Contacts of the helix formed by residues 162 - 167 (chain C) in PDB entry 5W4A
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 GLU 162 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A LYS* 2.6 45.9 + - - +
162A GLU* 3.8 2.1 - - - +
131C LYS* 3.3 26.6 + - - +
143C ILE* 3.7 26.1 - - + +
146C LYS* 6.0 0.9 - - + -
158C THR* 4.1 9.9 - - - +
159C GLU* 3.0 28.5 + - - +
160C LEU 3.0 1.0 - - - -
161C SER* 1.3 77.2 - - - +
163C LEU* 1.3 61.6 + - - +
165C GLY* 2.9 18.8 + - - +
166C LEU* 4.0 2.4 + - - +
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Residues in contact with LEU 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C PHE* 3.8 27.1 - - + -
140C ILE* 5.5 3.4 - - + -
143C ILE* 3.8 28.2 - - + +
160C LEU* 2.9 41.1 + - + +
162C GLU* 1.3 78.9 - - - +
164C CYS* 1.3 55.7 + - - +
166C LEU* 3.0 14.6 + - + +
168C LEU* 3.0 57.5 + - + +
171C ASP* 4.1 10.3 - - + -
172C ALA* 4.0 19.7 - - + +
175C PHE* 4.2 3.1 - - + -
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Residues in contact with CYS 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LYS 5.9 0.7 - - - +
132A LEU* 4.0 18.4 - - + +
134A LYS* 3.0 26.0 + - - +
139A LYS* 5.0 3.4 + - - -
161C SER 3.0 17.8 + - - +
163C LEU* 1.3 76.6 - - - +
165C GLY* 1.3 56.0 + - - +
167C ASP* 3.1 9.2 + - - +
169C ASP* 3.3 33.7 - - - +
172C ALA* 4.0 13.5 - - - -
193C ILE* 3.7 33.2 - - - -
196C ASN* 4.8 1.8 - - - +
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Residues in contact with GLY 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A LYS* 4.5 17.4 + - - -
161C SER 4.3 0.6 + - - -
162C GLU* 2.9 15.1 + - - +
164C CYS* 1.3 77.8 - - - +
166C LEU* 1.3 61.8 + - - +
167C ASP* 3.4 3.2 + - - +
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Residues in contact with LEU 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ILE* 4.5 4.7 - - + -
15C ARG* 2.9 27.5 + - - +
136C GLU* 4.5 18.4 - - + +
139C LYS* 4.0 35.7 - - + -
140C ILE* 3.8 29.4 - - + -
143C ILE* 3.9 26.2 - - + -
162C GLU 4.7 0.9 - - - +
163C LEU* 3.0 10.0 + - + +
165C GLY* 1.3 79.7 - - - +
167C ASP* 1.3 66.3 + - - +
168C LEU* 3.1 16.2 + - + +
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Residues in contact with ASP 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A LYS* 2.8 31.3 + - - +
15C ARG* 3.3 36.6 - - - +
164C CYS 3.1 8.5 + - - +
165C GLY 3.4 2.5 - - - -
166C LEU* 1.3 80.3 - - - +
168C LEU* 1.3 54.1 + - - +
169C ASP* 3.3 19.0 + - - +
170C PHE 5.2 0.3 + - - -
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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
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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