Contacts of the helix formed by residues 152 - 162 (chain E) in PDB entry 4DHJ
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 THR 152 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102E LEU* 5.3 0.4 - - - -
149E GLY 4.7 7.9 - - - +
150E VAL 3.8 4.1 + - - +
151E HIS* 1.3 77.7 - - - +
153E GLU* 1.3 66.3 + - - +
154E GLU* 3.4 12.2 + - - +
155E ALA* 3.1 23.6 + - - +
156E VAL* 3.0 22.8 + - - +
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Residues in contact with GLU 153 (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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102E LEU* 4.1 27.9 - - + +
152E THR* 1.3 72.7 - - - +
154E GLU* 1.3 62.1 + - - +
156E VAL* 3.1 17.5 + - - +
157E TYR* 3.3 47.4 + - + -
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Residues in contact with GLU 154 (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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152E THR* 3.2 9.9 + - - +
153E GLU* 1.3 80.4 - - - +
155E ALA* 1.3 60.5 + - - +
157E TYR* 3.4 7.7 + - - +
158E THR* 2.8 32.8 + - - +
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Residues in contact with ALA 155 (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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150E VAL 5.4 0.9 - - - +
151E HIS* 4.3 16.4 - - + +
152E THR* 3.1 29.0 + - - +
154E GLU* 1.3 73.1 + - - +
156E VAL* 1.3 67.9 + - - +
158E THR* 3.4 8.0 + - - -
159E ILE* 2.9 31.2 + - + +
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Residues in contact with VAL 156 (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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98E ILE* 3.8 20.4 - - + -
102E LEU* 4.4 13.2 - - + -
142E PHE* 3.9 12.1 - - + -
146E ILE* 3.9 27.8 - - + -
151E HIS* 4.0 8.5 - - + +
152E THR 3.0 17.9 + - - +
153E GLU* 3.1 12.1 + - - +
155E ALA* 1.3 75.6 - - - +
157E TYR* 1.3 61.4 + - + +
159E ILE* 3.1 8.5 + - - +
160E LEU* 2.8 46.4 + - + +
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Residues in contact with TYR 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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44E VAL* 4.4 13.2 - - + -
80E ARG* 3.5 34.5 + - - -
95E VAL* 4.6 11.0 - - + -
98E ILE* 6.3 0.9 - - + -
99E GLU* 2.9 35.8 + - + +
102E LEU* 4.3 11.0 - - + +
153E GLU* 3.3 52.7 + - + -
154E GLU* 3.4 6.7 + - - +
155E ALA 3.3 0.2 - - - -
156E VAL* 1.3 75.2 - - + +
158E THR* 1.3 64.5 + - - +
160E LEU* 3.7 14.6 - - + +
161E ASN* 2.9 36.8 + - - +
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Residues in contact with THR 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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154E GLU* 2.8 23.4 + - - +
155E ALA* 3.5 11.3 - - - -
157E TYR* 1.3 76.6 - - - +
159E ILE* 1.3 61.6 + - + +
161E ASN* 3.1 15.2 + - - +
162E ASP* 3.2 17.3 + - + +
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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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138E PHE* 5.7 2.0 - - + -
142E PHE* 3.7 24.5 - - + -
151E HIS* 3.4 43.5 - - + +
155E ALA* 2.9 20.3 + - + +
156E VAL 3.4 6.7 - - - +
158E THR* 1.3 75.5 - - + +
160E LEU* 1.3 61.8 + - - +
161E ASN 3.1 1.3 + - - -
162E ASP* 3.4 7.7 + - - -
165E SER* 3.3 27.8 + - - +
166E ALA* 3.7 8.0 + - - -
169E ILE* 3.8 17.7 - - + -
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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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43E LEU* 3.8 13.0 - - - +
44E VAL* 3.8 18.7 - - + +
91E ARG* 4.9 1.7 + - - +
94E LEU* 3.6 25.1 - - + -
95E VAL* 4.6 14.4 - - + -
98E ILE* 4.1 23.8 - - + -
142E PHE* 4.3 10.5 - - + -
156E VAL* 2.8 41.7 + - + +
157E TYR* 3.7 21.3 - - + +
158E THR 3.3 0.4 - - - -
159E ILE* 1.3 71.8 - - - +
161E ASN* 1.3 57.8 + - - +
162E ASP 3.6 0.4 - - - -
166E ALA* 3.5 18.6 - - + +
169E ILE* 4.4 14.8 - - + -
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Residues in contact with ASN 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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42E PRO* 3.6 8.8 - - - +
43E LEU* 3.2 23.2 + - - +
44E VAL* 2.8 51.3 + - - +
83E ARG* 5.9 0.5 + - - -
157E TYR* 2.9 29.7 + - - +
158E THR* 3.1 7.5 + - - +
160E LEU* 1.3 78.4 - - - +
162E ASP* 1.3 59.6 + - - +
163E ASP* 3.7 6.5 + - - +
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Residues in contact with ASP 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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158E THR* 3.2 15.0 + - + +
159E ILE* 3.4 2.6 + - - -
160E LEU 3.6 0.2 - - - -
161E ASN* 1.3 76.0 - - - +
163E ASP* 1.3 57.9 + - - +
164E GLY* 3.8 4.1 + - - -
165E SER* 2.9 32.4 + - - +
166E ALA* 2.7 33.7 + - - +
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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