Contacts of the helix formed by residues 155 - 166 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A MSE 2.9 29.8 + - + +
153A LYS* 3.0 14.3 + - + +
154A ASP* 1.3 69.5 - - - +
156A TRP* 1.3 57.2 + - - +
157A ASP 3.4 2.5 - - - -
158A GLN* 3.0 38.3 + - + +
159A ILE* 2.9 29.9 + - - +
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Residues in contact with TRP 156 (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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151A ILE* 4.2 26.0 - - + -
154A ASP* 3.0 41.5 + - - +
155A ALA* 1.3 68.5 - - - +
157A ASP* 1.3 67.9 + - - +
158A GLN 3.1 2.1 + - - -
159A ILE* 3.4 37.1 + - + +
160A THR* 3.6 15.2 + - - -
206B TYR* 4.1 11.9 - + - -
207B PRO* 6.5 0.2 - - + -
210B ARG* 5.0 7.3 - - + +
214B ARG* 3.0 56.3 - - - +
217B THR* 3.8 28.3 - - + -
218B ILE* 3.7 30.3 - - + -
221B LEU* 4.6 13.2 - - + -
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Residues in contact with ASP 157 (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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155A ALA 3.4 0.8 - - - -
156A TRP* 1.3 79.5 - - - +
158A GLN* 1.3 64.3 + - + +
160A THR* 4.1 13.1 - - - -
161A ARG* 4.3 9.9 + - - +
214B ARG* 5.5 2.8 + - - -
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Residues in contact with GLN 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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150A MSE 3.4 12.9 - - + +
155A ALA* 3.0 32.0 + - - +
157A ASP* 1.3 81.8 - - + +
159A ILE* 1.3 65.9 + - - +
160A THR 3.2 2.2 - - - -
161A ARG* 3.4 8.9 + - - +
162A PHE* 3.0 22.5 + - - +
168A THR* 4.6 10.0 + - - -
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Residues in contact with ILE 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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147A LEU* 3.9 18.4 - - + -
150A MSE 3.8 22.2 - - + -
151A ILE* 3.9 31.2 - - + +
155A ALA 2.9 21.7 + - - +
156A TRP* 3.4 45.7 + - + +
158A GLN* 1.3 77.3 - - - +
160A THR* 1.3 58.5 + - - +
162A PHE* 3.1 3.5 + - - +
163A LEU* 2.8 52.8 + - + +
221B LEU* 5.0 5.4 - - + -
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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 TRP 3.6 11.8 + - - -
157A ASP* 4.1 9.0 + - - -
158A GLN 3.2 0.2 - - - -
159A ILE* 1.3 81.3 - - - +
161A ARG* 1.3 64.0 + - + +
163A LEU* 3.6 16.3 + - - +
164A LYS* 3.8 9.2 + - - +
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Residues in contact with ARG 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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157A ASP 4.4 10.8 - - - +
158A GLN* 3.4 11.0 + - - +
159A ILE 3.3 0.2 - - - -
160A THR* 1.3 76.6 - - + +
162A PHE* 1.3 61.1 + - - +
164A LYS* 3.0 9.5 + - - +
165A THR* 2.9 36.5 + - + +
167A THR 5.9 0.7 - - - +
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Residues in contact with PHE 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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143A PHE* 3.5 42.1 - + - -
146A PHE* 3.5 36.3 - + + -
147A LEU* 4.1 22.2 - - + -
150A MSE 3.6 20.4 - - + -
158A GLN 3.0 18.4 + - - +
159A ILE* 3.1 3.6 + - - +
161A ARG* 1.3 73.9 - - - +
163A LEU* 1.3 64.9 + - - +
165A THR* 3.6 6.3 - - - -
166A GLN* 2.7 46.2 + - - -
167A THR 3.5 27.1 - - - +
168A THR* 3.9 8.1 - - - -
181A ALA* 4.1 4.3 - - + -
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Residues in contact with LEU 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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143A PHE* 3.9 31.8 - - + -
147A LEU* 4.1 18.4 - - + -
159A ILE* 2.8 39.7 + - + +
160A THR* 3.9 11.9 - - + +
161A ARG 3.2 0.4 - - - -
162A PHE* 1.3 72.8 - - + +
164A LYS* 1.3 59.4 + - - +
166A GLN* 4.6 3.8 - - - +
183A LYS* 4.7 6.8 + - - -
221B LEU* 4.1 28.3 - - + -
224B GLU* 5.2 10.8 - - - +
225B LEU* 6.1 0.7 - - + -
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Residues in contact with LYS 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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160A THR 3.8 6.2 + - - +
161A ARG* 3.0 10.5 + - - +
163A LEU* 1.3 81.6 - - - +
165A THR* 1.3 66.6 + - + +
166A GLN* 3.8 5.0 + - - +
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Residues in contact with THR 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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161A ARG* 2.9 29.8 + - + +
162A PHE* 3.6 2.4 - - - -
164A LYS* 1.3 77.9 - - + +
166A GLN* 1.3 69.5 + - - +
167A THR* 3.0 41.2 + - - -
180A TYR* 3.4 12.1 - - - -
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Residues in contact with GLN 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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143A PHE* 3.8 15.9 - - + -
162A PHE* 2.7 41.7 + - - +
163A LEU 4.6 3.1 - - - +
164A LYS 4.5 7.2 - - - +
165A THR* 1.3 73.8 - - - +
167A THR* 1.3 55.6 + - - +
179A SER 3.6 0.3 - - - +
180A TYR* 3.2 23.6 + - + -
181A ALA* 2.7 58.9 + - - +
183A LYS* 3.4 27.5 + - + +
185A GLU* 4.6 5.0 - - - +
186A ASP* 2.8 25.7 + - - +
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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