Contacts of the helix formed by residues 158 - 170 (chain X) in PDB entry 2ZG8
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 158 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154X LEU 3.2 5.7 + - - +
155X VAL 3.8 1.1 + - - -
157X SER* 1.3 90.9 + - - +
159X ALA* 1.3 56.1 + - - +
160X GLY 3.6 1.1 - - - +
161X LEU* 3.8 35.3 - - + +
162X GLY* 2.7 34.8 + - - -
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Residues in contact with ALA 159 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155X VAL* 3.8 25.7 + - + +
158X GLN* 1.3 71.4 - - - +
160X GLY* 1.3 65.4 + - - +
162X GLY* 3.8 0.2 - - - -
163X GLU* 2.9 35.3 + - - +
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Residues in contact with GLY 160 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158X GLN* 3.6 0.4 - - - +
159X ALA* 1.3 78.9 - - - +
161X LEU* 1.3 62.8 + - - +
163X GLU* 3.4 4.9 + - - +
164X TYR* 3.1 23.6 + - - +
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Residues in contact with LEU 161 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158X GLN* 3.8 34.6 + - + +
159X ALA 3.4 0.2 - - - -
160X GLY* 1.3 74.8 - - - +
162X GLY* 1.3 58.6 + - - +
164X TYR* 3.4 10.0 + - + +
165X LEU* 2.9 59.5 + - + +
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Residues in contact with GLY 162 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151X ILE* 4.2 2.7 - - - -
154X LEU* 3.7 37.6 - - - +
155X VAL* 4.4 0.7 - - - -
158X GLN* 2.7 24.1 + - - +
159X ALA 3.8 0.2 - - - -
161X LEU* 1.3 75.9 - - - +
163X GLU* 1.3 56.0 + - - +
165X LEU* 3.3 0.4 + - - -
166X PHE* 3.0 31.0 + - - +
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Residues in contact with GLU 163 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44X LEU* 3.8 13.3 - - + +
91X THR* 3.4 18.7 - - - +
92X THR* 2.7 33.9 + - - +
93X PRO* 4.1 3.3 - - - +
151X ILE* 3.8 12.7 - - + +
155X VAL* 3.8 15.8 - - + +
159X ALA* 2.9 25.2 + - - +
160X GLY* 3.9 4.3 - - - +
162X GLY* 1.3 75.7 - - - +
164X TYR* 1.3 62.1 + - - +
166X PHE* 3.5 2.4 + - - +
167X GLU* 3.1 24.4 + - - +
184X EDO 2.7 31.2 + - - -
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Residues in contact with TYR 164 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44X LEU* 4.6 12.3 - - + +
160X GLY 3.1 16.6 + - - +
161X LEU* 3.6 10.5 - - + +
163X GLU* 1.3 76.3 - - - +
165X LEU* 1.3 79.0 + - + +
167X GLU* 3.3 8.0 + - - +
168X ARG* 3.0 63.2 + - + +
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Residues in contact with LEU 165 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154X LEU* 4.5 19.7 - - + -
161X LEU* 2.9 47.9 + - + +
162X GLY 3.9 3.6 - - - +
164X TYR* 1.3 89.9 - - + +
166X PHE* 1.3 58.3 + - - +
168X ARG* 4.5 2.9 - - + -
169X LEU* 2.8 58.7 + - + +
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Residues in contact with PHE 166 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47X VAL* 5.5 0.7 - - + -
92X THR* 4.4 14.6 - - + -
96X MET* 4.7 4.0 - - + -
147X HIS* 3.7 38.6 - + + -
150X ASN* 3.7 27.6 - - + -
151X ILE* 3.6 28.5 - - + -
154X LEU* 3.7 14.3 - - + +
162X GLY 3.0 17.6 + - - +
163X GLU 3.9 2.0 - - - +
164X TYR 3.3 0.2 - - - -
165X LEU* 1.3 77.4 - - - +
167X GLU* 1.3 64.1 + - + +
169X LEU* 5.4 0.2 - - - -
170X THR* 2.9 53.9 + - + +
171X LEU* 3.2 33.9 + - + -
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Residues in contact with GLU 167 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43X ALA 5.4 0.6 - - - +
44X LEU* 3.9 29.1 - - + +
45X GLU 3.5 8.6 + - - -
46X GLY* 2.8 34.7 + - - +
47X VAL* 4.1 9.9 - - + +
163X GLU 3.1 14.9 + - - +
164X TYR* 3.7 6.8 - - - +
166X PHE* 1.3 80.9 - - - +
168X ARG* 1.3 103.2 + - - +
171X LEU* 4.3 9.0 - - - -
172X LYS* 2.9 36.6 + - - +
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Residues in contact with ARG 168 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45X GLU* 5.1 5.3 - - - +
164X TYR* 3.0 59.2 + - + +
165X LEU* 3.8 5.6 - - + +
167X GLU* 1.3 111.8 + - - +
169X LEU* 1.3 75.7 + - + +
170X THR 3.7 0.2 - - - -
172X LYS* 3.2 47.1 + - - +
190X EDO 2.9 33.3 + - - -
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Residues in contact with LEU 169 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165X LEU* 2.8 40.6 + - + +
168X ARG* 1.3 92.1 - - + +
170X THR* 1.3 62.3 + - - +
172X LYS 5.9 0.2 - - - -
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Residues in contact with THR 170 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147X HIS* 3.7 26.2 + - + +
150X ASN* 5.2 5.6 + - - +
166X PHE* 2.9 46.9 + - + -
169X LEU* 1.3 81.8 + - - +
171X LEU* 1.3 65.8 + - + +
172X LYS 3.8 3.0 - - - +
180X SO4 5.3 2.9 - - - +
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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