Contacts of the helix formed by residues 167 - 178 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118B THR* 4.9 2.5 - - - -
131B MET* 5.4 6.3 - - + -
165B GLY 3.6 4.0 + - - +
166B ILE* 1.3 73.9 - - - +
168B HIS* 1.3 67.2 + - - +
169B ARG* 4.5 4.5 - - + +
170B GLU* 3.1 40.2 + - + +
171B ILE* 3.0 21.7 + - - +
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Residues in contact with HIS 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ILE* 2.8 36.5 + - + +
117B GLN* 3.3 35.8 + - - +
118B THR* 3.4 29.7 + - + +
167B ARG* 1.3 71.1 - - - +
169B ARG* 1.3 99.0 + - + +
171B ILE* 3.3 3.4 + - - +
172B VAL* 2.9 42.9 + - + +
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Residues in contact with ARG 169 (chain B).
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* 4.6 1.1 - - - +
117B GLN* 5.7 2.8 + - - +
167B ARG* 3.4 5.8 - - + +
168B HIS* 1.3 115.6 + - - +
170B GLU* 1.3 63.4 - - + +
172B VAL* 3.6 6.9 + - + +
173B ASP* 3.1 32.3 + - - +
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Residues in contact with GLU 170 (chain B).
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* 4.7 6.6 - - - +
170A GLU* 3.6 40.0 + - + +
173A ASP* 2.3 42.2 - - - +
166B ILE* 3.6 11.7 - - + +
167B ARG* 3.1 30.3 + - + +
169B ARG* 1.3 76.7 - - + +
171B ILE* 1.3 55.0 + - - +
173B ASP* 3.1 4.0 + - - +
174B ILE* 2.7 42.1 + - + +
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Residues in contact with ILE 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ILE* 3.6 22.9 - - + -
133B THR* 3.8 22.0 - - + +
155B ILE* 6.1 0.7 - - + -
158B VAL* 5.4 2.5 - - + -
163B VAL* 4.8 16.8 - - + +
166B ILE* 3.4 28.7 - - + +
167B ARG 3.0 18.3 + - - +
168B HIS* 3.3 6.3 + - - +
170B GLU* 1.3 72.1 - - - +
172B VAL* 1.3 67.4 + - - +
174B ILE* 3.2 9.2 + - + +
175B ILE* 2.9 35.8 + - + +
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Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ILE* 4.1 17.9 - - + -
168B HIS* 2.9 44.4 + - + +
169B ARG* 3.7 7.9 - - + +
171B ILE* 1.3 77.8 - - - +
173B ASP* 1.3 60.5 + - - +
175B ILE* 3.2 4.9 + - - +
176B LYS* 3.0 55.4 + - + +
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Residues in contact with ASP 173 (chain B).
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* 4.9 6.1 - - + +
170A GLU* 2.6 41.4 - - - +
169B ARG* 3.1 15.9 + - - +
170B GLU 3.4 3.8 - - - +
172B VAL* 1.3 79.3 - - - +
174B ILE* 1.3 64.1 + - - +
176B LYS* 3.4 16.2 + - - +
177B ALA* 3.0 24.1 + - - +
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Residues in contact with ILE 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A LEU* 3.3 32.6 - - + +
166A ILE* 5.4 0.7 - - + -
170A GLU* 5.1 5.8 - - + +
174A ILE* 3.7 35.9 - - + +
158B VAL* 4.6 15.3 - - + -
161B LEU* 4.3 7.9 - - + -
163B VAL* 5.3 4.9 - - + -
166B ILE* 4.1 29.8 - - + -
170B GLU* 2.7 32.0 + - + +
171B ILE* 3.6 8.7 - - + +
173B ASP* 1.3 72.0 - - - +
175B ILE* 1.3 65.8 + - + +
177B ALA* 3.1 14.0 + - - +
178B SER 3.3 8.1 + - - -
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Residues in contact with ILE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B PHE* 4.5 13.3 - - + -
114B PHE* 4.2 24.7 - - + -
116B ILE* 4.1 13.2 - - + -
155B ILE* 4.6 11.0 - - + -
158B VAL* 4.5 22.2 - - + -
171B ILE* 2.9 37.4 + - + +
172B VAL* 3.8 4.7 - - - +
174B ILE* 1.3 73.9 - - + +
176B LYS* 1.3 69.2 + - + +
178B SER* 3.1 21.1 + - - -
179B GLY 4.4 1.2 + - - -
182B LEU* 3.8 26.6 - - + +
184B LEU* 5.8 0.7 - - + -
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Residues in contact with LYS 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B PHE* 6.2 0.2 - - - -
172B VAL* 3.0 41.8 + - + +
173B ASP* 3.8 15.1 + - - +
175B ILE* 1.3 78.7 - - + +
177B ALA* 1.3 58.7 + - - +
178B SER 3.1 1.1 + - - -
179B GLY* 3.7 9.9 + - - +
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Residues in contact with ALA 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A GLY 4.4 0.5 - - - +
161A LEU* 3.8 6.9 - - + -
162A ASN* 3.2 50.6 + - - +
166A ILE* 4.1 15.3 - - + -
173B ASP 3.0 17.8 + - - +
174B ILE* 3.5 7.9 - - - +
175B ILE 3.1 0.4 - - - -
176B LYS* 1.3 72.9 - - - +
178B SER* 1.3 60.2 + - - +
179B GLY* 3.1 8.2 + - - -
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Residues in contact with SER 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A GLY 4.3 9.8 - - - +
161A LEU* 3.5 16.4 - - - -
112B PHE* 5.1 0.2 - - - -
159B ASN* 2.7 27.5 + - - +
174B ILE 3.3 3.3 + - - -
175B ILE 3.1 16.7 + - - -
177B ALA* 1.3 76.4 - - - +
179B GLY* 1.3 63.2 + - - +
180B ASN 3.3 1.7 + - - -
181B VAL* 3.0 29.0 + - - +
182B LEU* 3.1 21.3 - - - +
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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