Contacts of the helix formed by residues 167 - 178 (chain A) in PDB entry 2PNT
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 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A MET* 4.3 13.5 - - + -
165A GLY 3.9 1.8 + - - -
166A ILE* 1.3 81.2 - - - +
168A HIS* 1.3 66.2 + - - +
169A ARG* 4.0 7.6 - - + +
170A GLU* 3.1 45.4 + - + +
171A ILE* 3.2 11.5 + - - +
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Residues in contact with HIS 168 (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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116A ILE* 3.4 43.3 - - + +
117A GLN* 4.0 4.0 - - - -
118A THR* 2.9 40.8 + - + +
131A MET* 5.2 2.5 - - + +
166A ILE 4.0 0.4 + - - -
167A ARG* 1.3 74.5 - - - +
169A ARG* 1.3 65.9 + - - +
171A ILE* 3.3 5.1 + - - +
172A VAL* 3.1 36.0 + - + +
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Residues in contact with ARG 169 (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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167A ARG* 3.3 8.3 - - + +
168A HIS* 1.3 83.1 - - + +
170A GLU* 1.3 61.9 + - + +
172A VAL* 3.4 7.4 + - - +
173A ASP* 3.0 31.6 + - - +
170B GLU* 4.7 8.5 - - - +
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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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166A ILE* 3.4 26.2 - - + +
167A ARG* 3.1 23.6 + - + +
169A ARG* 1.3 77.1 - - + +
171A ILE* 1.3 54.1 + - - +
173A ASP* 3.3 2.1 + - - +
174A ILE* 2.7 42.4 + - + +
169B ARG* 4.6 1.2 - - - +
170B GLU* 3.6 40.9 + - + +
173B ASP* 2.6 46.7 - - - +
174B ILE* 4.7 2.9 + - + +
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Residues in contact with ILE 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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116A ILE* 4.4 11.2 - - + -
133A THR* 3.0 35.2 - - + +
155A ILE* 5.4 2.0 - - + -
158A VAL* 4.6 5.4 - - + -
163A VAL* 3.5 47.1 - - + +
166A ILE* 3.4 25.6 - - + +
167A ARG 3.2 8.1 + - - +
168A HIS* 3.3 5.6 + - - +
170A GLU* 1.3 72.9 - - - +
172A VAL* 1.3 59.9 + - - +
174A ILE* 3.6 7.0 - - + +
175A ILE* 3.0 46.2 + - + +
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Residues in contact with VAL 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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1A CL 4.4 11.0 - - + -
116A ILE* 3.9 18.8 - - + -
168A HIS* 3.1 36.8 + - + +
169A ARG* 3.7 9.6 - - - +
171A ILE* 1.3 76.8 - - - +
173A ASP* 1.3 60.6 + - - +
175A ILE* 3.3 5.6 + - - +
176A LYS* 3.0 53.9 + - + +
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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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169A ARG* 3.0 17.9 + - - +
170A GLU 3.5 3.4 - - - +
172A VAL* 1.3 76.4 - - - +
174A ILE* 1.3 60.7 + - - +
176A LYS* 3.3 9.1 + - - +
177A ALA* 2.8 33.5 + - - +
166B ILE* 4.5 19.4 - - + +
170B GLU* 2.3 45.0 - - - +
174B ILE* 5.9 0.4 - - + -
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Residues in contact with ILE 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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158A VAL* 3.8 30.7 - - + -
161A LEU* 4.5 9.2 - - + -
163A VAL* 4.2 10.5 - - + -
166A ILE* 4.0 25.8 - - + -
170A GLU* 2.7 27.4 + - + +
171A ILE* 3.6 7.4 - - - +
173A ASP* 1.3 74.9 - - - +
175A ILE* 1.3 62.8 + - - +
177A ALA* 3.2 11.0 + - - +
178A SER 3.3 8.0 + - - -
161B LEU* 3.6 27.4 - - + +
174B ILE* 3.7 36.8 - - + -
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Residues in contact with ILE 175 (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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112A PHE* 4.5 15.6 - - + -
114A PHE* 4.3 23.8 - - + -
116A ILE* 4.1 17.0 - - + -
155A ILE* 4.7 8.3 - - + -
158A VAL* 4.4 14.1 - - + -
171A ILE* 3.0 35.1 + - + +
172A VAL* 3.8 4.5 - - - +
174A ILE* 1.3 75.4 - - - +
176A LYS* 1.3 64.1 + - + +
178A SER* 3.1 19.4 + - - -
179A GLY 4.2 1.7 + - - +
182A LEU* 3.7 37.4 - - + +
184A LEU* 5.1 0.7 - - + -
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Residues in contact with LYS 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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1A CL 3.4 29.3 - - - +
172A VAL* 3.0 34.4 + - + +
173A ASP* 3.8 9.4 - - - +
175A ILE* 1.3 78.0 - - + +
177A ALA* 1.3 58.3 + - - +
178A SER 3.1 1.1 + - - -
179A GLY* 3.6 9.9 + - - +
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Residues in contact with ALA 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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173A ASP 2.8 17.8 + - - +
174A ILE* 3.5 7.0 - - - +
175A ILE 3.2 0.2 - - - -
176A LYS* 1.3 71.8 - - - +
178A SER* 1.3 58.4 + - - +
179A GLY 3.2 6.3 + - - -
160B GLY 4.2 0.5 - - - +
161B LEU* 3.7 8.2 - - + -
162B ASN* 3.0 57.6 + - - +
166B ILE* 3.9 16.6 - - + -
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Residues in contact with SER 178 (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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159A ASN* 3.2 19.1 + - - -
174A ILE 3.3 7.5 + - - -
175A ILE 3.1 17.3 + - - -
177A ALA* 1.3 77.1 - - - +
179A GLY* 1.3 64.4 + - - +
180A ASN 3.5 1.2 + - - -
181A VAL* 2.8 37.5 + - - +
182A LEU* 3.2 23.0 - - - +
160B GLY 4.2 8.1 - - - +
161B LEU* 3.9 10.3 - - - -
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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