Contacts of the helix formed by residues 166 - 173 (chain E) in PDB entry 2ZSU
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 VAL 166 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49E ASP* 5.7 4.5 - - - +
163E THR* 5.5 1.9 + - - +
164E ASP* 2.7 26.1 + - + +
165E PRO* 1.3 73.0 - - - +
167E GLY* 1.3 67.7 + - - +
168E PRO* 3.4 7.3 - - - +
169E ALA* 4.1 5.0 + - - +
170E GLU 4.2 0.6 - - - +
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Residues in contact with GLY 167 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166E VAL* 1.3 76.1 - - - +
168E PRO* 1.3 65.3 - - - +
170E GLU* 2.9 37.6 + - - +
171E MET* 4.5 3.1 + - - +
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Residues in contact with PRO 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E TYR* 6.1 7.4 - - + +
108E ILE* 6.1 5.2 - - + -
146E VAL* 5.6 0.9 - - - +
166E VAL 3.6 6.5 - - - +
167E GLY* 1.3 79.1 - - - +
169E ALA* 1.3 59.3 + - - +
170E GLU 2.9 10.1 + - - -
171E MET* 3.2 22.2 + - + +
172E LEU* 4.7 0.7 + - - +
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Residues in contact with ALA 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E SER* 4.5 7.4 - - - -
163E THR* 3.2 36.8 - - - +
164E ASP 3.6 13.9 - - - +
165E PRO* 4.2 1.8 - - - -
166E VAL 4.1 3.2 + - - +
167E GLY 3.6 0.4 - - - -
168E PRO* 1.3 79.3 - - - +
170E GLU* 1.3 57.2 + - - +
171E MET 3.1 0.4 - - - -
172E LEU* 2.9 36.5 + - + +
173E PHE* 3.8 6.4 - - - -
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Residues in contact with GLU 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E PRO* 3.8 33.0 - - + +
167E GLY* 2.9 27.7 + - - +
168E PRO 2.9 0.6 + - - -
169E ALA* 1.3 78.1 - - - +
171E MET* 1.3 79.7 + - + +
173E PHE* 3.0 18.6 + - + +
174E SER* 3.6 5.2 + - - -
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Residues in contact with MET 171 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146E VAL* 3.7 27.8 - - + +
167E GLY 4.7 2.7 - - - +
168E PRO* 3.2 12.5 + - + +
169E ALA 3.1 1.0 + - - -
170E GLU* 1.3 104.8 - - + +
172E LEU* 1.3 57.2 + - - +
173E PHE 3.0 7.6 + - - -
174E SER* 2.8 35.3 + - - +
177E PHE* 3.0 13.7 - - - +
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Residues in contact with LEU 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E ILE* 3.9 29.2 - - + -
144E ASP* 5.4 2.2 - - - +
145E GLY* 4.8 0.9 - - - +
146E VAL* 3.6 27.1 - - + +
160E VAL* 4.1 10.2 - - + +
162E SER* 3.5 29.2 - - - -
168E PRO 5.5 0.2 - - - +
169E ALA* 2.9 21.9 + - + +
171E MET* 1.3 76.5 - - - +
173E PHE* 1.3 68.7 + - + +
177E PHE* 3.1 46.5 - - + -
178E TYR* 3.9 3.1 + - - -
191E TYR* 3.7 7.8 + - - -
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Residues in contact with PHE 173 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160E VAL* 5.6 0.7 - - + -
162E SER* 3.7 20.0 - - - -
163E THR 4.3 1.1 - - - -
165E PRO* 3.5 33.7 - - + -
169E ALA 3.8 7.9 - - - -
170E GLU* 3.0 10.2 + - + +
171E MET 3.0 0.6 - - - -
172E LEU* 1.3 87.3 - - + +
174E SER* 1.4 56.3 + - - +
178E TYR* 3.3 38.2 - - - +
193E THR* 3.7 16.2 - - + -
194E GLN* 3.4 36.6 - - - -
195E ALA* 4.4 7.0 - - + -
204E GLU* 3.9 18.6 - - + -
208E ALA* 4.1 15.5 - - + -
211E LYS* 3.5 20.1 + - - +
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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