Contacts of the helix formed by residues 159 - 171 (chain A) in PDB entry 3ADL
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 HIS 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A GLY* 4.2 16.2 + - - -
158A SER* 1.3 76.4 + - - +
160A GLU* 1.3 61.3 + - - +
161A VAL 3.5 2.0 - - - -
162A GLY* 4.2 6.1 - - - +
163A ALA* 2.9 34.6 + - + +
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Residues in contact with GLU 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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154A VAL* 3.4 38.4 - - + +
155A PRO* 4.3 8.4 - - - +
158A SER* 2.9 24.1 + - - +
159A HIS* 1.3 72.0 + - - +
161A VAL* 1.3 63.3 + - - +
164A LEU* 3.0 25.6 + - - +
215A ARG* 3.7 28.0 - - + +
218A ALA* 3.7 7.1 - - + +
219A ALA* 3.3 24.3 - - - +
222A LEU* 3.6 20.1 - - + +
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Residues in contact with VAL 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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159A HIS 3.5 0.2 - - - -
160A GLU* 1.3 75.5 - - - +
162A GLY* 1.3 59.6 + - - +
164A LEU* 3.8 2.4 - - - +
165A GLN* 3.0 30.8 + - + +
178A TYR* 3.9 15.8 + - + +
214A LYS* 4.0 47.1 - - + +
215A ARG* 4.3 11.2 - - + +
218A ALA* 3.8 15.9 - - + -
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Residues in contact with GLY 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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159A HIS* 3.6 10.2 + - - +
161A VAL* 1.3 77.1 - - - +
163A ALA* 1.3 60.3 + - - +
165A GLN* 3.3 7.1 + - - +
166A GLU* 2.9 45.7 + - - +
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Residues in contact with ALA 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 HIS* 2.9 23.1 + - + +
160A GLU* 3.9 4.7 - - - +
162A GLY* 1.3 77.3 - - - +
164A LEU* 1.3 56.2 + - - +
166A GLU* 3.8 8.2 - - - +
167A LEU* 2.9 30.7 + - - +
222A LEU* 4.2 16.3 - - + +
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Residues in contact with LEU 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 GLU 3.0 18.1 + - - +
161A VAL 3.8 3.4 - - - +
163A ALA* 1.3 73.1 - - - +
165A GLN* 1.3 66.4 + - - +
167A LEU* 3.3 6.7 + - + -
168A VAL* 2.9 44.7 + - + +
176A PRO* 3.8 14.1 - - + -
178A TYR* 3.4 21.8 - - - +
196A CYS* 3.7 11.9 - - - -
218A ALA* 4.1 7.2 - - + -
221A MET* 3.7 38.8 - - + +
222A LEU* 3.7 30.4 - - + +
225A VAL* 4.8 3.4 - - + -
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Residues in contact with GLN 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 VAL* 3.0 22.3 + - + +
162A GLY* 3.8 7.4 - - - +
163A ALA 3.3 0.2 - - - -
164A LEU* 1.3 78.3 - - - +
166A GLU* 1.3 64.3 + - + +
168A VAL* 3.4 8.0 - - - +
169A VAL* 3.2 28.1 + - + +
175A LEU* 3.9 34.5 - - + +
176A PRO* 4.5 10.8 - - + +
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Residues in contact with GLU 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 GLY* 2.9 34.5 + - - +
163A ALA* 3.9 6.5 - - - +
165A GLN* 1.3 80.0 - - + +
167A LEU* 1.3 64.9 + - - +
169A VAL* 3.6 6.7 + - - +
170A GLN* 3.2 29.2 + - + +
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Residues in contact with LEU 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 ALA 2.9 19.3 + - - +
164A LEU* 3.7 7.6 - - + +
166A GLU* 1.3 76.8 - - - +
168A VAL* 1.3 64.4 + - + +
170A GLN* 3.1 8.4 + - + +
171A LYS* 3.0 34.6 + - + +
222A LEU* 3.7 16.4 - - + -
225A VAL* 3.9 25.1 - - + -
226A HIS* 3.3 43.3 - - + +
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Residues in contact with VAL 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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164A LEU* 2.9 43.1 + - + +
165A GLN* 3.4 11.0 - - - +
167A LEU* 1.3 76.4 - - + +
169A VAL* 1.3 63.1 + - - +
171A LYS* 3.2 3.9 + - - +
172A GLY 3.1 4.5 + - - -
173A TRP* 2.9 62.6 + - + +
174A ARG 3.8 18.6 - - - +
175A LEU* 4.2 5.6 - - + -
176A PRO* 3.9 16.4 - - + -
198A VAL* 4.0 11.2 - - + -
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Residues in contact with VAL 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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165A GLN* 3.2 23.5 + - + +
166A GLU* 3.8 7.0 - - - +
168A VAL* 1.3 76.4 - - - +
170A GLN* 1.3 69.2 + - - +
172A GLY* 3.0 18.5 + - - -
173A TRP 4.2 6.5 - - - +
175A LEU* 3.5 26.0 - - + -
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Residues in contact with GLN 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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166A GLU* 3.2 15.6 + - + +
167A LEU* 3.1 12.7 + - + +
169A VAL* 1.3 86.4 - - - +
171A LYS* 1.3 63.3 + - + +
172A GLY 3.2 1.1 + - - -
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Residues in contact with LYS 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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167A LEU* 3.0 30.5 + - + +
168A VAL 3.2 8.0 + - - +
170A GLN* 1.3 77.8 - - + +
172A GLY* 1.3 59.7 + - - +
173A TRP* 3.5 54.4 + - + +
225A VAL* 4.0 19.6 + - + +
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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