Contacts of the helix formed by residues 162 - 173 (chain A) in PDB entry 2BZG
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 ASP 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A PHE* 3.7 27.2 - - + -
158A ILE* 3.5 12.5 - - + +
159A ASN* 2.8 39.0 + - - +
161A GLY* 1.3 78.4 - - - +
163A ARG* 1.3 56.5 + - - +
164A LYS 3.3 2.5 - - - -
165A CYS* 3.2 11.2 + - + +
166A TYR* 2.8 27.5 + - - +
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Residues in contact with ARG 163 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A GLN* 4.6 1.4 + - - +
155A LEU* 4.1 17.9 + - + +
158A ILE* 4.2 12.4 + - + -
159A ASN 3.6 0.4 + - - +
160A PRO* 3.2 41.0 + - - +
161A GLY 3.3 0.8 - - - -
162A ASP* 1.3 78.1 - - - +
164A LYS* 1.3 58.5 + - - +
166A TYR* 3.3 8.4 + - - +
167A ALA* 2.8 30.3 + - - +
197A PHE* 3.4 31.5 - - - +
198A TYR 3.5 17.8 + - - -
199A VAL* 3.8 19.8 - - - +
200A PRO* 5.3 0.8 - - - +
203A GLU* 3.1 41.9 + - - +
206A ARG* 4.3 1.3 - - - +
207A LEU* 3.8 14.2 - - + +
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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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161A GLY 4.6 4.2 + - - +
162A ASP 3.3 0.6 - - - -
163A ARG* 1.3 77.6 - - - +
165A CYS* 1.3 59.4 + - - +
167A ALA* 3.1 4.0 + - + +
168A ASP* 2.8 66.2 + - - +
206A ARG* 4.2 25.1 - - - +
207A LEU* 3.7 13.3 - - + +
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Residues in contact with CYS 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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136A PHE* 3.6 26.7 - - + -
161A GLY 5.3 0.8 + - - +
162A ASP* 3.2 13.0 + - + +
164A LYS* 1.3 78.2 - - - +
166A TYR* 1.3 57.7 + - - +
168A ASP* 3.3 8.8 + - - +
169A THR* 2.8 37.0 + - - -
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Residues in contact with TYR 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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68A PRO* 3.2 31.7 - - + +
69A LEU* 4.4 3.8 - - + -
135A ILE* 4.4 20.4 - - + -
136A PHE* 3.9 10.5 - - + -
151A ASP* 2.7 31.5 + - - -
154A ALA* 3.4 4.5 - - - +
155A LEU* 3.5 33.2 - - + -
158A ILE* 3.5 32.8 - - + -
162A ASP 2.8 14.7 + - - +
163A ARG* 3.4 10.5 - - - +
165A CYS* 1.3 77.1 - - - +
167A ALA* 1.3 59.5 + - - +
169A THR* 3.1 6.3 + - - -
170A MSE 2.8 50.5 + - + +
180A TYR* 3.8 3.1 - - - -
208A PHE* 5.1 0.7 - + - -
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Residues in contact with ALA 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 ARG 2.8 19.7 + - - +
164A LYS* 3.1 5.6 + - + +
166A TYR* 1.3 74.5 - - + +
168A ASP* 1.3 66.4 + - - +
170A MSE 3.2 7.1 + - - +
171A PHE* 3.0 28.7 + - + -
207A LEU* 4.0 35.9 - - + +
208A PHE* 4.0 19.2 - - + -
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Residues in contact with ASP 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 LYS* 2.8 53.5 + - - +
165A CYS* 3.7 7.2 - - - +
167A ALA* 1.3 76.4 - - - +
169A THR* 1.3 62.8 + - - +
171A PHE* 3.3 16.0 + - - +
172A SER* 3.1 22.5 + - - -
207A LEU 5.5 0.7 - - - +
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Residues in contact with THR 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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135A ILE* 3.9 27.8 - - + +
136A PHE* 4.4 4.8 - - - -
138A LEU* 4.8 2.0 - - + -
139A PRO* 3.9 30.3 - - + +
165A CYS* 2.8 31.9 + - - -
166A TYR* 3.1 11.7 + - - -
168A ASP* 1.3 75.5 - - - +
170A MSE 1.3 63.5 + - + +
172A SER* 2.7 25.3 + - - +
173A LEU* 3.3 21.5 + - + +
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Residues in contact with MSE 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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66A PHE* 3.6 32.1 - - + -
68A PRO* 4.1 14.1 - - + -
135A ILE* 4.2 7.4 - - + -
149A ILE* 3.9 15.2 - - + +
166A TYR* 2.8 49.5 + - + +
167A ALA* 3.2 9.2 + - - +
169A THR* 1.3 77.0 - - - +
171A PHE* 1.3 61.7 + - + +
173A LEU* 3.0 21.5 + - + +
174A LEU* 3.4 19.0 + - + +
180A TYR* 3.7 31.6 - - + +
208A PHE* 4.7 1.3 - - + -
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Residues in contact with PHE 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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145A LYS* 4.6 1.7 + - - -
167A ALA* 3.0 27.7 + - + -
168A ASP* 3.3 16.4 + - - +
170A MSE 1.3 74.8 - - + +
172A SER* 1.3 62.6 + - - +
173A LEU 3.1 0.7 + - - -
174A LEU* 3.3 33.3 + - + +
178A PHE* 4.9 1.8 - + - -
180A TYR* 5.8 0.4 - + - -
207A LEU 3.4 22.0 - - - -
208A PHE* 3.5 29.8 - + - -
211A ILE* 3.6 56.8 - - + -
212A CYS* 3.7 13.2 - - - -
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Residues in contact with SER 172 (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 PRO* 4.7 12.4 - - - +
144A GLY 4.6 1.2 - - - +
145A LYS* 2.9 25.8 + - - +
168A ASP 3.1 13.2 + - - -
169A THR* 2.7 26.1 + - - +
171A PHE* 1.3 77.7 - - - +
173A LEU* 1.3 64.3 + - - +
174A LEU 3.4 0.2 - - - -
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Residues in contact with LEU 173 (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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66A PHE* 3.7 35.9 - - + -
135A ILE* 5.3 0.2 - - + -
138A LEU* 4.5 9.9 - - + +
139A PRO* 6.4 0.4 - - + -
143A ILE* 3.4 34.8 - - + -
144A GLY 3.6 10.1 - - - +
145A LYS* 3.2 5.5 - - - -
146A PHE* 2.7 46.5 + - + +
149A ILE* 5.2 4.0 - - + -
169A THR* 3.3 25.6 - - + +
170A MSE 3.0 18.2 + - + +
172A SER* 1.3 86.6 - - - +
174A LEU* 1.3 53.7 + - - +
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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