Contacts of the helix formed by residues 169 - 175 (chain A) in PDB entry 4IXU
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 ARG 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A PRO 4.7 8.3 + - - -
167A LEU 3.5 1.0 + - - -
168A LEU* 1.3 71.0 - - - +
170A GLU* 1.3 70.7 + - - +
171A LEU 3.1 1.2 + - - -
172A GLN* 3.2 31.0 + - - +
186A PRO* 3.8 35.1 + - + +
187A CYS* 3.3 26.1 + - - +
188A ILE 2.8 14.3 + - - +
189A SER* 4.0 22.3 - - - +
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Residues in contact with GLU 170 (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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168A LEU* 3.3 2.4 - - + +
169A ARG* 1.3 77.3 + - - +
171A LEU* 1.3 63.7 + - + +
172A GLN* 3.5 0.6 - - - +
173A ASP* 3.7 11.1 - - - +
189A SER* 3.1 28.7 + - - -
190A SER* 2.9 38.8 + - - +
212A TYR* 3.4 33.4 - - + -
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Residues in contact with LEU 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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148A ILE* 4.1 9.9 - - + -
150A THR* 4.6 10.1 - - + -
165A SER* 3.9 35.4 - - - +
168A LEU* 3.3 30.4 + - + +
169A ARG 3.1 1.4 + - - -
170A GLU* 1.3 78.7 - - + +
172A GLN* 1.3 54.0 + - - +
173A ASP* 3.2 4.9 - - - -
174A LYS* 2.9 29.3 + - + +
175A VAL* 3.3 14.2 - - + +
208A ILE* 4.0 19.3 - - + -
212A TYR* 3.5 47.3 - - + -
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Residues in contact with GLN 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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165A SER 5.8 0.4 - - - -
168A LEU 4.0 3.5 + - - -
169A ARG* 3.2 24.2 + - - +
170A GLU 3.5 1.0 - - - -
171A LEU* 1.3 75.4 - - - +
173A ASP* 1.3 64.0 + - + +
174A LYS 3.0 1.4 + - - -
175A VAL* 3.1 24.4 + - - +
186A PRO* 3.5 31.5 - - + +
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Residues in contact with ASP 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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170A GLU 3.7 16.9 - - - +
171A LEU 3.7 0.5 - - - +
172A GLN* 1.3 78.0 - - + +
174A LYS* 1.3 90.0 + - - +
175A VAL 3.5 0.7 - - - -
212A TYR* 4.5 0.5 + - - -
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Residues in contact with LYS 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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150A THR* 4.2 14.0 + - + -
152A LEU* 3.7 17.5 - - + +
171A LEU* 2.9 11.4 + - + +
173A ASP* 1.3 109.5 + - - +
175A VAL* 1.3 60.3 + - + +
176A PRO* 3.5 9.9 - - - +
212A TYR* 3.9 21.1 + - - +
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Residues in contact with VAL 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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150A THR* 4.0 20.9 - - + -
151A PRO* 4.2 4.3 - - + -
165A SER* 3.5 23.1 - - - +
166A PHE* 3.7 33.2 - - + -
171A LEU* 3.3 17.9 - - + +
172A GLN* 3.1 18.2 + - - +
173A ASP 3.5 0.8 - - - -
174A LYS* 1.3 81.1 - - - +
176A PRO* 1.3 77.9 - - + +
177A GLN* 3.8 0.5 + - - -
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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