Contacts of the helix formed by residues 183 - 191 (chain E) in PDB entry 4QOZ
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 SER 183 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139E CYS 3.0 26.0 + - - -
140E GLU* 4.3 13.1 - - - -
141E GLU* 5.8 0.9 - - - -
181E GLN 3.5 3.6 + - - -
182E LEU* 1.3 77.8 - - - +
184E ASP* 1.3 64.1 + - - +
185E PHE* 3.5 7.2 + - - +
186E CYS* 3.1 16.9 + - - +
187E ILE* 3.1 20.4 + - - +
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Residues in contact with ASP 184 (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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141E GLU* 5.8 1.1 - - - +
183E SER* 1.3 71.4 - - - +
185E PHE* 1.3 60.8 + - - +
187E ILE* 3.2 12.6 + - - +
188E SER* 2.9 31.8 + - - -
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Residues in contact with PHE 185 (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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26D A 3.5 44.6 - + - -
139E CYS* 3.9 7.0 - - - -
140E GLU 3.6 16.6 - - - -
141E GLU* 3.3 58.7 + - + +
183E SER* 3.3 5.5 + - - +
184E ASP* 1.3 78.8 - - - +
186E CYS* 1.3 59.1 + - - +
188E SER* 3.8 4.5 - - - -
189E LEU* 2.9 59.5 + - + +
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Residues in contact with CYS 186 (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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137E ALA 3.9 22.2 - - - -
138E THR* 3.9 13.0 - - - -
139E CYS* 3.6 22.4 - - - +
152E ILE* 3.9 16.6 - - - -
182E LEU* 4.1 15.0 - - + -
183E SER* 3.1 27.4 + - - +
185E PHE* 1.3 78.3 - - - +
187E ILE* 1.3 62.1 + - - +
189E LEU* 3.8 0.2 - - - -
190E THR* 3.0 32.6 + - - +
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Residues in contact with ILE 187 (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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182E LEU* 3.7 26.9 - - + +
183E SER 3.1 18.5 + - - +
184E ASP* 3.7 12.6 - - - +
186E CYS* 1.3 75.5 - - - +
188E SER* 1.3 59.4 + - - +
190E THR* 4.4 0.2 - - - -
191E GLY* 3.0 30.0 + - - -
192E ILE 3.6 25.1 - - - +
193E THR* 4.7 7.0 - - + -
194E GLN* 4.3 20.6 - - + +
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Residues in contact with SER 188 (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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184E ASP 2.9 17.3 + - - -
185E PHE* 4.0 5.2 - - - -
187E ILE* 1.3 79.3 - - - +
189E LEU* 1.3 57.9 + - - +
191E GLY* 4.8 0.2 - - - -
291E ARG* 3.0 20.3 + - - -
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Residues in contact with LEU 189 (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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26D A 4.1 31.2 - - + +
139E CYS* 3.9 15.3 - - - -
185E PHE* 2.9 52.1 + - + +
186E CYS 3.8 2.2 - - - +
188E SER* 1.3 77.8 - - - +
190E THR* 1.3 61.9 + - + +
291E ARG* 3.2 13.3 + - - -
292E PRO 4.2 0.2 - - - +
293E HIS* 3.2 52.3 - - + +
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Residues in contact with THR 190 (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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26D A 4.3 8.3 - - - +
136E GLU* 3.7 22.9 - - + +
137E ALA 4.3 11.4 - - - +
139E CYS* 5.1 0.2 - - - -
152E ILE* 4.4 3.0 - - + +
153E GLU* 5.2 0.2 - - - +
186E CYS* 3.0 23.1 + - - +
187E ILE* 4.1 0.3 + - - -
189E LEU* 1.3 85.9 - - + +
191E GLY* 1.3 58.6 + - - +
192E ILE* 3.1 41.3 + - + +
291E ARG* 3.8 8.2 + - - -
293E HIS 3.7 18.0 - - - +
294E CYS* 4.0 9.0 - - - +
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Residues in contact with GLY 191 (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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187E ILE* 3.0 15.9 + - - -
190E THR* 1.3 76.1 - - - +
192E ILE* 1.3 61.7 + - - +
193E THR* 3.7 9.6 + - - +
196E GLN* 4.0 5.0 + - - +
291E ARG* 3.4 22.9 - - - +
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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