Contacts of the helix formed by residues 182 - 188 (chain A) in PDB entry 4BM9
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 CYS 182 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A PRO 3.7 0.8 - - - -
181A SER* 1.3 84.3 - - - +
183A TRP* 1.3 67.5 + - - +
184A ASP* 3.9 12.8 - - - +
185A ASP* 3.3 42.5 + - - +
186A VAL 3.9 1.6 + - - -
463A PHE* 3.6 23.8 - - - -
465A VAL* 4.2 10.8 - - + -
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Residues in contact with TRP 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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145A SER 4.3 9.2 - - - -
146A PHE* 3.8 32.5 - + + -
147A TYR 5.4 1.6 - - - -
182A CYS* 1.3 73.6 - - - +
184A ASP* 1.3 65.9 + - - +
186A VAL* 3.0 19.1 + - + +
187A LEU* 3.0 44.4 + - + +
210A PHE* 3.5 26.9 - + - -
225A ALA* 3.8 21.1 - - + -
226A LEU 5.1 1.8 - - - -
227A HIS* 3.4 44.1 + + + +
229A ILE 5.5 2.5 - - - -
463A PHE* 3.8 15.5 - + - -
465A VAL* 4.7 21.6 + - + +
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Residues in contact with ASP 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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182A CYS* 3.4 11.7 - - - -
183A TRP* 1.3 77.7 - - - +
185A ASP* 1.3 61.9 + - - +
187A LEU* 4.7 4.2 - - - +
188A ILE* 3.1 48.6 + - + +
191A ARG* 3.4 29.4 + - - +
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Residues in contact with ASP 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLY 4.5 0.5 - - - +
180A PRO* 3.7 10.7 - - + +
181A SER* 2.9 32.9 + - - -
182A CYS* 3.3 21.7 + - - +
183A TRP 3.1 1.0 + - - -
184A ASP* 1.3 77.5 - - - +
186A VAL* 1.3 58.3 + - - +
188A ILE 4.5 1.8 - - - +
191A ARG* 3.7 30.8 + - - +
192A MET* 3.6 29.8 - - - +
208A PHE* 3.6 17.2 - - - -
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Residues in contact with VAL 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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162A LEU* 4.1 7.6 - - + -
180A PRO* 3.6 29.6 - - + -
183A TRP* 3.2 35.7 - - + +
185A ASP* 1.3 76.5 - - - +
187A LEU* 1.3 69.0 + - + +
188A ILE 3.8 1.3 - - - -
208A PHE* 3.6 48.8 + - + +
210A PHE* 4.0 9.8 - - + -
463A PHE* 3.8 19.1 - - + -
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Residues in contact with LEU 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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183A TRP* 3.0 46.7 + - + +
184A ASP* 4.5 3.6 - - - +
186A VAL* 1.3 98.5 - - + +
188A ILE* 1.3 63.5 + - + +
189A PRO* 3.4 10.6 - - - +
210A PHE* 4.3 10.3 - - + -
225A ALA* 4.8 7.0 - - + +
227A HIS* 4.2 22.7 - - + -
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Residues in contact with ILE 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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184A ASP* 3.1 47.7 + - + +
185A ASP 4.5 2.8 - - - +
186A VAL 5.0 0.7 - - - -
187A LEU* 1.3 80.5 + - + +
189A PRO* 1.3 81.7 - - + +
190A ASN 3.4 0.3 + - - -
191A ARG* 3.3 47.2 + - + +
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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