Contacts of the helix formed by residues 163 - 167 (chain A) in PDB entry 4DTZ
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 ASN 163 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A GLN* 5.1 4.9 + - - +
151A ASP* 3.2 9.4 + - - -
161A ARG* 3.2 20.0 + - - +
162A PHE* 1.3 77.8 - - - +
164A SER* 1.3 65.8 + - - +
165A PHE 3.1 3.1 - - - -
166A TYR* 3.0 42.0 + - + +
167A ARG* 3.5 16.7 - - - +
129B LYS 5.4 0.6 + - - -
132B ARG* 2.9 47.5 + - - +
133B LEU* 4.3 11.1 - - - +
137B GLU* 4.3 7.9 + - - -
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Residues in contact with SER 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ARG* 3.6 39.3 + - - -
150A LEU* 4.8 1.6 - - - +
151A ASP* 2.6 36.2 + - - -
162A PHE* 3.2 3.2 + - - +
163A ASN* 1.3 75.1 - - - +
165A PHE* 1.3 59.8 + - - -
166A TYR 3.1 1.8 + - - -
167A ARG* 3.4 27.3 + - - +
170A PRO* 5.5 4.6 - - - +
174A ILE* 3.6 20.4 - - - +
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Residues in contact with PHE 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ILE* 4.0 25.4 - - + -
125A GLN* 3.8 34.5 + - + +
126A LEU* 3.7 39.5 - - + -
129A LYS* 3.8 19.0 + - + +
144A ASP* 3.8 21.8 - - - -
147A ARG* 3.5 33.7 - - + +
148A LEU* 3.8 10.3 - - - -
151A ASP* 4.3 5.4 + - - -
163A ASN 3.1 1.2 - - - -
164A SER* 1.3 76.9 - - - +
166A TYR* 1.3 60.2 + - + +
167A ARG 3.4 2.7 - - - -
165B PHE 3.9 0.5 - - - +
166B TYR* 3.1 42.5 - - + +
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Residues in contact with TYR 166 (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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125A GLN* 3.8 19.7 - - - -
163A ASN* 3.0 44.0 + - + +
165A PHE* 1.3 82.3 - - + +
167A ARG* 1.3 61.7 + - + +
125B GLN* 4.7 2.9 + - + -
128B GLN* 4.0 2.3 - - - +
129B LYS* 3.5 59.9 + - + -
132B ARG* 2.9 34.6 + - + -
147B ARG* 5.4 1.6 + - - -
165B PHE* 3.1 37.3 - - + +
166B TYR* 3.9 4.9 - + - -
167B ARG 3.8 14.7 + - - +
168B ASP* 4.6 3.3 - - - +
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Residues in contact with ARG 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ARG* 3.8 15.8 + - - -
162A PHE 3.0 26.7 + - - -
163A ASN* 3.5 17.9 + - - +
164A SER* 3.4 16.9 - - - +
165A PHE 3.4 2.5 + - - -
166A TYR* 1.3 86.6 - - + +
168A ASP* 1.3 59.4 + - - +
169A GLN 3.3 25.5 + - - +
170A PRO* 3.9 4.4 + - + -
171A HIS* 3.5 44.9 - - - +
172A PRO* 4.5 5.9 - - - +
137B GLU* 4.0 13.3 + - - -
166B TYR 3.9 13.5 + - - +
168B ASP* 3.5 13.4 + - - +
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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