Contacts of the strand formed by residues 177 - 184 (chain E) in PDB entry 3EI4
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 177 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125E ASP* 5.0 0.2 + - - -
126E PRO* 6.2 0.4 - - - +
169E PHE* 3.6 7.0 - - - -
170E LEU* 2.7 51.3 + - + +
173E CYS* 3.4 22.6 - - - +
175E ALA 2.7 19.1 + - - -
176E PRO* 1.3 71.8 - - - +
178E ILE* 1.3 60.7 + - - +
192E THR* 4.8 0.7 - - - -
193E TYR 3.5 11.0 - - - +
194E GLU* 3.2 17.9 + - + +
205E GLY* 4.5 0.7 - - - -
206E PRO* 3.7 32.4 - - + +
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Residues in contact with ILE 178 (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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123E ILE* 4.1 6.3 - - + -
140E PHE* 3.5 43.7 - - + -
167E VAL* 3.8 22.2 - - + -
168E LYS 3.9 9.4 - - - +
169E PHE* 3.8 17.2 - - + -
176E PRO 4.1 0.8 + - - -
177E THR* 1.3 72.9 - - - +
179E CYS* 1.3 63.1 + - - +
180E PHE* 4.9 6.7 - - + -
192E THR* 3.2 8.5 - - - +
193E TYR* 3.0 60.8 + - + +
195E VAL* 4.2 11.0 - - + -
202E PHE* 4.5 7.2 - - + -
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Residues in contact with CYS 179 (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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166E ASP 3.8 0.3 - - - +
167E VAL* 3.4 1.0 - - - +
168E LYS 2.9 37.3 + - - +
170E LEU* 3.8 17.7 - - + -
177E THR 4.1 0.2 + - - -
178E ILE* 1.3 75.8 - - - +
180E PHE* 1.3 64.2 + - - +
190E VAL* 3.8 22.4 - - - -
191E LYS 3.8 0.2 - - - -
192E THR* 3.5 17.3 - - + -
207E TRP* 5.0 4.5 - - - -
219E VAL* 3.8 20.9 - - + +
229E ALA* 4.3 17.3 - - - -
231E ILE* 5.7 0.9 - - - -
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Residues in contact with PHE 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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159E LEU* 4.2 10.3 - - + -
161E GLU* 3.7 19.5 - - + -
164E VAL* 4.3 8.3 - - + -
166E ASP 3.1 8.1 - - - +
167E VAL* 3.2 33.0 - - + -
178E ILE* 4.9 9.4 - - + -
179E CYS* 1.3 77.2 - - - +
181E VAL* 1.3 64.0 + - - +
182E TYR* 3.4 40.6 - + + -
190E VAL* 3.3 5.6 - - - +
191E LYS* 2.9 54.3 + - + -
192E THR* 4.9 0.9 - - - -
193E TYR* 3.8 38.1 - + - -
202E PHE* 6.3 0.2 - + - -
219E VAL* 4.6 1.6 - - - -
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Residues in contact with VAL 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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164E VAL* 3.7 2.6 - - - +
165E ILE* 2.7 40.1 + - + -
166E ASP* 3.2 9.2 + - + +
180E PHE* 1.3 77.0 - - - +
182E TYR* 1.3 67.6 + - - +
188E ARG* 4.1 13.7 - - + -
189E HIS 3.3 8.1 - - - +
190E VAL* 4.4 4.3 - - + -
212E VAL* 4.7 2.7 - - + -
216E ALA* 3.7 26.2 - - + +
217E SER 6.0 0.4 - - - +
218E MET 4.9 0.9 - - - +
219E VAL* 3.8 21.7 - - + +
231E ILE* 4.1 31.4 - - + -
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Residues in contact with TYR 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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161E GLU* 3.5 30.9 + - + -
163E HIS 3.2 15.3 - - - +
164E VAL* 4.3 0.9 - - - -
165E ILE* 4.1 4.3 - - - +
180E PHE* 3.4 27.4 - + + -
181E VAL* 1.3 74.7 - - - +
183E GLN* 1.3 78.3 + - - +
184E ASP* 4.1 15.3 + - + -
188E ARG* 3.2 29.5 - - - +
189E HIS* 2.9 57.4 + + + +
191E LYS* 3.7 25.6 - - + -
209E GLN* 2.4 30.9 + - - -
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Residues in contact with GLN 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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162E LEU* 4.4 8.7 + - - +
163E HIS* 2.7 58.3 + - + +
165E ILE* 4.7 1.6 - - + -
182E TYR* 1.3 82.8 - - - +
184E ASP* 1.3 71.5 + - - +
187E GLY* 3.4 18.5 + - - +
188E ARG* 2.7 44.3 + - + +
214E ALA 5.3 1.0 + - - -
58F ALA* 4.0 16.9 + - + +
61F GLN* 5.8 0.8 + - - -
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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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162E LEU* 5.6 4.3 - - + -
182E TYR* 4.1 13.3 + - + -
183E GLN* 1.3 82.7 + - - +
185E PRO* 1.4 76.0 - - + +
186E GLN* 3.0 23.6 + - - +
187E GLY* 3.0 19.1 + - - +
189E HIS* 3.0 33.1 + - - -
58F ALA* 4.2 10.6 - - - +
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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