Contacts of the helix formed by residues 158 - 161 (chain O) in PDB entry 2WQT
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 158 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42O GLN* 3.3 22.9 - - + +
45O ASN* 6.6 0.2 - - + -
46O VAL* 5.1 3.6 - - - -
80O GLY* 3.9 0.2 - - - -
81O THR* 2.7 49.5 + - - +
83O PHE* 4.8 8.1 - - - -
86O MET* 5.0 2.4 - - - +
143O ARG* 5.0 2.2 - - - +
155O VAL 3.0 9.7 + - - -
156O ALA 3.0 5.5 + - - -
157O ASP* 1.3 78.8 - - - +
159O ALA* 1.3 67.6 + - - +
161O CYS* 3.1 28.9 + - + +
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Residues in contact with ALA 159 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42O GLN* 4.0 0.4 - - - +
60O LYS* 3.0 33.5 + - + -
78O ASP* 3.6 18.2 - - - +
79O PHE 3.5 22.0 - - - +
80O GLY* 3.6 11.4 - - - +
154O THR* 2.8 29.0 + - - -
155O VAL* 3.5 5.9 + - - +
158O ASN* 1.3 71.9 - - - +
160O SER* 1.3 62.2 + - - +
1262O PO4 3.9 3.6 + - - -
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Residues in contact with SER 160 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140O VAL* 3.2 13.0 - - - +
141O GLY 2.9 38.1 + - - -
142O SER* 4.9 3.2 + - - -
143O ARG* 3.7 0.9 - - - +
147O TRP* 3.9 23.6 - - - -
149O ILE* 4.9 3.3 - - - +
154O THR* 2.5 35.1 + - - +
157O ASP* 3.1 15.1 + - - -
159O ALA* 1.3 77.5 - - - +
161O CYS* 1.3 59.9 + - - +
1262O PO4 5.3 2.7 - - - -
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Residues in contact with CYS 161 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60O LYS* 3.7 18.4 - - - -
81O THR 4.2 4.9 - - - -
82O LEU* 4.0 11.2 - - - -
86O MET* 3.6 25.4 - - + -
138O GLU* 3.6 19.3 - - - -
141O GLY 4.1 0.9 - - - -
143O ARG* 2.9 29.8 + - - +
158O ASN* 3.1 35.3 + - + +
159O ALA 3.3 0.4 - - - -
160O SER* 1.3 76.3 - - - +
162O GLY* 1.3 59.3 + - - +
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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
------------------------------------------------------------
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