Contacts of the helix formed by residues 169 - 180 (chain A) in PDB entry 3PEJ
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 GLY 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A GLU* 3.5 20.1 + - - -
166A ALA 4.8 1.2 + - - -
167A LYS* 3.7 1.8 - - - +
168A SER* 1.3 77.8 - - - +
170A THR* 1.3 63.3 + - - +
171A SER 3.2 2.9 - - - -
172A ASN* 3.1 35.6 + - - +
173A PHE* 3.5 10.4 - - - -
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Residues in contact with THR 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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80A GLU* 3.0 8.6 + - - -
84A LEU* 4.2 2.0 - - + -
165A ILE* 5.1 1.9 + - - -
168A SER* 3.4 16.9 - - - -
169A GLY* 1.3 71.3 - - - +
171A SER* 1.3 64.4 + - - +
173A PHE* 3.0 25.9 + - + +
174A LEU* 3.0 13.2 + - + +
190A PHE* 3.7 44.6 + - + -
192A VAL* 3.9 28.9 - - + +
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Residues in contact with SER 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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80A GLU* 2.6 33.7 + - - -
83A ARG* 3.0 45.4 + - - -
84A LEU* 3.7 16.4 - - - +
87A ILE* 3.4 8.7 - - - +
169A GLY 4.3 0.2 - - - -
170A THR* 1.3 76.7 - - - +
172A ASN* 1.4 55.8 + - - +
174A LEU* 3.3 2.2 + - - -
175A GLU* 2.7 36.7 + - - +
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Residues in contact with ASN 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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83A ARG* 2.6 33.6 + - - +
169A GLY* 3.1 23.1 + - - +
170A THR 3.1 0.2 - - - -
171A SER* 1.4 80.1 + - - +
173A PHE* 1.3 67.7 + - + +
175A GLU* 3.4 4.7 + - - +
176A ALA* 3.0 24.3 + - - +
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Residues in contact with PHE 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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168A SER 4.6 9.6 - - - -
169A GLY 3.5 16.2 - - - -
170A THR* 3.0 15.6 + - + +
172A ASN* 1.3 80.1 - - + +
174A LEU* 1.4 50.8 + - - +
176A ALA* 3.4 6.6 + - - +
177A ILE* 2.9 41.9 + - + +
190A PHE* 3.9 29.4 - + + -
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Residues in contact with LEU 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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84A LEU* 3.8 27.6 - - + +
87A ILE* 3.8 17.7 - - + -
88A ILE* 4.1 15.3 - - + -
170A THR* 3.0 16.8 + - + +
171A SER* 3.7 5.8 - - - +
173A PHE* 1.4 72.7 - - - +
175A GLU* 1.4 53.0 + - - +
177A ILE* 3.1 13.0 + - + +
178A SER* 2.8 36.0 + - - -
184A MET* 3.8 12.4 - - + +
186A LEU* 5.7 0.7 - - + -
187A ILE* 4.0 30.3 - - + +
190A PHE* 3.8 30.1 - - + -
192A VAL* 4.2 4.7 - - + -
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Residues in contact with GLU 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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83A ARG* 2.8 41.7 + - - +
87A ILE* 3.8 16.7 - - + +
171A SER 2.7 19.7 + - - +
172A ASN* 3.6 5.8 - - - +
174A LEU* 1.4 71.3 - - - +
176A ALA* 1.3 56.9 + - - +
178A SER* 3.3 4.4 + - - -
179A LYS* 2.9 70.7 + - + +
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Residues in contact with ALA 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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172A ASN 3.0 17.5 + - - +
173A PHE* 3.5 7.4 - - - +
175A GLU* 1.3 75.8 - - - +
177A ILE* 1.4 59.9 + - + +
179A LYS* 3.5 8.3 + - - +
180A SER* 2.8 33.9 + - - +
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Residues in contact with ILE 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 PHE* 2.9 28.6 + - + +
174A LEU* 3.1 14.1 + - + +
176A ALA* 1.4 76.0 - - + +
178A SER* 1.3 56.5 + - - +
180A SER* 3.2 10.6 + - - -
182A GLY* 2.8 42.8 + - - -
183A ASP 3.3 27.4 - - - +
184A MET* 3.9 7.6 - - + -
186A LEU* 4.4 15.9 - - + -
190A PHE* 3.9 26.7 - - + -
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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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87A ILE* 4.2 11.2 - - - +
90A ASN* 4.4 9.4 + - - -
91A SER* 3.0 25.3 + - - -
174A LEU 2.8 18.9 + - - -
175A GLU* 3.6 4.5 - - - -
177A ILE* 1.3 74.6 - - - +
179A LYS* 1.3 61.6 + - - +
181A GLY* 3.1 14.7 + - - -
182A GLY 4.5 8.2 - - - +
184A MET* 4.4 1.6 - - - -
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Residues in contact with LYS 179 (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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175A GLU* 2.9 51.5 + - + +
176A ALA* 3.9 7.2 - - - +
178A SER* 1.3 76.3 - - - +
180A SER* 1.3 58.5 + - - +
181A GLY 3.4 0.8 + - - -
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Residues in contact with SER 180 (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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176A ALA* 2.8 23.2 + - - +
177A ILE* 3.7 6.3 - - - -
178A SER 3.1 0.4 - - - -
179A LYS* 1.3 76.2 - - - +
181A GLY* 1.3 59.8 + - - +
182A GLY* 3.3 1.9 + - - -
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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