Contacts of the helix formed by residues 172 - 175 (chain J) in PDB entry 3LUE
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 PRO 172 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40H HIS* 6.0 3.8 - - - +
64H ILE* 5.9 0.9 - - + -
170J ALA* 3.1 13.7 - - + +
171J LEU* 1.3 83.2 - - + +
173J HIS* 1.3 66.7 + - - +
174J ALA 3.3 0.4 + - - -
175J ILE* 3.4 33.2 + - + +
375J PHE* 4.5 29.4 - - + +
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Residues in contact with HIS 173 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64H ILE* 3.5 21.6 - - + +
265I SER 5.7 5.2 - - - +
268I GLY* 5.3 9.6 - - - -
171J LEU* 3.4 33.8 + - + -
172J PRO* 1.3 78.5 - - - +
174J ALA* 1.3 66.3 + - + +
175J ILE 3.4 4.9 + - - +
284J LYS* 3.4 48.7 + - + +
285J CYS* 4.4 5.1 - - - -
286J ASP 5.3 0.6 + - - -
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Residues in contact with ALA 174 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164J PRO* 3.5 25.7 - - + +
171J LEU* 2.9 12.0 + - + +
173J HIS* 1.3 81.0 - - + +
175J ILE* 1.4 56.6 + - - +
176J LEU* 3.8 2.9 - - - +
281J SER* 2.7 41.3 + - - +
284J LYS* 3.6 16.6 - - + -
285J CYS* 3.6 16.2 - - - -
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Residues in contact with ILE 175 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191I LYS* 6.1 0.7 - - - -
195I GLU* 5.5 2.8 - - - +
136J ILE* 5.6 2.0 - - + -
139J VAL* 5.4 0.2 - - + -
161J HIS* 3.3 29.6 - - + +
162J THR 3.3 9.4 - - - +
163J VAL* 4.0 36.6 - - + -
164J PRO* 4.4 0.2 - - + -
170J ALA* 4.3 4.5 - - + -
171J LEU 3.9 10.8 - - - +
172J PRO* 3.7 24.6 - - + +
173J HIS 3.4 6.4 - - - +
174J ALA* 1.4 78.8 - - - +
176J LEU* 1.3 68.3 + - - +
177J ARG* 5.8 0.2 - - + -
375J PHE* 3.5 33.2 - - + -
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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
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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