Contacts of the helix formed by residues 155 - 166 (chain B) in PDB entry 2AVN
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 ALA 155 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A ARG* 4.0 0.4 - - - +
249A PO4 3.4 13.2 - - - +
153B LYS 4.2 0.4 + - - -
154B ASP* 1.3 76.1 - - - +
156B TRP* 1.3 66.0 + - - +
157B ASP* 4.3 9.2 - - + +
158B GLN* 2.9 33.6 + - + +
159B ILE* 3.4 4.6 + - - +
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Residues in contact with TRP 156 (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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206A TYR* 4.2 15.0 - + - -
210A ARG* 3.5 40.0 - - + +
214A ARG* 3.5 46.9 - - - +
217A THR* 3.3 28.8 - - + +
218A ILE* 3.5 33.4 - - + -
221A LEU* 4.1 20.4 - - + -
249A PO4 2.8 10.7 + - - +
151B ILE* 4.3 10.3 - - + -
155B ALA* 1.3 71.3 - - - +
157B ASP* 1.3 63.5 + - - +
159B ILE* 3.0 36.2 + - + +
160B THR* 3.0 20.0 + - - +
163B LEU* 5.5 2.6 - - - +
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Residues in contact with ASP 157 (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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214A ARG* 5.0 8.4 + - - -
249A PO4 4.7 0.9 + - - -
155B ALA* 3.1 7.3 + - + +
156B TRP* 1.3 80.5 - - - +
158B GLN* 1.3 67.8 + - - +
160B THR* 3.6 11.0 + - - +
161B ARG* 3.4 20.3 + - - +
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Residues in contact with GLN 158 (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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150B MSE 3.4 17.5 - - + +
154B ASP* 4.4 7.9 - - + +
155B ALA* 2.9 28.3 + - + +
157B ASP* 1.3 80.8 - - - +
159B ILE* 1.3 65.7 - - - +
161B ARG* 3.4 6.9 + - - +
162B PHE* 3.0 24.4 + - - +
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Residues in contact with ILE 159 (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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210A ARG* 4.1 3.8 - - - +
221A LEU* 5.2 1.1 - - + -
147B LEU* 3.8 23.1 - - + -
150B MSE 3.7 44.9 - - + +
151B ILE* 3.8 19.5 - - + -
154B ASP* 4.1 6.1 - - + +
155B ALA 3.4 3.6 + - - +
156B TRP* 3.0 50.1 + - + +
158B GLN* 1.3 78.4 - - - +
160B THR* 1.3 57.3 + - - +
162B PHE* 3.2 4.0 + - - +
163B LEU* 2.9 37.6 + - + +
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Residues in contact with THR 160 (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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156B TRP* 3.0 24.7 + - - -
157B ASP* 3.6 14.9 + - - +
159B ILE* 1.3 79.7 - - - +
161B ARG* 1.3 63.5 + - - +
163B LEU* 3.4 19.4 + - - +
164B LYS* 3.5 17.8 + - + +
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Residues in contact with ARG 161 (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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157B ASP 3.4 10.4 + - - +
158B GLN* 3.4 10.9 + - - +
159B ILE 3.3 0.6 - - - -
160B THR* 1.3 80.1 - - - +
162B PHE* 1.3 59.5 + - - +
164B LYS* 3.1 8.9 + - + +
165B THR* 3.0 44.4 + - + +
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Residues in contact with PHE 162 (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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143B PHE* 3.5 46.1 - + - -
146B PHE* 3.5 34.3 - + + -
147B LEU* 4.0 21.1 - - + -
150B MSE 3.6 25.1 - - + -
158B GLN 3.0 17.1 + - - +
159B ILE 3.5 3.6 - - - +
161B ARG* 1.3 74.2 - - - +
163B LEU* 1.3 61.9 + - - +
165B THR* 3.8 5.6 - - - -
166B GLN* 2.8 49.5 + - - -
167B THR 3.5 26.2 - - - +
168B THR* 4.1 4.0 - - - -
181B ALA* 4.2 2.0 - - + -
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Residues in contact with LEU 163 (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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221A LEU* 4.2 25.6 - - + -
225A LEU* 6.2 0.7 - - + -
143B PHE* 3.9 27.7 - - + -
147B LEU* 3.8 31.2 - - + -
156B TRP* 5.5 2.7 - - - +
159B ILE* 2.9 31.2 + - + +
160B THR* 3.7 14.6 - - + +
161B ARG 3.3 0.4 - - - -
162B PHE* 1.3 76.8 - - - +
164B LYS* 1.3 62.0 + - + +
166B GLN* 4.6 3.6 + - - +
183B LYS* 4.8 6.8 + - - -
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Residues in contact with LYS 164 (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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160B THR* 3.5 18.4 + - + +
161B ARG* 3.1 9.5 + - + +
163B LEU* 1.3 80.2 - - + +
165B THR* 1.3 65.8 + - + +
166B GLN* 4.8 3.7 - - - +
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Residues in contact with THR 165 (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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161B ARG* 3.0 29.8 + - + +
162B PHE* 3.8 2.3 - - - -
164B LYS* 1.3 83.4 - - + +
166B GLN* 1.3 67.6 + - - +
167B THR* 2.9 44.0 + - - -
180B TYR* 3.7 9.5 - - - -
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Residues in contact with GLN 166 (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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143B PHE* 3.7 17.5 - - + -
162B PHE* 2.8 32.5 + - - +
163B LEU 4.7 5.6 - - - +
164B LYS 4.8 3.0 - - - +
165B THR* 1.3 78.7 + - - +
167B THR* 1.3 55.1 + - - +
179B SER 3.7 0.2 - - - +
180B TYR* 3.3 23.3 + - + -
181B ALA* 2.7 54.2 + - - +
183B LYS* 3.6 26.8 + - + +
186B ASP* 2.9 24.5 + - - +
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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