Contacts of the helix formed by residues 152 - 161 (chain E) in PDB entry 5U07
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 PRO 152 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130E ILE* 6.0 2.5 - - + -
134E HIS* 3.7 25.4 - - + +
150E ILE 3.5 2.9 - - - +
151E LEU* 1.3 87.2 - - + +
153E ALA* 1.3 61.9 + - - +
154E ASP* 4.1 15.0 - - - +
155E ARG* 3.6 31.2 - - + +
156E ILE* 3.0 26.3 + - + +
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Residues in contact with ALA 153 (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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93E SER 3.9 16.8 - - - +
94E VAL* 5.8 0.7 - - - -
151E LEU 3.3 4.4 + - - +
152E PRO* 1.3 72.9 - - - +
154E ASP* 1.3 59.8 + - - +
156E ILE* 3.1 9.0 - - + +
157E THR* 2.6 40.2 + - - +
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Residues in contact with ASP 154 (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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152E PRO* 4.1 7.1 - - - +
153E ALA* 1.3 79.7 - - - +
155E ARG* 1.3 94.0 + - - +
157E THR* 3.8 4.2 - - - -
158E GLU* 2.9 31.2 + - - +
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Residues in contact with ARG 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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130E ILE* 3.5 32.5 - - + +
133E GLU* 3.3 29.7 + - - +
134E HIS* 4.6 0.2 + - - -
152E PRO* 3.6 27.7 + - + +
153E ALA 3.4 0.2 - - - -
154E ASP* 1.3 98.0 + - - +
156E ILE* 1.3 65.0 + - + +
158E GLU* 3.2 7.4 + - - +
159E VAL* 2.9 28.0 + - + +
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Residues in contact with ILE 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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90E VAL* 5.1 4.9 - - + +
93E SER* 4.2 11.9 - - - +
94E VAL* 3.2 35.2 - - + -
127E LEU* 4.2 12.0 - - + +
130E ILE* 3.4 36.8 - - + -
151E LEU* 4.6 7.6 - - + -
152E PRO* 3.0 22.4 + - + +
153E ALA* 3.1 16.2 - - + +
155E ARG* 1.3 76.0 - - + +
157E THR* 1.3 75.7 + - - +
159E VAL* 2.9 24.8 + - - +
160E LEU* 2.9 20.3 + - + +
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Residues in contact with THR 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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94E VAL* 4.6 3.8 - - - +
153E ALA* 2.6 27.0 + - - +
154E ASP* 4.0 4.5 - - - -
156E ILE* 1.3 87.4 - - - +
158E GLU* 1.3 61.1 + - - +
160E LEU* 3.4 16.6 + - - +
161E LYS* 3.4 18.4 + - - +
177E LEU* 4.4 19.5 - - + +
179E SER* 3.5 25.4 - - - +
180E THR* 4.1 3.8 - - + +
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Residues in contact with GLU 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 ASP 2.9 20.0 + - - +
155E ARG* 3.6 6.5 - - - +
156E ILE 3.1 0.2 - - - -
157E THR* 1.3 75.9 - - - +
159E VAL* 1.3 72.3 + - - +
161E LYS* 3.3 28.6 + - + +
162E SER* 4.1 2.9 + - - -
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Residues in contact with VAL 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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123E ALA* 3.9 31.1 - - + +
126E GLU* 4.5 19.5 - - + +
127E LEU* 3.9 16.6 - - + -
130E ILE* 5.3 10.8 - - + -
155E ARG* 2.9 19.0 + - + +
156E ILE* 2.9 13.5 + - - +
158E GLU* 1.3 81.7 - - - +
160E LEU* 1.3 61.4 - - + +
161E LYS 3.0 6.5 + - - -
162E SER* 3.2 23.1 + - - -
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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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94E VAL* 4.7 12.3 - - + -
117E PHE* 4.7 13.5 - - + -
119E LEU* 3.9 30.5 - - + +
123E ALA* 5.9 1.3 - - + -
127E LEU* 4.1 24.5 - - + -
156E ILE* 2.9 20.5 + - + +
157E THR* 3.9 10.8 - - - +
158E GLU 3.4 0.6 - - - -
159E VAL* 1.3 76.7 - - + +
161E LYS* 1.3 57.8 + - - +
162E SER* 3.3 1.6 + - - +
172E ARG* 2.9 29.1 + - - +
174E LEU* 5.3 2.5 - - + -
177E LEU* 3.6 29.6 - - + -
180E THR* 3.8 13.3 - - + +
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Residues in contact with LYS 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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157E THR* 3.4 17.0 + - - +
158E GLU* 3.3 21.6 + - + +
159E VAL 3.0 1.4 - - - -
160E LEU* 1.3 76.4 - - - +
162E SER* 1.3 66.8 + - - +
163E ARG* 3.3 26.4 + - - +
172E ARG* 4.4 2.8 + - - +
179E SER* 3.5 44.5 + - - +
180E THR* 3.6 19.3 - - + +
182E VAL* 5.5 0.7 - - - +
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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