Contacts of the helix formed by residues 162 - 168 (chain B) in PDB entry 1OE4
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 GLN 162 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B TRP* 3.5 6.4 - - - -
160B CYS* 2.8 7.8 + - - +
161B GLY* 1.3 89.2 + - - -
163B PRO* 1.3 78.5 - - + +
164B GLU* 3.3 13.6 - - + +
165B THR* 3.1 28.6 + - - +
166B PHE 3.6 3.5 + - - -
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Residues in contact with PRO 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B TYR* 3.6 28.9 - - + +
118B TRP* 3.4 55.2 - - + +
119B LEU* 4.3 3.4 - - + -
120B GLN* 6.1 0.4 - - + +
162B GLN* 1.3 92.7 - - + +
164B GLU* 1.3 76.5 + - - +
166B PHE* 3.1 3.1 + - - +
167B PHE* 3.0 33.6 + - + -
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Residues in contact with GLU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B TYR* 4.9 13.4 + - + -
162B GLN* 3.3 12.9 - - + +
163B PRO* 1.3 95.7 - - - +
165B THR* 1.3 56.3 + - - +
167B PHE* 3.8 4.6 - - - +
168B LYS* 3.0 31.8 + - - +
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Residues in contact with THR 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B CYS* 3.4 20.3 + - + +
162B GLN* 3.1 20.2 + - - +
163B PRO 3.1 0.8 - - - -
164B GLU* 1.3 80.2 - - - +
166B PHE* 1.3 60.7 + - - +
168B LYS* 3.8 14.0 + - - +
169B HIS 4.9 0.2 + - - -
278B LEU 4.1 12.6 - - - +
279B LEU* 3.7 20.2 - - - +
280B THR* 3.8 20.9 - - + +
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Residues in contact with PHE 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B PHE* 3.8 22.7 - + - -
118B TRP* 4.4 10.3 - - + -
153B TRP* 3.9 9.6 - + - -
156B PHE* 3.5 51.1 - + + -
160B CYS* 3.7 22.8 - - + +
162B GLN 3.6 1.8 + - - -
163B PRO 3.1 7.8 + - - +
165B THR* 1.3 78.9 - - - +
167B PHE* 1.3 96.8 + + - +
168B LYS 3.5 0.5 + - - -
169B HIS 3.9 0.7 + - - -
170B CYS* 3.2 37.9 + - + +
172B VAL* 3.7 25.4 - - + -
278B LEU 5.6 0.2 - - - +
279B LEU* 4.1 8.3 - - + +
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Residues in contact with PHE 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B TYR* 3.7 34.3 - + - -
83B TYR* 3.2 49.1 - + + +
88B LYS* 2.6 31.2 + - - -
119B LEU* 3.7 23.6 - - + -
153B TRP* 3.6 24.2 - + - -
163B PRO* 3.0 29.2 + - + +
164B GLU* 3.8 3.1 - - - +
166B PHE* 1.3 94.4 - + - +
168B LYS* 1.3 60.6 + - - +
169B HIS 3.2 3.0 + - - -
170B CYS 3.4 18.3 - - - +
171B PHE* 4.1 8.1 - + - -
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Residues in contact with LYS 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B SER* 4.1 15.2 + - - -
87B LYS 4.2 5.7 - - - +
88B LYS* 4.4 0.7 + - - +
164B GLU 3.0 17.5 + - - +
165B THR* 3.9 11.4 - - - +
166B PHE 3.3 1.2 - - - -
167B PHE* 1.3 78.9 - - - +
169B HIS* 1.3 93.7 + - + +
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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