Contacts of the helix formed by residues 158 - 168 (chain E) in PDB entry 3J7Y
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 ALA 158 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156E ARG 4.2 0.4 + - - -
157E LYS* 1.3 77.2 - - - +
159E THR* 1.3 61.9 + - - +
160E SER* 3.2 10.3 - - - +
161E ILE* 3.1 26.9 + - + +
162E LEU* 2.9 27.1 + - - +
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Residues in contact with THR 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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3097 HIS* 5.9 4.9 - - + +
3107 PHE* 4.4 18.6 - - + -
157E LYS 3.8 0.6 + - - +
158E ALA* 1.3 73.6 - - - +
160E SER* 1.3 65.1 + - - +
162E LEU* 3.2 13.2 + - + +
163E GLU* 2.9 36.4 + - - +
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Residues in contact with SER 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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3207A A 5.2 6.9 + - - +
158E ALA* 4.1 11.1 - - - +
159E THR* 1.3 83.9 + - - +
161E ILE* 1.3 70.4 + - - +
163E GLU* 3.4 12.9 + - - +
164E PHE* 3.2 21.1 + - - +
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Residues in contact with ILE 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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3207A A 3.7 52.9 - - + +
157E LYS* 4.5 20.9 - - + +
158E ALA* 3.1 29.3 + - + +
160E SER* 1.3 84.2 + - - +
162E LEU* 1.3 62.4 - - - +
164E PHE* 3.2 9.8 + - - +
165E TYR* 2.9 55.8 + - + -
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Residues in contact with LEU 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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3097 HIS* 4.7 6.1 - - + +
3107 PHE* 3.6 44.0 - - + -
3117 THR* 4.7 3.6 - - + -
154E ARG* 3.2 46.9 - - + +
157E LYS* 3.1 32.3 - - + +
158E ALA 2.9 15.9 + - - +
159E THR* 3.5 9.4 - - + +
161E ILE* 1.3 76.2 - - - +
163E GLU* 1.3 56.5 + - - +
165E TYR* 3.2 8.1 + - + +
166E ARG* 2.9 28.4 + - - +
172E PRO* 4.4 6.1 - - + -
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Residues in contact with GLU 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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3107 PHE* 3.6 25.4 - - + -
159E THR* 2.9 17.9 + - - +
160E SER* 3.5 14.3 - - - +
161E ILE 3.2 0.2 - - - -
162E LEU* 1.3 76.0 - - - +
164E PHE* 1.3 58.5 + - - +
166E ARG* 3.2 24.5 + - - +
167E GLU* 2.9 35.8 + - + +
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Residues in contact with PHE 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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3207A A 4.1 32.5 - + - -
130E LEU* 4.2 27.1 - - + -
131E LYS* 4.6 19.7 - - + -
160E SER 3.2 10.7 + - - +
161E ILE* 3.4 11.2 - - - +
163E GLU* 1.3 78.0 - - - +
165E TYR* 1.3 71.6 - + - +
167E GLU* 3.2 18.6 + - + +
168E LEU* 3.0 39.6 + - + +
176E VAL* 5.9 1.1 - - + -
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Residues in contact with TYR 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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3207A A 3.3 23.8 + + - -
130E LEU* 3.5 38.7 - - + +
161E ILE* 2.9 45.1 + - + -
162E LEU* 3.7 8.5 - - + +
164E PHE* 1.3 85.9 - + - +
166E ARG* 1.3 50.0 + - - +
168E LEU* 2.8 25.6 + - + +
169E GLY 2.7 23.9 - - - +
170E LEU* 4.0 19.0 - - + +
171E PRO 4.1 12.3 - - - -
172E PRO* 3.4 34.8 - - + -
173E LYS* 3.5 19.6 + - + +
176E VAL* 3.7 2.9 - - - +
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Residues in contact with ARG 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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3107 PHE* 3.7 19.1 - - + -
3147 ASP* 3.0 40.1 + - - +
3177 LEU* 5.8 1.6 - - - +
72E GLN* 6.0 0.8 + - - +
154E ARG* 6.4 0.7 - - - +
162E LEU 2.9 13.2 + - - +
163E GLU* 3.2 32.4 + - - +
165E TYR* 1.3 76.8 - - - +
167E GLU* 1.3 56.7 + - - +
168E LEU 2.6 17.0 - - - +
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Residues in contact with GLU 167 (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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163E GLU* 2.9 18.6 + - + +
164E PHE* 3.4 22.0 - - + +
166E ARG* 1.3 78.4 - - + +
168E LEU* 1.3 59.3 + - - +
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Residues in contact with LEU 168 (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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72E GLN* 4.8 1.9 + - - +
76E LYS* 4.5 3.8 - - - +
130E LEU* 3.2 39.0 - - + +
164E PHE* 3.0 29.2 + - + +
165E TYR* 2.8 13.9 + - + +
166E ARG* 2.6 24.6 - - - +
167E GLU* 1.3 76.9 - - - +
169E GLY* 1.3 79.1 + - - +
170E LEU* 3.7 28.7 - - + -
189E PRO* 4.3 7.6 - - + -
190E GLY* 3.8 22.4 - - - +
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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