Contacts of the helix formed by residues 158 - 168 (chain F) in PDB entry 2ZU6
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 THR 158 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417E LEU 3.6 3.1 + - - -
418E ASP* 3.2 33.3 + - - +
107F ALA 3.4 14.1 - - - +
108F PRO 3.6 3.4 - - - +
109F THR* 3.4 37.7 - - - +
110F ARG* 3.5 5.6 - - - +
113F ALA* 5.2 0.9 - - + +
157F GLY* 1.3 72.6 - - - -
159F PRO* 1.3 75.8 - - - +
160F GLY 2.7 2.6 + - - -
161F ARG* 3.0 15.7 + - - +
162F VAL* 3.3 8.0 + - - +
192F PHE* 3.7 10.5 - - - -
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Residues in contact with PRO 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F LEU* 3.8 18.8 - - + -
107F ALA 3.5 13.0 - - - +
157F GLY 3.9 2.6 - - - +
158F THR* 1.3 85.2 - - - +
160F GLY* 1.3 56.3 + - - +
162F VAL* 4.0 1.8 - - + -
163F PHE* 2.9 30.5 + - - +
187F MET* 3.5 24.5 - - - -
192F PHE* 3.8 26.0 - - + -
195F GLN* 3.7 19.7 - - + -
196F ILE* 4.1 8.3 - - + -
199F ILE* 3.2 16.4 - - + +
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Residues in contact with GLY 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417E LEU* 3.0 34.2 - - - +
158F THR 2.7 7.1 + - - -
159F PRO* 1.3 76.9 - - - +
161F ARG* 1.3 56.6 + - - -
163F PHE* 4.0 6.2 - - - +
164F ASP* 3.7 11.6 + - - +
192F PHE* 3.5 11.7 - - - -
195F GLN* 4.1 14.5 - - - +
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Residues in contact with ARG 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414E ASP* 2.5 46.0 + - - -
417E LEU* 3.5 29.8 + - + +
418E ASP* 2.6 50.7 + - - +
134F CYS* 3.4 29.2 - - + -
135F ILE 3.6 8.4 + - - -
136F GLY* 3.7 15.3 - - - -
140F VAL* 4.6 3.6 - - - +
157F GLY* 6.0 0.2 - - - -
158F THR* 3.0 17.2 + - - +
160F GLY* 1.3 74.3 - - - +
162F VAL* 1.3 68.7 + - + +
163F PHE 3.4 0.4 - - - -
164F ASP* 3.0 4.7 + - - +
165F MET* 3.0 46.0 + - - +
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Residues in contact with VAL 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F LEU* 3.9 31.6 - - + -
106F LEU* 4.0 12.3 - - + -
134F CYS* 5.0 5.6 - - - -
155F ILE* 4.7 8.7 - - + -
157F GLY* 3.6 37.7 - - - +
158F THR 3.3 6.5 + - - +
159F PRO 3.9 2.9 - - - +
161F ARG* 1.3 74.3 - - + +
163F PHE* 1.3 67.0 + - - +
165F MET* 2.9 7.6 + - - +
166F LEU* 2.9 25.6 + - + +
171F LEU* 4.6 9.3 - - + +
199F ILE* 3.9 15.9 - - + -
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Residues in contact with PHE 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159F PRO 2.9 19.4 + - - +
160F GLY 4.0 7.2 - - - +
162F VAL* 1.3 76.3 - - - +
164F ASP* 1.3 67.8 + - + +
166F LEU* 4.2 3.6 - - + +
167F ASN* 3.1 37.9 + - - +
195F GLN* 4.6 14.4 - - + -
198F ASP* 3.1 48.9 - - + -
199F ILE* 3.5 22.8 - - + +
202F LYS* 4.8 17.8 - - + -
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Residues in contact with ASP 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417E LEU* 3.8 30.7 - - + +
160F GLY 3.7 5.7 + - - +
161F ARG 3.0 12.0 + - - +
163F PHE* 1.3 85.7 - - + +
165F MET* 1.3 60.5 + - + +
167F ASN* 2.9 21.9 - - - +
168F ARG* 3.2 46.7 + - - +
170F TYR* 4.3 2.5 - - - -
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Residues in contact with MET 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F CYS* 4.4 22.2 - - + -
140F VAL* 6.2 1.3 - - + -
143F GLU* 3.5 29.2 - - + +
144F VAL* 6.1 5.8 - - + -
147F LEU* 4.8 18.6 - - + -
161F ARG* 3.0 41.8 + - - +
162F VAL* 2.9 6.5 + - - +
164F ASP* 1.3 78.7 - - + +
166F LEU* 1.3 65.5 + - - +
167F ASN 3.2 0.9 - - - -
168F ARG 3.7 0.3 - - - -
169F ARG 3.2 2.6 + - - -
170F TYR* 3.0 38.9 + - + +
171F LEU* 2.9 27.9 + - + -
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Residues in contact with LEU 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F LEU* 4.8 3.8 - - + -
162F VAL* 2.9 16.5 + - + +
163F PHE* 4.2 3.8 - - + +
165F MET* 1.3 72.6 - - - +
167F ASN* 1.3 70.9 + - - +
169F ARG* 3.3 7.3 + - - +
171F LEU* 3.5 36.9 - - + +
172F SER 4.2 0.4 - - - -
173F PRO* 3.3 42.7 - - + +
176F ILE* 5.3 0.4 - - + -
199F ILE* 4.4 17.7 - - + +
202F LYS* 4.3 25.5 + - + +
203F LEU* 4.2 25.1 - - + -
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Residues in contact with ASN 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163F PHE* 3.1 34.5 + - + +
164F ASP* 2.9 17.9 - - - +
166F LEU* 1.3 75.1 - - - +
168F ARG* 1.3 91.6 + - - +
169F ARG* 2.5 28.7 + - - +
202F LYS* 4.2 21.6 + - - +
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Residues in contact with ARG 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F ASP* 3.2 49.0 + - - -
165F MET 3.7 1.1 + - - -
167F ASN* 1.3 89.2 - - - +
169F ARG* 1.3 57.4 + - - +
170F TYR* 2.7 62.2 + - + +
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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