Contacts of the helix formed by residues 156 - 166 (chain E) in PDB entry 5L08
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 LYS 156 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101E TYR* 4.9 0.9 - - - -
150E VAL* 3.4 31.1 + - + +
151E ILE* 3.5 27.2 - - - +
152E LEU 4.0 3.1 - - - +
153E GLY* 2.9 20.4 + - - +
155E GLY* 1.3 86.5 + - - +
157E LEU* 1.3 65.5 + - - +
158E ASP* 3.1 4.3 - - - -
159E ILE* 2.9 38.5 + - + +
160E LEU* 3.6 4.5 + - - +
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Residues in contact with LEU 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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101E TYR* 4.2 15.3 - - + -
153E GLY 3.2 7.4 + - - +
154E GLU 4.2 13.5 - - - +
155E GLY 3.5 1.2 - - - -
156E LYS* 1.3 78.1 - - - +
158E ASP* 1.3 64.8 + - - +
160E LEU* 3.1 36.8 + - + +
161E LYS* 3.2 11.7 + - - +
175E ILE* 3.6 44.6 - - + +
178E TYR* 4.2 22.4 - - + -
179E GLU* 5.9 0.4 - - - +
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Residues in contact with ASP 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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155E GLY 5.3 3.1 + - - +
156E LYS* 3.1 2.4 + - - -
157E LEU* 1.3 80.2 - - - +
159E ILE* 1.3 62.9 + - + +
161E LYS* 3.2 19.6 + - - +
162E ARG* 3.0 23.1 + - - +
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Residues in contact with ILE 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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127E GLU* 4.5 5.6 - - + +
146E MET* 4.8 8.7 - - + -
151E ILE* 3.6 41.7 - - + +
156E LYS* 2.9 35.6 + - + +
158E ASP* 1.3 78.7 - - + +
160E LEU* 1.3 63.7 + - - +
162E ARG* 3.2 36.1 + - - +
163E VAL* 2.9 31.8 + - + +
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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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101E TYR* 3.6 12.8 - - + +
105E LEU* 3.8 13.7 - - + -
108E ILE* 4.7 10.1 - - + -
120E PHE* 6.1 2.9 - - + -
143E PHE* 4.2 17.0 - - + -
146E MET* 4.1 16.6 - - + -
151E ILE 5.6 0.4 - - - +
152E LEU* 3.6 34.3 - - + -
156E LYS 3.6 4.4 + - - +
157E LEU* 3.1 25.9 + - + +
159E ILE* 1.3 77.6 - - + +
161E LYS* 1.3 57.3 + - - +
163E VAL* 3.2 11.8 + - + +
164E CYS* 2.8 33.6 + - - -
175E ILE* 3.7 13.0 - - + -
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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
----------------------------------------------------------
157E LEU* 3.2 6.9 + - - +
158E ASP* 3.4 19.9 + - - +
159E ILE 3.2 0.4 - - - -
160E LEU* 1.3 76.8 - - - +
162E ARG* 1.3 64.6 + - - +
164E CYS* 3.1 4.2 + - - +
165E ALA* 3.0 21.0 + - - +
172E LEU* 4.2 28.9 - - + +
175E ILE* 3.4 28.7 - - + +
176E ASN* 3.1 28.2 + - - +
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Residues in contact with ARG 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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127E GLU* 2.8 40.4 + - - +
158E ASP 3.0 14.0 + - - +
159E ILE* 3.5 34.0 - - - +
161E LYS* 1.3 75.0 - - - +
163E VAL* 1.3 56.6 + - - +
165E ALA* 3.4 11.3 - - + +
166E GLN* 2.7 27.7 - - - +
5F ARG* 4.6 25.5 - - - +
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Residues in contact with VAL 163 (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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120E PHE* 3.4 36.6 - - + -
123E LEU* 3.6 27.0 - - + +
124E LEU* 5.9 5.6 - - + -
127E GLU* 4.7 20.6 - - + +
146E MET* 5.5 5.4 - - + -
159E ILE* 2.9 29.5 + - + +
160E LEU* 3.2 15.9 + - + +
162E ARG* 1.3 76.3 - - - +
164E CYS* 1.3 62.8 + - - +
166E GLN 3.0 12.5 + - - -
167E ILE* 3.4 8.5 - - - +
5F ARG* 6.4 0.4 - - - +
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Residues in contact with CYS 164 (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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108E ILE* 5.8 4.7 - - - -
120E PHE* 5.5 2.2 - - - -
160E LEU* 2.8 27.8 + - - -
161E LYS* 3.1 10.1 + - - +
163E VAL* 1.3 75.3 - - - +
165E ALA* 1.3 57.5 + - - +
167E ILE* 2.8 24.9 + - - -
168E ASN 2.9 29.6 + - - +
169E LYS* 5.4 0.8 - - - +
171E LEU* 3.4 30.7 - - - -
172E LEU* 4.0 12.6 - - + +
175E ILE* 3.4 20.2 - - + -
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Residues in contact with ALA 165 (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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51C LYS* 5.3 3.1 + - - -
161E LYS 3.0 11.3 + - - +
162E ARG* 3.4 17.0 - - + +
163E VAL 3.1 0.2 - - - -
164E CYS* 1.3 76.7 - - - +
166E GLN* 1.3 70.9 + - - +
167E ILE 3.3 1.4 + - - -
168E ASN* 5.0 0.5 + - - -
169E LYS* 4.5 23.9 + - - +
172E LEU* 5.9 1.5 - - + +
9F ASP* 5.4 0.3 - - - +
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Residues in contact with GLN 166 (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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51C LYS* 5.0 4.5 + - - -
123E LEU* 3.7 14.6 - - + +
162E ARG* 2.7 28.2 - - - +
163E VAL* 3.0 10.1 + - - +
165E ALA* 1.3 87.6 + - - +
167E ILE* 1.3 61.9 + - - +
5F ARG* 3.6 35.9 - - + +
6F ASN* 5.3 1.2 + - - -
8F TYR* 2.8 44.8 + - + -
9F ASP* 3.1 36.0 + - - +
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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