Contacts of the helix formed by residues 159 - 169 (chain E) in PDB entry 1IES
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 159 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155E VAL* 3.7 31.2 + - + +
158E GLN* 1.3 73.2 + - - +
160E GLY* 1.3 58.5 + - - +
163E GLU* 3.0 33.8 + - - +
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Residues in contact with GLY 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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153C ARG* 3.6 36.9 - - - -
157C SER* 3.5 12.3 + - - -
159E ALA* 1.3 73.5 - - - +
161E LEU* 1.3 67.7 + - - +
163E GLU* 3.2 5.9 + - - +
164E TYR* 3.0 20.0 + - - +
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Residues in contact with LEU 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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153C ARG 4.2 0.6 + - - -
154C LEU* 3.5 41.3 - - + +
157C SER* 3.3 18.4 + - - +
158C GLN* 5.1 3.1 - - + +
161C LEU* 4.0 24.7 - - + -
162C GLY* 4.6 3.6 - - - +
165C LEU* 3.9 15.5 - - + -
158E GLN* 4.0 20.9 - - + +
160E GLY* 1.3 76.5 - - - +
162E GLY* 1.3 62.0 + - - +
164E TYR* 3.3 1.7 + - - +
165E LEU* 3.0 47.2 + - + +
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Residues in contact with GLY 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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151E ILE* 6.2 0.2 - - - -
154E LEU* 3.7 36.8 - - - +
155E VAL* 4.3 2.7 - - - -
158E GLN 2.7 24.0 + - - -
159E ALA 3.7 1.3 - - - -
160E GLY 3.3 0.2 - - - -
161E LEU* 1.3 73.1 - - - +
163E GLU* 1.3 62.6 + - - +
165E LEU* 3.4 1.2 + - - -
166E PHE* 3.1 25.4 + - - +
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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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153C ARG* 4.4 16.4 + - - +
44E LEU* 3.5 21.1 - - + +
91E THR* 4.0 21.4 - - - +
92E THR* 2.7 46.9 + - - +
93E LEU 5.7 0.4 - - - +
151E ILE* 5.5 1.6 - - + -
155E VAL* 4.2 14.4 - - + +
159E ALA 3.0 16.1 + - - +
160E GLY* 3.2 8.5 + - - +
162E GLY* 1.3 74.5 - - - +
164E TYR* 1.3 64.0 + - - +
166E PHE* 3.8 5.5 - - - +
167E GLU* 3.3 23.6 + - - +
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Residues in contact with TYR 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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150C ASN* 3.6 24.9 - - - -
153C ARG* 4.1 10.5 - - - +
154C LEU* 3.4 46.7 - - + -
165C LEU* 3.4 15.5 + - + -
166C PHE* 3.5 6.2 - + - -
169C LEU* 3.5 23.7 - - + +
170C THR* 2.6 42.3 + - - -
44E LEU* 4.7 2.9 - - - -
160E GLY 3.0 16.5 + - - +
161E LEU 3.7 2.5 - - - +
163E GLU* 1.3 78.6 - - - +
165E LEU* 1.3 66.2 + - + +
167E GLU* 3.3 7.8 + - - +
168E ARG* 2.8 46.8 + - + +
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Residues in contact with LEU 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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165C LEU* 4.4 17.3 - - + -
169C LEU* 3.7 28.5 - - + -
154E LEU* 5.0 17.5 - - + -
161E LEU* 3.0 43.1 + - + +
162E GLY* 4.1 2.7 - - - +
164E TYR* 1.3 79.3 - - + +
166E PHE* 1.3 57.5 + - - +
168E ARG* 3.9 3.1 - - - -
169E LEU* 2.7 52.1 + - + +
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Residues in contact with PHE 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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92E THR* 4.2 10.1 - - + -
96E MET* 4.7 1.8 - - + -
147E HIS* 3.7 23.3 - + + -
150E ASN* 4.1 18.4 - - + -
151E ILE* 3.6 42.0 - - + -
154E LEU* 3.7 21.7 - - + +
162E GLY 3.1 17.7 + - - +
163E GLU* 3.8 6.3 - - - +
165E LEU* 1.3 72.1 - - - +
167E GLU* 1.3 62.5 + - + +
170E THR* 2.8 65.8 + - + +
171E LEU* 3.0 36.2 + - + -
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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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150C ASN* 5.5 0.7 + - - -
43E ALA 5.4 0.4 - - - +
44E LEU* 4.1 22.7 - - + +
45E GLU* 3.4 8.7 + - - +
46E GLY* 2.7 37.3 + - - +
47E VAL* 4.0 16.2 - - + +
163E GLU 3.3 14.6 + - - +
164E TYR* 3.5 6.5 - - - +
166E PHE* 1.3 80.2 - - - +
168E ARG* 1.3 96.9 + - - +
171E LEU* 3.4 11.1 - - - -
172E LYS* 2.6 37.1 + - - +
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Residues in contact with ARG 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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169C LEU* 3.3 43.3 + - + +
170C THR* 3.8 11.2 + - - +
173C HIS 4.3 0.6 + - - -
174C ASP* 3.6 19.6 - - - +
45E GLU* 4.1 8.1 + - - +
164E TYR* 2.8 35.9 + - + +
165E LEU* 3.7 8.5 - - - +
167E GLU* 1.3 115.5 + - - +
169E LEU* 1.3 56.9 + - + +
172E LYS* 2.9 52.7 - - - +
173E HIS* 2.5 36.9 + - + +
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Residues in contact with LEU 169 (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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169C LEU* 4.5 22.9 - - + -
165E LEU* 2.7 41.2 + - + +
168E ARG* 1.3 81.0 - - + +
170E THR* 1.3 61.7 + - - +
173E HIS* 3.4 29.9 - - + +
174E ASP* 4.7 1.2 - - - +
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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