Contacts of the helix formed by residues 152 - 163 (chain A) in PDB entry 5JEI
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 ILE 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A PHE* 4.6 8.7 - - + -
150A SER* 3.2 16.2 + - - +
151A LYS* 1.3 76.2 - - - +
153A ALA* 1.3 68.3 + - - +
154A CYS* 4.3 6.5 - - + +
155A PHE* 3.0 39.6 + - + -
156A ASP 2.9 19.6 + - - -
215A LEU 5.8 0.2 - - - +
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Residues in contact with ALA 153 (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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151A LYS 3.3 7.2 + - - -
152A ILE* 1.3 73.9 - - - +
154A CYS* 1.3 63.8 + - - +
156A ASP* 3.4 5.0 + - - +
157A LYS* 3.0 24.7 + - - +
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Residues in contact with CYS 154 (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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124A ALA* 3.8 25.1 - - - -
125A GLU* 3.7 29.4 - - - +
128A SER* 3.8 21.3 - - - -
152A ILE* 3.3 5.3 - - + +
153A ALA* 1.3 79.9 - - - +
155A PHE* 1.3 68.7 + - + +
157A LYS* 3.4 8.4 + - - +
158A MET* 3.0 42.2 + - - +
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Residues in contact with PHE 155 (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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124A ALA* 4.3 4.9 - - + -
146A PHE* 3.6 26.7 - + + -
147A PHE* 3.7 13.9 - + + +
150A SER* 3.7 18.4 - - - +
152A ILE* 3.0 35.1 + - + +
154A CYS* 1.3 92.9 - - + +
156A ASP* 1.3 58.8 + - - +
158A MET* 3.3 13.0 + - - +
159A TRP* 2.9 29.5 + - - +
215A LEU* 3.5 60.1 - - + -
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Residues in contact with ASP 156 (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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150A SER 3.5 18.0 + - - +
151A LYS* 3.2 40.6 + - - +
152A ILE 2.9 15.8 + - - +
153A ALA* 3.7 6.0 - - - +
155A PHE* 1.3 74.0 - - - +
157A LYS* 1.3 65.4 + - - +
159A TRP* 3.3 9.1 + - - +
160A THR* 2.9 38.3 + - - -
163A ARG* 5.8 0.3 + - - -
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Residues in contact with LYS 157 (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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128A SER* 3.6 34.7 + - - +
129A LYS* 4.0 26.7 - - - +
135A TYR* 5.1 0.2 - - - -
153A ALA 3.0 13.8 + - - +
154A CYS* 3.5 10.8 - - - +
156A ASP* 1.3 76.7 - - - +
158A MET* 1.3 62.0 + - - +
160A THR* 3.3 7.5 + - - -
161A TYR* 3.1 22.4 + - + +
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Residues in contact with MET 158 (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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124A ALA* 4.1 15.0 - - + +
127A LEU* 4.2 11.2 - - + -
128A SER* 3.8 11.0 - - - -
135A TYR* 3.6 29.8 - - + +
147A PHE* 3.9 13.0 - - + -
154A CYS* 3.0 35.6 + - - +
155A PHE* 3.6 20.6 - - - +
156A ASP 3.3 0.4 - - - -
157A LYS* 1.3 77.0 - - - +
159A TRP* 1.3 56.5 + - - +
161A TYR* 3.2 3.3 + - - +
162A MET* 2.8 35.4 + - + +
191A LEU* 3.5 40.4 - - + -
215A LEU* 4.6 0.4 - - + -
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Residues in contact with TRP 159 (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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137A THR* 6.3 0.4 - - + -
144A LYS* 3.9 22.2 - - + -
147A PHE* 3.3 36.1 - - + +
148A ARG* 3.6 40.3 - - + +
155A PHE 2.9 13.5 + - - +
156A ASP* 3.7 7.4 - - - +
158A MET* 1.3 75.6 - - - +
160A THR* 1.3 60.0 + - - +
162A MET* 4.1 11.4 - - + +
163A ARG* 2.9 61.5 + - + +
170A PHE* 3.8 23.8 - + - -
302A PO4 2.8 32.9 + - - -
307A PG4 3.6 26.9 - - - -
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Residues in contact with THR 160 (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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156A ASP* 2.9 28.0 + - - -
157A LYS* 3.6 8.7 - - - -
158A MET 3.3 0.2 - - - -
159A TRP* 1.3 75.7 - - - +
161A TYR* 1.3 61.4 + - - +
163A ARG* 3.6 44.8 + - - +
164A SER* 4.1 8.8 + - - -
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Residues in contact with TYR 161 (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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134A ALA* 3.2 31.5 - - - +
135A TYR* 3.4 60.2 + + - +
157A LYS* 3.1 12.3 + - + +
158A MET 3.6 4.0 - - - +
160A THR* 1.3 76.4 - - - +
162A MET* 1.3 77.9 + - + +
164A SER* 3.2 5.0 + - - -
165A ALA* 3.1 39.7 + - + +
169A VAL* 3.7 6.6 - - - +
313A PEG 3.4 35.1 - - - -
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Residues in contact with MET 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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135A TYR* 3.4 20.2 - - + +
136A GLY* 3.7 23.8 - - - -
137A THR* 4.0 9.4 - - + -
147A PHE* 3.6 48.5 - - + -
158A MET* 2.8 27.6 + - + +
159A TRP* 3.1 8.9 + - + +
161A TYR* 1.3 82.6 - - + +
163A ARG* 1.3 63.2 + - - +
164A SER 3.1 0.9 + - - -
165A ALA* 3.3 9.9 + - - +
169A VAL* 3.6 12.9 - - + +
170A PHE* 3.4 26.8 - - + -
191A LEU* 3.8 16.6 - - + -
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Residues in contact with ARG 163 (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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156A ASP* 5.8 0.4 + - - -
159A TRP* 2.9 55.2 + - + +
160A THR* 3.6 39.4 + - - +
162A MET* 1.3 78.1 - - - +
164A SER* 1.3 65.7 + - - +
165A ALA 3.6 0.6 - - - +
170A PHE* 4.2 11.8 - - - -
302A PO4 2.9 39.4 + - - +
307A PG4 4.4 16.9 - - - +
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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