Contacts of the helix formed by residues 163 - 173 (chain E) in PDB entry 1I43
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 TYR 163 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139E MET* 3.9 11.7 - - - -
161E ASP 4.5 0.4 - - - -
162E CYS* 1.3 70.8 - - - +
164E ARG* 1.3 73.2 + - + +
165E LYS* 3.5 24.8 - - + +
166E THR* 2.8 38.2 + - - +
167E ARG 2.9 10.0 + - - -
207E GLU* 3.4 21.7 + - - +
211E ASN* 4.4 22.0 - - - +
500E PLP 3.7 40.4 - + + +
604E PMC 3.3 62.2 + + - -
110G ARG* 3.4 13.6 + - - -
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Residues in contact with ARG 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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162E CYS 3.2 6.2 + - - -
163E TYR* 1.3 76.7 - - + +
165E LYS* 1.3 68.2 + - + +
167E ARG* 2.6 31.5 + - - +
168E ILE* 2.9 33.5 + - + +
211E ASN* 5.7 0.8 - - - +
403E SER* 2.9 28.1 + - - -
404E TYR* 3.4 37.9 + - + +
406E ASP* 3.0 36.5 + - - -
407E LEU* 3.7 25.2 - - - +
604E PMC 5.6 3.6 - - - +
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Residues in contact with LYS 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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139E MET* 4.0 12.6 - - + +
163E TYR* 3.5 21.2 - - + +
164E ARG* 1.3 88.4 - - + +
166E THR* 1.3 61.3 + - - +
168E ILE* 3.3 25.1 + - - +
169E PHE* 3.1 21.3 + - - +
604E PMC 4.3 13.9 + - - +
110G ARG* 4.3 12.3 - - - +
111G TYR* 3.4 31.5 + - - +
289G HIS* 4.6 5.3 + - - +
290G ILE* 4.3 28.2 - - + +
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Residues in contact with THR 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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139E MET* 3.9 16.4 - - + +
142E SER* 4.5 15.7 + - - -
146E LEU* 4.8 6.3 - - + -
162E CYS* 4.2 5.6 - - - -
163E TYR* 2.8 32.2 + - - +
165E LYS* 1.3 72.7 - - - +
167E ARG* 1.3 63.9 + - - +
169E PHE* 3.3 5.5 + - + +
170E ILE* 2.9 49.2 + - + +
205E PHE* 3.9 26.4 - - + -
207E GLU* 5.7 0.2 + - - -
500E PLP 4.8 2.9 - - - -
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Residues in contact with ARG 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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158E THR* 6.1 0.9 - - - -
159E THR 5.2 1.6 - - - -
160E THR* 3.5 21.2 + - - +
162E CYS* 4.5 20.4 - - + +
163E TYR 2.9 9.8 + - - +
164E ARG* 2.6 23.3 + - + +
166E THR* 1.3 72.6 - - - +
168E ILE* 1.3 55.2 + - + +
170E ILE* 3.3 8.2 + - - +
171E GLU* 2.9 68.9 + - - +
183E VAL* 4.3 25.2 - - - +
415E TYR* 2.9 51.6 + - - -
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Residues in contact with ILE 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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164E ARG* 2.9 34.5 + - + +
165E LYS* 3.5 37.5 - - + +
167E ARG* 1.3 75.8 - - + +
169E PHE* 1.3 64.5 + - - +
171E GLU* 4.5 2.9 - - - +
172E THR* 2.8 51.9 + - + +
290G ILE* 3.9 21.8 - - + -
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Residues in contact with PHE 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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139E MET* 5.2 1.6 - - + -
143E THR* 3.8 32.3 - - + +
146E LEU* 3.5 34.3 - - + -
147E LEU* 3.7 28.5 - - + -
165E LYS 3.1 13.8 + - - +
166E THR* 3.6 11.0 - - + +
168E ILE* 1.3 75.7 - - - +
170E ILE* 1.3 60.1 + - + +
173E ILE* 2.9 64.0 + - + +
174E LEU* 3.2 29.3 + - + -
290G ILE* 4.1 18.6 - - + +
291G LEU* 3.9 10.5 - - + -
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Residues in contact with ILE 170 (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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146E LEU* 4.2 13.9 - - + -
156E ILE* 4.2 10.3 - - + -
158E THR* 4.4 25.8 - - + +
162E CYS* 4.5 6.7 - - - -
166E THR* 2.9 34.4 + - + +
167E ARG* 3.7 5.4 - - - +
169E PHE* 1.3 78.6 - - + +
171E GLU* 1.3 60.9 + - + +
174E LEU* 3.6 28.8 - - + +
175E PRO* 3.1 20.4 - - - +
179E ILE* 5.0 2.9 - - + +
181E ALA* 4.1 26.7 - - + +
205E PHE* 4.9 2.0 - - + -
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Residues in contact with GLU 171 (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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167E ARG* 2.9 61.5 + - - +
168E ILE* 3.2 3.1 + - - +
170E ILE* 1.3 80.1 - - + +
172E THR* 1.3 67.5 + - + +
175E PRO* 3.8 10.4 - - - +
183E VAL* 5.0 6.1 - - + +
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Residues in contact with THR 172 (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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168E ILE* 2.8 39.0 + - + +
170E ILE 3.4 0.6 - - - -
171E GLU* 1.3 87.9 - - + +
173E ILE* 1.3 80.0 + - - +
175E PRO* 3.6 11.1 - - - +
176E LYS* 3.8 18.7 - - - +
290G ILE* 5.4 0.7 - - - +
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Residues in contact with ILE 173 (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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147E LEU* 5.4 7.0 - - + -
169E PHE* 2.9 48.0 + - + +
172E THR* 1.3 94.3 - - - +
174E LEU* 1.3 67.4 + - - +
175E PRO* 3.2 2.0 - - - -
176E LYS* 2.9 45.5 + - + +
177E MET* 4.0 3.5 + - + +
147G LEU* 5.7 9.0 - - + -
177G MET* 5.2 7.4 - - + +
287G LEU* 4.0 28.0 - - + -
290G ILE* 5.5 5.6 - - + -
291G LEU* 5.9 0.9 - - + -
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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