Contacts of the helix formed by residues 185 - 191 (chain B) in PDB entry 3D0E
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 LYS 185 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B LEU 3.6 1.2 + - - -
184B ARG* 1.3 70.9 - - - +
186B GLU* 1.3 57.1 + - - +
188B ILE* 3.2 9.7 + - - +
189B ILE* 2.9 41.5 + - + +
220B GLN* 2.7 29.9 + - - -
221B THR 2.9 25.7 + - - +
222B HIS 3.9 9.4 - - - +
223B ASP* 2.9 22.3 + - - +
224B ARG 3.6 11.0 - - - +
225B LEU* 3.7 18.6 - - + -
468B THR* 2.7 43.2 + - - +
469B HIS* 4.3 0.4 - - - +
470B PHE* 3.7 20.2 - - + -
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Residues in contact with GLU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ARG* 3.3 30.6 + - + +
185B LYS* 1.3 80.0 - - - +
187B VAL* 1.3 62.2 + - + +
189B ILE* 4.0 7.1 - - - +
190B ALA* 3.1 25.1 + - + +
223B ASP* 4.5 3.0 + - + +
453B PRO* 5.9 0.3 - - - +
454B ASP* 3.0 38.8 - - - +
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Residues in contact with VAL 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B THR* 3.8 18.6 - - + +
163B PHE* 4.7 8.7 - - - +
184B ARG* 3.3 48.7 + - + +
186B GLU* 1.3 72.6 - - + +
188B ILE* 1.3 62.6 + - + +
190B ALA* 3.4 5.3 + - - +
191B LYS* 2.9 59.7 + - + +
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Residues in contact with ILE 188 (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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163B PHE 5.4 3.4 - - - +
183B LEU* 3.4 35.7 - - + -
184B ARG 3.2 12.4 + - - +
185B LYS* 3.6 8.7 - - - +
187B VAL* 1.3 79.1 - - + +
189B ILE* 1.3 59.0 + - - +
191B LYS* 3.5 4.1 + - - -
192B ASP 3.2 3.3 + - - -
193B GLU* 3.0 48.5 + - + +
194B VAL* 3.9 12.1 + - + +
197B THR* 3.7 20.0 - - - +
225B LEU* 3.3 30.7 - - + -
470B PHE* 4.3 9.2 - - + -
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Residues in contact with ILE 189 (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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185B LYS* 2.9 28.2 + - + +
186B GLU* 4.0 5.8 - - - +
188B ILE* 1.3 73.8 - - - +
190B ALA* 1.3 66.8 + - - +
192B ASP* 3.0 14.0 + - - +
194B VAL* 4.1 22.8 - - + +
468B THR* 5.3 5.4 - - - +
470B PHE* 4.3 17.9 - - + -
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Residues in contact with ALA 190 (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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186B GLU* 3.1 17.7 + - + +
187B VAL* 3.7 6.3 - - - +
189B ILE* 1.3 79.8 - - - +
191B LYS* 1.3 63.1 + - + +
192B ASP* 3.4 2.9 + - - +
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Residues in contact with LYS 191 (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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162B THR* 3.2 46.0 + - - +
163B PHE* 3.8 6.6 - - - +
187B VAL* 2.9 39.0 + - + +
188B ILE* 4.0 5.2 - - - +
190B ALA* 1.3 76.8 - - + +
192B ASP* 1.3 70.6 + - - +
193B GLU* 3.5 22.2 + - + +
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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
------------------------------------------------------------
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