Contacts of the helix formed by residues 180 - 191 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A TYR* 4.1 1.3 - - - -
178A HIS* 2.8 30.2 + - + +
179A GLY* 1.3 74.6 - - - +
181A THR* 1.3 63.6 + - - +
182A ASN* 2.9 24.2 + - - +
183A GLU* 3.0 28.5 + - + +
184A VAL* 3.5 8.1 + - - +
440B SER* 3.9 15.3 - - - -
441B LYS* 4.0 9.0 + - - +
442B GLN* 3.3 34.3 + - - +
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Residues in contact with THR 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A TYR* 3.9 13.5 + - - -
179A GLY 3.2 4.6 + - - -
180A ASP* 1.3 70.6 + - - +
182A ASN* 1.3 62.5 + - - +
184A VAL* 3.3 5.2 + - - +
185A ALA* 3.0 27.1 + - + +
221A LYS* 4.3 1.6 + - - +
222A LEU* 3.7 30.3 + - + +
225A ASP* 2.9 47.5 + - + +
226A LEU* 4.6 1.6 - - + +
402B LYS* 5.3 2.5 + - - -
442B GLN* 3.2 17.9 + - - +
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Residues in contact with ASN 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ASP* 2.9 9.7 + - - +
181A THR* 1.3 80.5 - - - +
183A GLU* 1.3 64.2 + - - +
185A ALA* 3.2 10.2 + - - +
186A GLU* 2.8 50.5 + - - +
189A ARG* 5.4 4.9 - - - +
441B LYS* 5.6 5.4 - - - -
442B GLN* 3.4 16.6 - - + +
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Residues in contact with GLU 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A GLU* 5.1 3.3 - - - +
178A HIS* 3.7 31.2 + - - +
180A ASP* 3.0 28.5 + - - +
181A THR 3.3 0.2 - - - -
182A ASN* 1.3 77.7 - - - +
184A VAL* 1.3 62.0 + - - +
186A GLU* 3.4 12.0 + - - +
187A MET* 3.1 44.6 + - + +
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Residues in contact with VAL 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ILE* 3.9 23.8 - - + +
172A ILE* 6.0 1.8 - - + -
175A TYR* 3.6 34.5 - - + -
178A HIS* 4.2 5.4 - - + +
180A ASP 3.6 13.9 - - - +
181A THR 3.3 6.9 + - - +
183A GLU* 1.3 72.2 - - - +
185A ALA* 1.3 67.1 + - - +
187A MET* 3.2 10.3 + - + +
188A LEU* 3.0 39.6 + - + +
200A VAL* 6.0 0.4 - - + -
222A LEU* 3.8 24.5 - - + -
226A LEU* 4.4 0.7 - - + -
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Residues in contact with ALA 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A THR* 3.0 16.3 + - + +
182A ASN* 3.2 17.7 + - - +
184A VAL* 1.3 76.5 - - - +
186A GLU* 1.3 62.0 + - - +
188A LEU* 3.3 0.7 + - - +
189A ARG* 3.1 33.9 + - - +
225A ASP 6.1 0.7 - - - +
226A LEU* 3.8 21.3 - - + +
229A THR* 5.0 6.3 - - + -
230A VAL* 3.7 18.7 - - + +
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Residues in contact with GLU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ASN* 2.8 43.7 + - - +
183A GLU* 3.7 10.4 - - + +
185A ALA* 1.3 76.0 - - - +
187A MET* 1.3 63.8 + - + +
189A ARG* 3.2 28.6 + - - +
190A ASP* 3.2 21.8 + - - +
441B LYS* 5.1 8.8 + - - -
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Residues in contact with MET 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ILE* 3.6 41.7 - - + +
174A GLU* 5.3 7.6 - - + +
178A HIS* 4.9 6.5 - - + -
183A GLU* 3.1 56.4 + - + +
184A VAL* 3.2 8.9 + - + +
186A GLU* 1.3 77.8 - - + +
188A LEU* 1.3 63.3 + - + +
190A ASP* 3.4 11.0 + - - +
191A LEU* 3.3 26.9 + - + +
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Residues in contact with LEU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A LEU* 3.9 27.8 - - + -
171A ILE* 4.5 14.1 - - + -
184A VAL* 3.0 27.5 + - + +
185A ALA 3.8 4.3 - - - +
187A MET* 1.3 75.2 - - - +
189A ARG* 1.3 64.3 + - - +
191A LEU* 3.4 25.2 + - + +
192A ASN* 3.6 7.3 + - - -
193A LEU* 4.3 17.1 + - + +
200A VAL* 3.8 28.0 - - + -
226A LEU* 3.9 25.1 - - + -
230A VAL* 4.4 16.1 - - + +
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Residues in contact with ARG 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ASN* 5.4 4.4 - - - +
185A ALA* 3.1 26.3 + - - +
186A GLU* 3.2 23.9 + - - +
188A LEU* 1.3 78.3 - - - +
190A ASP* 1.3 65.2 + - - +
192A ASN* 3.2 16.1 + - - +
229A THR* 3.7 28.6 + - - +
230A VAL* 4.5 11.4 - - + +
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Residues in contact with ASP 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A GLU* 3.2 16.8 + - - +
187A MET* 3.7 10.9 - - - +
188A LEU 3.3 0.2 - - - -
189A ARG* 1.3 80.5 - - - +
191A LEU* 1.3 64.0 + - + +
192A ASN* 3.2 4.0 + - - +
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Residues in contact with LEU 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A THR* 4.0 24.5 - - + -
168A LEU* 3.9 28.5 - - + -
171A ILE* 5.1 8.5 - - + -
187A MET* 3.3 15.9 + - + +
188A LEU* 3.8 22.9 - - + +
189A ARG 3.2 1.0 - - - -
190A ASP* 1.3 77.3 - - + +
192A ASN* 1.3 73.8 + - - +
193A LEU* 3.2 16.0 + - + +
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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