Contacts of the helix formed by residues 169 - 177 (chain A) in PDB entry 1AO3
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 ILE 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A TYR* 3.8 58.2 - - + +
24A GLU* 3.3 36.3 - - + +
25A MET* 4.2 14.8 - - + -
116A THR* 5.5 0.2 - - + -
142A ILE* 3.8 36.4 - - + +
168A ARG* 1.3 71.6 - - - +
170A GLU* 1.3 78.6 + - + +
172A LEU* 3.0 34.7 + - + +
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Residues in contact with GLU 170 (chain A).
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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24A GLU* 4.0 20.3 - - - +
168A ARG* 3.1 48.9 + - - +
169A ILE* 1.3 93.4 + - + +
171A ASP* 1.3 60.2 + - - +
172A LEU 3.2 0.8 + - - -
173A PRO* 3.9 12.7 - - - +
174A THR* 4.3 7.8 - - - -
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Residues in contact with ASP 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A LEU* 3.9 18.5 - - + +
167A GLN* 3.1 27.8 + - - +
168A ARG* 3.0 51.1 + - - +
170A GLU* 1.3 77.6 - - - +
172A LEU* 1.3 60.5 + - - +
174A THR* 2.9 31.5 - - + +
175A MET* 3.3 9.7 + - - +
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Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLU 4.7 0.2 - - - +
25A MET* 4.1 15.7 - - + +
28A PHE* 3.7 38.1 - - + -
114A LEU* 3.7 31.2 - - + -
140A ILE* 4.2 15.0 - - + -
142A ILE* 3.9 14.4 - - + -
166A LEU* 3.5 24.5 - - + +
168A ARG 4.0 0.2 + - - -
169A ILE* 3.0 22.5 + - + +
171A ASP* 1.3 75.0 - - - +
173A PRO* 1.3 70.7 - - + +
175A MET* 3.0 22.7 + - + +
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Residues in contact with PRO 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLU* 3.9 30.7 - - + +
27A SER* 4.0 13.0 - - - +
28A PHE* 3.9 30.1 - - + +
31A ALA* 5.3 0.4 - - + -
169A ILE 3.7 7.6 - - - +
170A GLU 3.9 7.2 - - - +
172A LEU* 1.3 95.2 - - + +
174A THR* 1.3 57.0 + - - +
175A MET 3.0 5.5 + - - -
176A VAL* 3.0 19.7 + - + +
177A THR* 3.1 18.1 + - + +
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Residues in contact with THR 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A GLU 4.3 7.4 - - - +
171A ASP* 2.9 35.9 + - + +
172A LEU 3.2 1.0 - - - -
173A PRO* 1.3 80.7 - - - +
175A MET* 1.3 57.9 + - - +
176A VAL 3.2 0.2 - - - -
177A THR* 3.1 13.2 + - - -
178A LEU* 3.0 56.7 + - + +
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Residues in contact with MET 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PHE* 3.7 21.8 - - + -
140A ILE* 3.6 28.0 - - + -
164A VAL* 3.9 27.1 - - - -
166A LEU* 4.1 16.4 - - + -
171A ASP 3.7 7.4 - - - +
172A LEU* 3.0 17.6 + - + +
173A PRO 3.0 0.4 + - - -
174A THR* 1.3 82.7 - - - +
176A VAL* 1.3 59.2 + - + +
178A LEU* 4.6 2.1 - - - -
179A GLY 3.9 8.6 - - - +
181A SER* 5.3 2.6 + - - -
182A PHE* 4.1 36.6 + - + +
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Residues in contact with VAL 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PHE* 3.5 36.6 - - + +
31A ALA* 3.2 35.0 - - + +
32A PHE* 3.9 19.5 - - + +
35A LYS* 3.1 25.5 - - - +
173A PRO 3.0 11.9 + - - +
175A MET* 1.3 85.5 - - + +
177A THR* 1.3 60.1 + - - +
178A LEU 3.6 0.2 - - - -
179A GLY 3.3 12.8 - - - +
182A PHE* 4.6 12.6 - - + -
183A LEU* 4.5 12.6 - - + +
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Residues in contact with THR 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ALA* 3.8 22.9 - - + -
35A LYS* 4.3 13.0 + - + +
173A PRO* 3.4 14.6 - - + +
174A THR* 3.1 22.3 + - - -
176A VAL* 1.3 77.1 - - - +
178A LEU* 1.3 62.7 + - - +
179A GLY 3.0 11.0 + - - -
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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