Contacts of the helix formed by residues 154 - 162 (chain E) in PDB entry 3BZE
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 GLU 154 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151E SER* 3.6 27.8 + - - +
152E GLU 2.6 6.1 + - - -
153E ALA* 1.3 75.3 - - - +
155E HIS* 1.3 70.0 + - + +
156E GLN 3.2 1.3 - - - -
157E ARG* 3.5 10.3 + - - +
158E ALA* 3.4 21.5 + - - +
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Residues in contact with HIS 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E ALA 4.9 4.0 - - - -
151E SER 4.0 13.2 - - - -
152E GLU* 2.9 32.1 + - - +
154E GLU* 1.3 81.1 + - + +
156E GLN* 1.3 59.7 + - + +
157E ARG 2.8 8.3 + - - -
158E ALA* 3.3 9.6 - - - +
159E TYR* 3.0 19.3 + - - +
5R ARG* 3.7 35.7 + - + -
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Residues in contact with GLN 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E TRP* 4.3 1.0 - - - -
114E GLU* 2.5 42.7 + - - +
126E LEU* 4.2 7.0 - - + +
133E TRP* 3.7 23.8 - - + -
152E GLU* 3.3 10.6 + - - +
153E ALA 4.5 5.4 - - - +
154E GLU 3.2 1.6 - - - -
155E HIS* 1.3 74.3 - - - +
157E ARG* 1.3 56.0 + - - +
159E TYR* 3.9 8.4 - - - +
160E LEU* 3.1 27.5 - - - +
3R ALA* 4.2 12.0 - - - +
5R ARG* 2.6 44.2 + - - +
6R THR* 4.1 7.7 + - - +
7R LEU* 5.2 3.6 - - + +
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Residues in contact with ARG 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E ASP 4.8 6.5 + - - -
130E LEU* 3.5 44.5 - - + +
131E ARG* 4.4 26.2 - - - +
153E ALA 4.2 5.6 - - - +
154E GLU* 3.5 14.6 + - - +
155E HIS 2.8 4.2 + - - -
156E GLN* 1.3 72.5 - - - +
158E ALA* 1.3 83.3 - - - +
159E TYR 2.6 1.2 - - - +
160E LEU* 2.7 8.7 + - - +
161E GLU* 2.4 65.3 + - - +
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Residues in contact with ALA 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154E GLU 3.6 9.4 - - - +
155E HIS* 3.3 14.8 - - - +
157E ARG* 1.3 91.8 - - - +
159E TYR* 1.4 58.2 + - - +
161E GLU* 5.4 0.7 - - - -
162E ASP* 3.1 34.7 + - - +
163E THR* 3.7 2.2 + - - -
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Residues in contact with TYR 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E TYR* 4.1 3.5 - - - -
99E HIS* 3.3 32.7 + + - -
155E HIS 3.0 16.6 + - - +
156E GLN* 4.3 9.6 - - - +
157E ARG 2.6 7.0 - - - +
158E ALA* 1.4 71.8 - - - +
160E LEU* 1.3 81.0 + - + +
163E THR* 3.3 33.3 + - + +
164E CYS* 2.8 52.1 + - + +
1R VAL 2.7 28.5 + - - -
2R MET 3.7 2.2 - - - -
3R ALA* 3.4 28.9 + - + -
4R PRO* 3.8 20.9 - - + -
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Residues in contact with LEU 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E HIS* 4.4 4.5 - - + -
100E GLY 3.9 29.2 - - - +
101E CYS* 3.4 23.5 - - + +
109E PHE* 3.8 2.4 - - + -
112E GLY* 4.7 4.7 - - - -
113E TYR 4.1 19.3 - - - +
114E GLU* 4.2 6.3 - - - +
126E LEU* 3.9 9.6 - - + -
130E LEU* 3.9 34.1 - - + -
156E GLN 3.1 21.8 - - - +
157E ARG* 2.7 12.0 + - - -
159E TYR* 1.3 96.1 - - + +
161E GLU* 1.3 60.2 + - - +
164E CYS* 3.5 7.4 - - - +
165E VAL* 3.6 4.0 - - - +
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Residues in contact with GLU 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109E PHE* 3.8 43.9 - - + +
130E LEU* 4.1 7.6 - - + +
157E ARG* 2.4 83.9 + - + +
158E ALA* 5.7 0.3 - - - -
160E LEU* 1.3 70.0 - - - +
162E ASP* 1.3 68.7 + - - +
165E VAL* 3.2 18.7 - - - +
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Residues in contact with ASP 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158E ALA* 3.1 22.8 + - - +
160E LEU 3.5 0.2 - - - -
161E GLU* 1.3 90.9 - - - +
163E THR* 1.3 59.2 + - - +
164E CYS 3.4 0.4 - - - -
165E VAL* 3.0 4.2 + - - +
166E GLU* 2.6 40.5 + - - +
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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