Contacts of the helix formed by residues 157 - 169 (chain A) in PDB entry 3PPA
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 THR 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A ALA 4.2 8.7 - - - +
156A ASP* 1.3 78.6 - - - +
158A ILE* 1.3 67.5 + - - +
159A ASP* 3.8 3.8 + - - +
160A THR* 2.8 43.9 + - + +
161A ILE* 3.0 12.5 + - - +
194A PRO 3.5 14.2 + - - -
195A ASP* 3.4 22.2 - - - +
196A SER 3.1 8.5 - - - +
197A THR* 4.7 4.3 - - + +
198A ILE* 5.7 0.4 - - - -
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Residues in contact with ILE 158 (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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157A THR* 1.3 70.7 - - - +
159A ASP* 1.3 64.6 + - - +
161A ILE* 3.1 12.9 + - + +
162A GLU* 2.9 36.4 + - - +
179A LEU* 4.5 7.2 - - + -
191A LEU* 3.4 41.1 - - + +
193A LYS 3.5 23.8 - - - +
194A PRO* 3.3 4.4 + - + +
196A SER 2.9 17.4 + - - +
198A ILE* 4.3 9.2 - - - -
201A ALA* 3.7 31.2 - - + -
203A LEU* 3.9 20.2 - - + -
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Residues in contact with ASP 159 (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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157A THR* 3.8 6.1 - - - +
158A ILE* 1.3 78.2 - - - +
160A THR* 1.3 58.6 + - + +
162A GLU* 3.5 5.8 + - - +
163A LYS* 2.8 50.0 + - - +
194A PRO* 2.9 33.8 + - + +
195A ASP* 5.3 3.8 - - - +
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Residues in contact with THR 160 (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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156A ASP* 3.6 15.1 - - - +
157A THR* 2.8 45.0 + - + +
159A ASP* 1.3 76.0 - - - +
161A ILE* 1.3 63.0 + - - +
163A LYS* 3.4 11.1 + - + +
164A GLU* 3.2 21.8 + - - +
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Residues in contact with ILE 161 (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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136A LEU* 4.8 4.0 - - + -
152A PHE* 3.4 49.6 - - + -
156A ASP* 5.1 5.8 - - + +
157A THR 3.0 11.1 + - - +
158A ILE* 3.1 34.8 - - + +
160A THR* 1.3 73.6 + - - +
162A GLU* 1.3 56.5 + - - +
164A GLU* 3.2 5.5 + - - +
165A ILE* 2.9 39.2 + - + +
179A LEU* 3.7 21.5 - - + -
198A ILE* 5.8 6.3 - - + -
203A LEU* 5.5 2.0 - - + -
209A LEU* 4.7 8.1 - - + -
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Residues in contact with GLU 162 (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 ILE* 2.9 26.6 + - - +
159A ASP* 3.7 6.8 - - - +
161A ILE* 1.3 73.1 - - - +
163A LYS* 1.4 56.1 + - + +
165A ILE* 3.2 10.3 + - - +
166A ARG* 2.9 43.4 + - - +
177A THR* 3.0 28.8 - - + +
178A ARG* 3.4 12.2 + - - -
179A LEU* 3.4 33.1 + - + +
191A LEU 4.5 3.3 - - - +
211A ILE* 3.8 17.7 - - + -
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Residues in contact with LYS 163 (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 ASP* 2.8 46.0 + - - +
160A THR* 3.6 9.6 - - + +
162A GLU* 1.4 75.5 - - + +
164A GLU* 1.3 57.0 + - - +
166A ARG* 3.4 42.8 + - - +
167A LYS* 3.1 25.3 + - - +
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Residues in contact with GLU 164 (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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152A PHE* 4.3 18.2 - - + -
160A THR 3.2 12.2 + - - +
161A ILE* 3.2 9.6 + - - +
163A LYS* 1.3 74.7 - - - +
165A ILE* 1.4 58.7 + - - +
167A LYS* 3.0 11.4 + - - +
168A ILE* 3.0 36.4 + - + +
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Residues in contact with ILE 165 (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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138A LEU* 3.7 37.7 - - + -
139A CYS 5.4 0.2 - - - +
152A PHE* 4.4 5.4 - - + -
161A ILE* 2.9 32.2 + - + +
162A GLU 3.2 4.9 + - - +
164A GLU* 1.4 74.1 - - - +
166A ARG* 1.4 51.0 + - - +
168A ILE* 3.3 6.6 + - - +
169A PHE* 2.8 48.6 + - + +
179A LEU* 3.8 16.6 - - + -
209A LEU* 3.8 17.7 - - + -
211A ILE* 3.7 36.1 - - + +
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Residues in contact with ARG 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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162A GLU* 2.9 21.3 + - - +
163A LYS* 3.4 54.2 + - - +
165A ILE* 1.4 74.3 - - - +
167A LYS* 1.4 58.9 + - - +
169A PHE 3.7 0.2 - - - -
170A SER 3.0 8.7 + - - -
171A ILE* 2.7 71.3 + - + +
173A ASP* 4.6 26.1 + - - +
175A LYS 4.7 4.7 + - - -
177A THR* 3.6 29.6 - - - +
211A ILE* 3.7 15.5 - - + -
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Residues in contact with LYS 167 (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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163A LYS 3.1 11.9 + - - +
164A GLU* 3.0 14.0 + - - +
166A ARG* 1.4 76.8 - - - +
168A ILE* 1.4 63.8 + - + +
170A SER* 3.4 10.1 + - - +
171A ILE 5.6 0.2 - - - -
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Residues in contact with ILE 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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138A LEU* 3.8 23.6 - - + -
148A VAL* 3.7 30.7 - - + -
150A ARG* 3.5 39.0 - - + +
152A PHE* 4.9 2.0 - - + -
164A GLU* 3.0 32.8 + - + +
165A ILE* 3.3 8.3 + - + +
167A LYS* 1.4 77.6 - - + +
169A PHE* 1.3 74.0 + - + +
170A SER* 3.4 8.0 + - - -
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Residues in contact with PHE 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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138A LEU* 3.4 45.1 - - + -
139A CYS* 3.6 15.0 - - - -
140A GLU* 3.4 46.3 - - + +
146A ASN* 4.1 24.5 - - + -
148A VAL* 4.0 22.0 - - + -
165A ILE* 2.8 40.9 + - + +
166A ARG 3.7 0.2 - - - -
168A ILE* 1.3 80.5 - - + +
170A SER* 1.4 71.0 + - - +
171A ILE* 3.5 11.2 - - + +
211A ILE* 4.2 1.3 - - + -
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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