Contacts of the strand formed by residues 173 - 176 (chain J) in PDB entry 1DU3
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 173 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150J LYS* 2.9 24.5 + - - -
169J LEU* 3.3 5.6 - - - +
170J ARG 2.9 36.8 + - - +
171J ASN* 3.1 14.2 - - - +
172J GLY* 1.3 80.1 - - - +
174J LEU* 1.3 64.4 + - - +
175J VAL* 3.4 5.4 + - + +
213J TYR* 3.9 18.8 - - - -
255J ARG* 3.1 42.2 + - + +
256J ILE 3.3 10.3 - - - +
257J PHE* 3.7 19.2 - - + -
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Residues in contact with LEU 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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124J ALA* 4.1 14.6 - - + -
126J ILE* 3.8 24.7 - - + -
164J LEU* 4.2 14.6 - - + -
167J LEU* 4.0 20.4 - - + -
168J HIS 3.4 4.5 - - - +
169J LEU* 3.7 1.3 - - + +
173J GLU* 1.3 70.9 - - - +
175J VAL* 1.3 61.5 + - - +
176J ILE 3.8 0.5 + - - -
255J ARG* 3.3 4.5 - - - -
256J ILE* 2.9 50.6 + - + +
275J PHE* 3.2 41.2 - - + -
276J GLY* 4.3 17.3 - - - -
277J ALA* 4.7 4.3 - - + +
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Residues in contact with VAL 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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167J LEU* 3.6 4.5 - - - -
168J HIS* 2.7 61.4 + - + +
170J ARG* 3.8 13.5 - - + +
173J GLU* 3.6 14.1 - - - +
174J LEU* 1.3 72.7 - - - +
176J ILE* 1.3 68.3 + - - +
177J HIS* 3.1 18.5 - - + -
253J ASN* 4.5 12.6 - - - +
254J ASP 3.8 9.2 - - - +
255J ARG* 3.9 19.1 - - + -
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Residues in contact with ILE 176 (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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167J LEU* 3.8 18.2 - - + -
175J VAL* 1.3 74.8 - - - +
177J HIS* 1.3 61.1 - - - +
178J GLU 2.9 31.9 - - - +
182J TYR* 3.5 36.6 - - + +
250J LEU* 3.8 27.8 - - + -
251J LYS 4.0 20.4 - - - +
252J GLU* 4.4 0.2 - - - +
253J ASN* 3.0 24.4 + - - +
254J ASP* 3.3 17.0 + - + +
256J ILE* 4.3 13.7 - - + -
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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