Contacts of the helix formed by residues 161 - 171 (chain A) in PDB entry 2BZN
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 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A TYR* 2.5 28.6 + - - +
159A VAL* 4.4 0.5 - - - +
160A VAL* 1.3 87.6 - - + +
162A GLY* 1.3 64.9 + - - +
163A GLU* 2.7 23.0 + - - -
164A MET* 3.3 5.7 + - - +
165A VAL* 3.1 21.5 + - - +
196A TYR* 3.9 22.0 - - + +
204A GLU* 3.3 12.8 - - - +
205A CYS* 3.5 6.6 - - - -
18B ARG* 3.3 30.7 + - + +
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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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161A THR* 1.3 69.5 - - - +
163A GLU* 1.3 65.9 + - - +
165A VAL* 3.1 5.9 + - - +
166A GLU* 3.0 30.4 + - - +
204A GLU* 2.8 24.5 + - - +
208A ALA* 3.5 24.0 - - - -
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Residues in contact with GLU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A TYR* 3.5 12.8 - - - -
161A THR* 2.7 27.4 + - - -
162A GLY* 1.3 75.2 - - - +
164A MET* 1.3 76.0 + - + +
166A GLU* 3.3 12.9 + - - +
167A GLU* 3.1 22.6 + - - +
204A GLU* 4.8 0.2 + - - -
18B ARG* 3.2 29.4 + - - -
20B LYS* 5.6 0.2 - - - +
21B ARG* 4.5 10.3 + - + +
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Residues in contact with MET 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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133A GLY 3.5 14.1 - - - +
134A TYR* 3.5 52.5 - - + +
139A VAL* 3.5 32.3 - - + -
159A VAL* 3.5 23.1 - - + -
161A THR 3.3 5.4 + - - +
162A GLY 3.2 0.2 - - - -
163A GLU* 1.3 83.2 + - - +
165A VAL* 1.3 67.8 + - - +
167A GLU* 3.5 21.3 + - - +
168A LEU* 3.0 34.5 + - + +
21B ARG* 4.1 15.7 - - - +
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Residues in contact with VAL 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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159A VAL* 3.9 12.6 - - + -
161A THR 3.1 15.8 + - - +
162A GLY* 3.1 10.0 + - - +
164A MET* 1.3 79.0 - - - +
166A GLU* 1.3 62.2 + - - +
168A LEU* 3.3 1.9 + - - +
169A ILE* 3.1 31.0 + - + +
176A ILE* 4.0 20.3 - - + +
205A CYS* 3.5 33.0 - - + +
208A ALA* 4.2 1.3 - - + -
209A ALA* 3.7 39.0 - - + +
216A ILE* 4.8 0.4 - - + -
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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 3.0 18.8 + - - +
163A GLU* 3.3 14.4 + - - +
165A VAL* 1.3 75.2 - - - +
167A GLU* 1.3 58.1 + - - +
169A ILE* 3.2 3.1 + - - +
170A LEU* 2.9 42.1 + - + +
208A ALA* 4.0 26.6 - - + +
212A LEU* 3.8 28.2 - - + +
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Residues in contact with GLU 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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139A VAL* 3.7 19.0 - - + +
143A LYS* 5.4 1.7 + - - -
163A GLU 3.1 13.9 + - - +
164A MET* 3.5 14.3 - - + +
166A GLU* 1.3 80.5 - - - +
168A LEU* 1.3 53.9 + - - +
170A LEU* 3.5 7.9 + - + +
171A SER* 2.6 43.7 + - - +
21B ARG* 2.7 50.5 + - - -
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Residues in contact with LEU 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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133A GLY 4.0 6.3 - - - +
138A PHE* 4.0 33.4 - - + -
139A VAL* 4.0 24.5 - - + -
142A VAL* 4.2 13.7 - - + +
156A ALA* 4.5 6.7 - - + +
157A GLY* 4.8 1.1 - - - -
159A VAL* 3.7 29.8 - - + -
164A MET* 3.0 22.0 + - + +
165A VAL 3.9 0.4 - - - +
167A GLU* 1.3 75.8 - - - +
169A ILE* 1.3 58.7 + - - +
171A SER* 3.4 5.7 + - - -
172A GLY 3.2 5.9 + - - -
173A ALA* 3.0 28.3 + - + +
176A ILE* 3.7 27.6 - - + -
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Residues in contact with ILE 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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39A ARG* 3.4 36.1 + - + +
40A ASN* 2.7 27.5 + - - -
165A VAL* 3.1 26.0 + - + +
166A GLU 3.7 2.9 - - - +
168A LEU* 1.3 75.3 - - - +
170A LEU* 1.3 58.5 + - - +
172A GLY 3.1 6.9 + - - -
173A ALA 3.3 15.5 - - - +
174A ASP 4.7 4.7 - - - +
176A ILE* 3.7 17.3 - - + -
209A ALA* 3.7 39.3 - - + +
212A LEU* 4.2 16.4 - - + +
214A GLY* 4.2 12.8 - - - -
215A HIS 4.7 0.4 - - - +
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Residues in contact with LEU 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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39A ARG* 3.6 31.4 + - - +
166A GLU* 2.9 29.6 + - + +
167A GLU* 3.9 6.3 - - - +
169A ILE* 1.3 75.4 - - - +
171A SER* 1.3 60.8 + - - +
172A GLY* 3.5 0.7 + - - -
212A LEU* 4.2 19.5 - - + -
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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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139A VAL* 3.4 27.9 - - - +
142A VAL* 4.0 6.0 - - - +
143A LYS* 3.5 53.8 + - - +
146A ARG* 4.3 2.9 - - - +
167A GLU* 2.6 25.4 + - - +
168A LEU* 3.7 8.7 - - - -
169A ILE 3.2 0.4 - - - -
170A LEU* 1.3 77.6 - - - +
172A GLY* 1.3 56.2 + - - +
173A ALA 3.8 0.2 - - - -
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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