 54.1 + - - +
88S LEU 2.4 17.7 + - - -
89S LYS* 2.7 53.4 + - + +
90S ARG* 3.6 9.5 + - - +
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Residues in contact with THR 87 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26R PHE* 4.0 14.4 - - + -
79S ARG* 3.5 25.9 + - - +
83S ASP* 3.2 16.5 + - - -
84S ILE* 3.5 6.5 + - - -
86S GLU* 1.3 76.1 - - - +
88S LEU* 1.3 57.7 + - - +
90S ARG* 4.5 9.6 + - - +
91S ARG* 3.5 40.7 - - - +
103Y SER* 5.2 8.3 + - - -
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Residues in contact with LEU 88 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26R PHE* 4.1 21.3 - - + -
30R LYS* 3.4 45.1 - - + +
33R TYR* 5.4 5.6 - - + -
84S ILE* 3.3 22.1 + - + +
85S LEU* 3.8 6.5 - - + +
86S GLU 2.4 15.6 + - - -
87S THR* 1.3 77.6 - - - +
89S LYS* 1.3 65.0 + - - +
90S ARG* 2.9 3.9 + - - -
91S ARG* 3.9 28.3 + - + +
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Residues in contact with LYS 89 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85S LEU* 2.9 39.9 + - + +
86S GLU* 2.7 57.1 + - + +
88S LEU* 1.3 71.6 - - - +
90S ARG* 1.3 63.9 + - + +
91S ARG 4.5 1.2 - - - +
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Residues in contact with ARG 90 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86S GLU 3.6 10.5 + - - +
87S THR* 4.6 8.1 - - - +
88S LEU 2.9 1.6 - - - -
89S LYS* 1.3 81.5 - - + +
91S ARG* 1.3 74.5 + - + +
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Residues in contact with ARG 91 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26R PHE* 3.3 49.6 - - - +
87S THR* 3.5 29.3 + - - +
88S LEU* 3.9 21.2 + - + +
89S LYS 4.5 1.4 - - - +
90S ARG* 1.3 94.5 - - + +
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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