Contacts of the helix formed by residues 158 - 161 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42S GLN* 3.3 23.5 - - + +
45S ASN* 6.6 0.4 - - + -
46S VAL* 5.1 3.4 - - - -
81S THR* 2.7 49.4 + - - -
83S PHE* 4.8 8.7 - - - -
86S MET* 5.0 2.6 - - - +
143S ARG* 4.9 2.0 - - - +
155S VAL 3.0 8.0 + - - -
156S ALA 3.0 7.9 + - - -
157S ASP* 1.3 79.5 - - - +
159S ALA* 1.3 67.1 + - - +
161S CYS* 3.1 30.1 + - + +
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Residues in contact with ALA 159 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42S GLN* 4.0 0.8 - - - +
60S LYS* 3.0 32.9 + - + -
78S ASP* 3.6 18.2 - - - +
79S PHE* 3.5 22.0 - - - +
80S GLY* 3.6 11.0 - - - +
154S THR* 2.7 28.4 + - - -
155S VAL* 3.5 5.0 + - - +
158S ASN* 1.3 73.2 - - - +
160S SER* 1.3 61.5 + - - +
1262S PO4 3.6 4.2 + - - -
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Residues in contact with SER 160 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140S VAL* 3.2 13.2 - - - +
141S GLY 3.0 37.8 + - - -
142S SER* 4.9 3.0 + - - -
143S ARG* 3.8 1.1 - - - +
147S TRP* 3.9 24.0 - - - -
149S ILE* 4.9 3.3 - - - +
154S THR* 2.5 35.3 + - - +
157S ASP* 3.1 15.6 + - - -
159S ALA* 1.3 76.5 - - - +
161S CYS* 1.3 58.5 + - - +
1262S PO4 5.1 2.2 + - - -
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Residues in contact with CYS 161 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60S LYS* 3.7 17.7 - - - -
81S THR 4.1 5.4 - - - -
82S LEU* 4.0 11.0 - - - -
86S MET* 3.6 26.7 - - + -
138S GLU* 3.7 19.1 - - - -
141S GLY 4.1 0.7 - - - -
143S ARG* 2.9 29.0 + - - +
158S ASN* 3.1 35.3 + - + +
159S ALA 3.3 0.8 - - - -
160S SER* 1.3 76.1 - - - +
162S GLY* 1.3 59.2 + - - +
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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
------------------------------------------------------------
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