Contacts of the helix formed by residues 164 - 167 (chain U) in PDB entry 5XS0
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 164 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69T HIS* 3.1 29.1 + - - +
72T ILE* 3.3 32.5 - - - +
73T ASN* 3.1 28.9 + - - +
156U ARG* 3.5 17.1 + - - +
159U GLY 3.1 25.0 + - - +
160U ASN* 3.5 3.3 + - - +
162U LEU 3.8 0.2 - - - -
163U GLY* 1.3 76.1 - - - +
165U CYS* 1.3 65.4 + - - +
167U LEU* 3.0 27.0 + - - +
168U ASP 4.4 0.3 + - - -
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Residues in contact with CYS 165 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69T HIS* 6.1 0.7 - - - -
46U ARG* 3.5 28.7 - - + +
47U LEU* 3.6 33.4 - - - -
66U ILE* 6.0 0.4 - - - -
160U ASN* 3.3 38.7 + - + +
163U GLY 4.8 0.4 - - - -
164U ASN* 1.3 78.8 - - - +
166U ILE* 1.3 65.1 + - - +
167U LEU 3.0 2.2 + - - -
168U ASP* 3.0 18.5 + - - +
171U TYR* 3.3 24.0 - - + -
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Residues in contact with ILE 166 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52U ILE* 3.6 33.4 - - + -
64U CYS* 3.6 40.6 - - + +
65U TYR* 4.4 7.4 - - - +
66U ILE* 5.0 10.1 - - + -
156U ARG* 4.7 7.6 - - - +
163U GLY* 3.1 23.9 + - - +
164U ASN 3.1 0.8 + - - -
165U CYS* 1.3 81.3 - - - +
167U LEU* 1.3 74.7 + - + +
168U ASP 3.3 0.6 + - - -
171U TYR* 4.0 14.1 - - + -
172U LEU* 3.9 20.9 - - + +
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Residues in contact with LEU 167 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67T GLU* 5.2 0.7 - - - +
68T GLY* 6.1 0.4 - - - -
69T HIS* 3.7 33.0 + - + +
72T ILE* 5.6 4.7 - - + -
156U ARG* 3.6 37.7 - - + +
164U ASN* 3.0 28.3 + - - +
165U CYS 3.0 1.4 - - - -
166U ILE* 1.3 90.6 - - + +
168U ASP* 1.3 61.2 + - - +
169U LYS* 3.5 9.7 + - - +
172U LEU* 5.7 1.1 - - - -
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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