Contacts of the helix formed by residues 181 - 187 (chain A) in PDB entry 4IM0
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 HIS 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A TYR 3.7 0.8 + - - -
180A LEU* 1.3 72.9 - - - +
182A PRO* 1.3 73.3 - - + +
183A ASP* 3.2 40.6 + - + -
184A MET* 2.8 9.2 + - + +
185A TYR* 2.4 35.3 + - - +
201A THR 5.2 1.8 + - - -
202A VAL* 3.6 34.2 + - + +
205A TRP* 3.6 37.6 - + + +
286A GLU 4.2 3.6 - - - -
287A ALA 3.8 18.0 + - - -
289A GLN* 3.2 32.8 + - + +
292A CYS* 5.8 3.4 - - - -
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Residues in contact with PRO 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 LEU 3.7 1.1 - - - +
181A HIS* 1.3 108.4 - - + +
183A ASP* 1.3 62.3 + - - +
185A TYR* 3.9 7.3 - - + +
186A GLU* 3.3 26.2 + - - +
205A TRP* 3.8 15.0 - - + -
235A TYR* 3.4 10.5 - - + -
238A ILE* 3.5 35.7 - - + -
239A THR* 4.3 18.8 - - + -
287A ALA* 4.7 11.7 - - + +
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Residues in contact with ASP 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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181A HIS* 3.2 15.0 + - + -
182A PRO* 1.3 80.3 - - - +
184A MET* 1.3 62.6 + - - +
186A GLU* 3.5 17.7 + - - +
187A ARG* 3.4 16.6 + - - +
202A VAL* 6.2 1.1 - - + -
235A TYR* 5.7 0.2 + - - -
287A ALA 5.4 0.4 - - - +
289A GLN* 2.8 28.1 + - - +
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Residues in contact with MET 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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180A LEU* 4.0 25.4 - - + +
181A HIS* 2.8 28.4 + - + +
183A ASP* 1.3 78.9 - - - +
185A TYR* 1.3 59.0 + - - +
187A ARG* 2.9 23.7 + - - +
191A ARG* 6.4 1.8 - - - -
202A VAL* 4.4 12.1 - - + +
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Residues in contact with TYR 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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177A GLU* 3.5 51.7 + - + +
180A LEU* 4.0 14.3 - - + +
181A HIS 2.4 30.2 + - - +
182A PRO* 3.9 10.8 - - + +
183A ASP 3.3 0.4 - - - -
184A MET* 1.3 66.4 - - - +
186A GLU* 1.3 64.4 - - - +
187A ARG* 4.3 2.8 - - - +
227A PRO* 3.9 20.4 + - - +
228A ARG* 5.0 0.3 - - - -
231A LYS* 3.7 28.0 - - + +
234A MET* 3.4 29.3 - - + +
235A TYR* 4.5 20.2 - + + -
238A ILE* 4.9 6.3 - - + -
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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 PRO 3.3 13.8 + - - +
183A ASP* 3.5 17.2 - - - +
185A TYR* 1.3 77.0 - - - +
187A ARG* 1.3 72.8 + - - +
235A TYR* 2.5 40.3 + - + -
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Residues in contact with ARG 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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180A LEU* 6.2 0.9 - - + -
183A ASP 3.4 7.2 + - - +
184A MET* 2.9 19.7 + - - +
185A TYR 4.3 2.5 - - - +
186A GLU* 1.3 91.0 - - - +
189A VAL 3.7 22.6 + - - -
190A LEU 5.8 1.8 - - - -
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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