Contacts of the helix formed by residues 180 - 192 (chain B) in PDB entry 3EIJ
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 ASP 180 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440A SER* 3.9 15.5 + - - -
441A LYS* 3.9 15.9 + - - +
442A GLN* 3.3 33.4 + - - +
175B TYR* 4.1 0.4 - - - -
178B HIS* 3.0 32.3 + - + -
179B GLY* 1.3 72.9 - - - +
181B THR* 1.3 61.8 + - - +
182B ASN* 2.8 24.9 + - - +
183B GLU* 3.0 25.0 + - + +
184B VAL* 3.4 10.0 - - - +
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Residues in contact with THR 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A LYS* 5.0 3.2 + - - -
442A GLN* 2.8 19.0 + - - +
175B TYR* 3.8 20.1 + - - -
179B GLY 3.0 4.6 + - - -
180B ASP* 1.3 70.7 - - - +
182B ASN* 1.3 62.6 + - - +
184B VAL* 3.4 6.9 + - - +
185B ALA* 3.0 26.8 + - + +
221B LYS* 4.5 1.0 - - - +
222B LEU* 3.9 20.6 + - + +
225B ASP* 3.1 45.9 + - + +
226B LEU* 4.6 4.4 - - + +
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Residues in contact with ASN 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A LYS* 4.8 13.0 + - - -
442A GLN* 3.3 17.2 - - + +
180B ASP* 2.8 11.0 + - - +
181B THR* 1.3 78.5 - - - +
183B GLU* 1.3 59.7 + - - +
185B ALA* 3.1 10.1 + - - +
186B GLU* 2.9 56.2 + - - +
189B ARG* 5.9 1.8 - - - +
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Residues in contact with GLU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B HIS* 3.7 32.4 + - - +
180B ASP* 3.0 26.5 + - - +
182B ASN* 1.3 77.9 + - - +
184B VAL* 1.3 61.7 + - - +
186B GLU* 3.4 9.3 + - + +
187B MET* 3.2 48.4 + - + +
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Residues in contact with VAL 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B ILE* 3.8 22.9 - - + -
172B ILE* 5.6 2.5 - - + -
175B TYR* 3.5 34.3 - - + -
178B HIS* 3.9 7.0 - - + +
180B ASP 3.4 16.4 - - - +
181B THR 3.4 6.5 + - - +
182B ASN 3.2 0.2 - - - -
183B GLU* 1.3 73.9 - - - +
185B ALA* 1.3 65.8 + - - +
187B MET* 3.3 9.4 + - + +
188B LEU* 3.1 37.6 + - + +
200B VAL* 6.3 0.2 - - + -
222B LEU* 3.8 24.0 - - + -
226B LEU* 4.7 1.8 - - + -
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Residues in contact with ALA 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B THR* 3.0 16.7 + - + +
182B ASN* 3.1 16.8 + - - +
184B VAL* 1.3 78.6 - - - +
186B GLU* 1.3 57.8 + - + +
188B LEU* 3.5 0.9 + - - -
189B ARG* 3.2 35.8 + - - +
225B ASP 6.1 0.4 - - - +
226B LEU* 3.9 21.0 - - + +
229B THR* 5.4 5.6 - - + -
230B VAL* 3.6 18.9 - - + +
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Residues in contact with GLU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A LYS* 5.3 7.9 + - - -
182B ASN* 2.9 45.8 + - - +
183B GLU* 3.9 8.1 - - - +
184B VAL 3.2 0.2 - - - -
185B ALA* 1.3 75.9 - - + +
187B MET* 1.3 61.6 + - + +
189B ARG* 3.7 22.2 + - - +
190B ASP* 3.0 32.6 + - - +
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Residues in contact with MET 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B ILE* 3.8 45.1 - - + +
174B GLU* 5.6 5.6 - - + +
178B HIS* 5.1 6.1 - - + -
183B GLU* 3.2 46.2 + - + +
184B VAL* 3.3 7.6 + - + +
186B GLU* 1.3 78.3 - - + +
188B LEU* 1.3 61.6 + - + +
190B ASP* 3.4 9.8 + - - +
191B LEU* 3.2 30.0 + - + +
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Residues in contact with LEU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B LEU* 3.9 24.2 - - + -
171B ILE* 4.5 15.5 - - + -
172B ILE* 6.5 0.4 - - + -
184B VAL* 3.1 24.0 + - + +
185B ALA 4.1 3.6 - - - +
187B MET* 1.3 74.6 - - + +
189B ARG* 1.3 63.9 + - - +
191B LEU* 3.6 21.7 + - + +
192B ASN* 3.5 13.7 + - - -
193B LEU* 4.4 16.1 + - + +
200B VAL* 3.9 33.0 - - + -
226B LEU* 4.2 19.3 - - + -
230B VAL* 4.8 14.4 - - + +
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Residues in contact with ARG 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B ASN* 5.9 1.8 - - - +
185B ALA* 3.2 22.6 + - - +
186B GLU* 3.8 22.4 - - - +
188B LEU* 1.3 77.6 - - - +
190B ASP* 1.3 66.8 + - - +
192B ASN* 3.3 16.0 + - - +
229B THR* 3.5 30.9 + - - +
230B VAL* 4.3 17.8 - - + +
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Residues in contact with ASP 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B GLU* 3.0 18.7 + - - +
187B MET* 3.7 11.2 - - - +
188B LEU 3.3 0.4 - - - -
189B ARG* 1.3 85.7 - - - +
191B LEU* 1.3 61.1 + - + +
192B ASN* 3.4 4.3 + - - +
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Residues in contact with LEU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B THR* 4.0 24.9 - - + -
168B LEU* 4.0 21.1 - - + -
171B ILE* 4.9 7.2 - - + -
187B MET* 3.2 21.1 + - + +
188B LEU* 3.9 27.8 - - + +
189B ARG 3.3 0.4 - - - -
190B ASP* 1.3 74.8 - - - +
192B ASN* 1.3 71.5 + - - +
193B LEU* 3.4 15.9 + - + +
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Residues in contact with ASN 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B LEU 3.5 4.1 + - - -
189B ARG 3.3 13.0 + - - +
190B ASP 3.2 6.7 - - - +
191B LEU* 1.3 81.4 - - - +
193B LEU* 1.3 68.2 + - - +
194B GLY* 3.3 3.8 + - - -
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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