Contacts of the helix formed by residues 146 - 157 (chain B) in PDB entry 1JEY
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 GLN 146 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74B TYR* 4.9 5.7 + - - +
108B LEU* 5.7 2.9 - - + +
109B ASP* 5.2 5.8 - - - +
112B ILE* 3.9 29.5 - - + +
143B SER* 5.2 5.5 + - - +
144B LYS* 3.3 1.0 - - - +
145B SER* 1.3 107.7 + - - +
147B LEU* 1.3 58.2 + - - +
148B ASP 3.4 2.2 - - - -
149B ILE* 3.2 31.3 + - + +
150B ILE* 2.8 38.6 + - + +
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B LEU* 3.8 24.3 - - + +
144B LYS* 3.6 30.9 - - + +
145B SER 3.4 2.6 - - - -
146B GLN* 1.3 77.6 - - - +
148B ASP* 1.3 70.6 + - - +
150B ILE* 3.2 6.6 + - + +
151B ILE* 3.0 33.8 + - + +
207B ILE* 4.0 30.5 - - + -
210B MET* 5.6 6.5 - - + -
211B VAL* 4.1 17.0 - - + -
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Residues in contact with ASP 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B SER 5.1 2.1 + - - +
146B GLN 3.4 0.6 - - - -
147B LEU* 1.3 78.7 - - - +
149B ILE* 1.3 63.6 + - + +
151B ILE* 4.0 6.3 - - - +
152B HIS* 3.0 27.2 + - - +
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Residues in contact with ILE 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ILE* 5.6 3.6 - - + -
145B SER 5.0 2.9 - - - +
146B GLN* 3.2 41.2 + - + +
148B ASP* 1.3 77.3 - - + +
150B ILE* 1.3 69.2 + - + +
152B HIS* 3.8 4.8 - - - +
153B SER* 3.1 30.7 + - - +
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Residues in contact with ILE 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B LEU* 4.0 38.1 - - + +
111B LEU* 3.8 13.5 - - + -
112B ILE* 3.8 36.1 - - + -
115B MET* 3.2 24.9 - - + +
146B GLN* 2.8 32.5 + - + +
147B LEU* 3.2 8.0 + - + +
149B ILE* 1.3 80.5 - - + +
151B ILE* 1.3 66.0 + - + +
153B SER* 3.4 2.7 + - - -
154B LEU* 3.1 30.5 + - + +
211B VAL* 5.6 4.3 - - + -
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Residues in contact with ILE 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B LEU* 3.0 22.9 + - + +
148B ASP* 4.1 6.5 - - - +
150B ILE* 1.3 78.9 - - + +
152B HIS* 1.3 63.1 + - - +
154B LEU* 3.3 6.8 + - + +
155B LYS* 3.1 50.3 + - + +
210B MET 5.4 0.2 - - - -
211B VAL* 4.3 29.4 - - + +
214B SER* 3.6 32.3 - - - +
215B LEU* 4.4 5.8 - - + -
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Residues in contact with HIS 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B ASP 3.0 20.2 + - - +
149B ILE* 3.8 5.6 + - - +
151B ILE* 1.3 77.2 - - - +
153B SER* 1.3 63.9 + - - +
155B LYS* 4.1 4.1 - - - +
156B LYS* 3.0 69.9 + - + +
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Residues in contact with SER 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B MET* 4.6 11.7 - - - -
119B GLN* 4.3 18.7 + - - -
149B ILE* 3.1 22.4 + - - +
150B ILE* 3.9 3.6 - - - -
152B HIS* 1.3 81.5 + - - +
154B LEU* 1.3 66.3 + - - +
156B LYS* 4.5 3.6 - - - +
157B CYS* 3.0 32.0 + - - +
159B ILE* 4.7 1.4 - - - +
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Residues in contact with LEU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B MET* 3.5 30.7 - - + -
132B ILE* 4.9 2.9 - - + -
150B ILE* 3.1 36.5 + - + +
151B ILE* 3.3 2.4 + - - +
153B SER* 1.3 76.2 - - - +
155B LYS* 1.3 58.5 + - - +
158B ASP* 3.0 8.0 + - - -
159B ILE* 2.9 61.4 + - + +
161B LEU* 4.1 20.2 - - + -
211B VAL* 5.0 2.5 - - + -
215B LEU* 3.7 40.4 - - + -
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Residues in contact with LYS 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B ILE* 3.1 31.2 + - + +
152B HIS* 4.1 4.7 - - - +
154B LEU* 1.3 75.6 - - - +
156B LYS* 1.3 64.9 + - + +
158B ASP* 3.2 14.4 + - - +
214B SER* 2.9 37.3 + - - +
215B LEU* 4.1 15.7 - - + +
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Residues in contact with LYS 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B HIS* 3.0 59.2 + - + +
153B SER* 4.3 4.0 - - - +
155B LYS* 1.3 77.8 - - + +
157B CYS* 1.3 62.6 + - - +
158B ASP* 3.3 1.8 + - - +
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Residues in contact with CYS 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B GLN* 3.3 32.8 - - + -
130B ARG* 2.9 22.1 + - - -
153B SER* 3.0 24.3 + - - +
156B LYS* 1.3 78.8 - - - +
158B ASP* 1.3 68.4 + - - +
159B ILE* 3.4 18.2 + - + +
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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