Contacts of the helix formed by residues 179 - 187 (chain E) in PDB entry 3E5Q
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 179 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177E PRO 3.9 2.0 - - - -
178E LEU* 1.3 74.8 - - - +
180E GLN* 1.3 58.3 + - - +
181E LYS* 3.6 27.4 - - - +
182E SER* 2.8 46.2 + - - -
183E ILE* 3.2 11.8 + - - +
209E LYS* 4.8 0.7 - - - +
155F ARG* 5.1 0.2 + - - -
159F GLU* 5.7 0.2 + - - -
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Residues in contact with GLN 180 (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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178E LEU 3.3 3.6 + - - -
179E SER* 1.3 69.5 - - - +
181E LYS* 1.3 59.8 + - - +
183E ILE* 3.2 27.2 + - + +
184E GLY 3.3 5.5 + - - -
191E HIS 5.2 0.2 + - - -
194E VAL* 3.5 18.9 - - + +
195E SER* 4.2 20.9 + - - +
198E LEU* 4.0 28.7 - - + +
209E LYS* 4.4 16.7 - - - +
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Residues in contact with LYS 181 (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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179E SER* 3.6 20.4 - - - +
180E GLN* 1.3 72.6 - - - +
182E SER* 1.3 65.4 + - - +
184E GLY* 3.1 5.6 + - - -
185E GLU* 3.0 43.5 + - - +
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Residues in contact with SER 182 (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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178E LEU* 4.7 5.2 - - - -
179E SER* 2.8 37.2 + - - -
181E LYS* 1.3 77.2 - - - +
183E ILE* 1.3 52.6 + - - -
185E GLU* 3.7 9.0 + - - -
186E ILE* 2.7 48.1 + - - +
155F ARG* 2.9 38.0 + - - +
159F GLU* 4.0 6.8 + - - -
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Residues in contact with ILE 183 (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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153E ILE* 3.7 35.2 - - + -
156E LEU* 3.9 23.8 - - + -
157E PHE* 4.8 12.6 - - + -
178E LEU* 4.1 25.4 - - + +
179E SER 3.2 20.1 + - - +
180E GLN* 3.2 11.6 + - + +
181E LYS 3.1 0.8 - - - -
182E SER* 1.3 77.0 - - - +
184E GLY* 1.3 61.4 + - - +
185E GLU 3.0 1.7 + - - -
187E THR* 2.4 36.0 + - - +
194E VAL* 3.6 27.6 - - + -
198E LEU* 4.6 8.5 - - + -
209E LYS* 5.4 4.7 - - + -
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Residues in contact with GLY 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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180E GLN 3.3 5.2 + - - -
181E LYS* 3.1 7.8 + - - -
183E ILE* 1.3 78.4 - - - +
185E GLU* 1.3 60.9 + - - +
188E GLY* 3.4 11.4 - - - -
189E VAL 2.9 29.0 - - - +
190E HIS* 5.3 0.2 - - - -
191E HIS* 5.5 1.1 - - - -
194E VAL* 3.6 7.5 - - - +
143F GLU* 5.8 5.0 - - - +
152F ARG* 5.3 0.2 - - - +
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Residues in contact with GLU 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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181E LYS* 3.0 43.5 + - - +
182E SER* 3.7 9.8 + - - +
184E GLY* 1.3 73.9 - - - +
186E ILE* 1.3 70.1 + - - +
187E THR 2.7 4.7 + - - -
188E GLY 2.9 11.1 + - - -
151F ILE* 5.1 13.9 - - + +
152F ARG* 3.1 19.6 - - - +
155F ARG* 3.4 32.0 + - + +
226F SER 4.4 12.0 - - - +
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Residues in contact with ILE 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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156E LEU* 4.1 17.3 - - + -
178E LEU* 4.7 6.7 - - + -
182E SER* 2.7 33.8 + - - +
185E GLU* 1.3 73.9 - - - +
187E THR* 1.3 71.8 + - + +
152F ARG* 3.1 32.1 - - - +
155F ARG* 3.2 23.3 - - + +
156F LEU* 3.2 37.0 - - + +
159F GLU* 3.3 31.9 - - + -
187F THR* 3.6 10.6 - - - +
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Residues in contact with THR 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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152E ARG* 2.7 26.1 + - - +
153E ILE* 4.5 1.7 - - - +
156E LEU* 3.6 24.7 - - + -
183E ILE* 2.4 24.1 + - - +
185E GLU 2.7 4.0 + - - -
186E ILE* 1.3 92.5 - - + +
188E GLY* 1.3 63.2 + - - +
189E VAL* 3.2 19.5 - - - +
186F ILE* 3.3 24.7 - - + +
187F THR 2.8 16.7 - - - +
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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