Contacts of the helix formed by residues 182 - 190 (chain A) in PDB entry 2ZPB
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 SER 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A GLY 3.6 2.0 + - - -
181A TRP* 1.3 75.6 - - - +
183A GLN* 1.3 66.2 + - - +
184A GLU* 3.5 9.1 + - - +
185A GLN* 2.9 39.4 + - - +
186A LEU* 3.0 22.8 + - - +
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Residues in contact with GLN 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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58A GLU* 4.7 1.9 - - - +
61A ALA* 3.6 12.8 - - + +
62A ARG* 3.7 34.5 + - - +
65A THR* 3.5 30.9 + - + +
66A ASP* 5.9 0.6 - - - +
84A TYR* 4.7 2.4 + - - -
182A SER* 1.3 73.4 - - - +
184A GLU* 1.3 57.1 + - - +
186A LEU* 3.3 2.8 + - - -
187A GLN* 2.8 50.0 + - - +
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Residues in contact with GLU 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 SER* 3.2 8.3 + - - +
183A GLN* 1.3 78.2 - - - +
185A GLN* 1.3 63.1 + - + +
187A GLN* 3.4 17.6 + - - +
188A GLU* 3.3 21.3 + - - +
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Residues in contact with GLN 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 TRP* 3.4 54.7 - - + +
182A SER* 2.9 42.2 + - - +
184A GLU* 1.3 76.3 - - + +
186A LEU* 1.3 62.2 + - - +
188A GLU* 3.5 25.2 + - - +
189A ILE* 3.9 1.7 + - - +
1303A MG 4.1 10.2 - - - -
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Residues in contact with LEU 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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61A ALA* 3.9 14.8 - - + +
64A TRP* 3.9 23.8 - - + -
65A THR* 3.5 31.2 - - + -
174A ARG* 3.8 22.2 - - - +
178A THR* 3.7 31.0 - - + -
181A TRP* 3.8 18.2 - - + +
182A SER 3.0 21.5 + - - +
183A GLN* 3.7 4.0 - - - +
185A GLN* 1.3 74.8 - - - +
187A GLN* 1.3 66.0 + - - +
189A ILE* 3.2 22.0 + - + +
190A VAL* 3.6 10.1 - - - +
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Residues in contact with GLN 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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54A ARG* 2.7 30.5 + - - +
57A ALA* 3.6 21.3 - - + +
58A GLU* 3.7 32.3 + - - +
61A ALA* 3.6 13.0 - - + +
183A GLN* 2.8 43.2 + - - +
184A GLU* 3.6 15.6 - - - +
185A GLN 3.4 0.2 - - - -
186A LEU* 1.3 77.2 - - - +
188A GLU* 1.3 58.4 + - - +
190A VAL* 3.1 13.3 + - - +
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Residues in contact with GLU 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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54A ARG* 4.0 10.0 + - - +
184A GLU 3.3 8.6 + - - +
185A GLN* 3.5 20.2 - - - +
186A LEU 3.1 0.8 - - - -
187A GLN* 1.3 79.3 - - - +
189A ILE* 1.3 63.3 + - + +
190A VAL 3.7 1.2 + - - +
191A THR* 4.8 6.8 - - - +
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Residues in contact with ILE 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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64A TRP* 4.4 8.5 - - + -
175A PRO* 3.8 31.9 - - + -
178A THR* 4.0 16.8 - - + -
181A TRP* 3.9 21.8 - - + -
185A GLN 4.2 2.5 - - - +
186A LEU* 3.2 17.0 + - + +
188A GLU* 1.3 82.8 - - + +
190A VAL* 1.3 60.2 + - - +
191A THR* 3.5 9.9 + - - +
194A CYS* 4.0 1.4 - - - -
201A PRO* 3.6 29.1 - - + +
202A GLN 3.4 26.2 + - - +
203A VAL* 4.4 0.7 - - + -
204A PRO* 4.8 6.5 - - + -
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Residues in contact with VAL 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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54A ARG* 3.0 21.8 + - - -
57A ALA* 3.4 29.6 - - + +
60A VAL* 3.8 27.4 - - + -
61A ALA 5.1 0.7 - - - +
64A TRP* 3.6 31.0 - - + -
172A PRO* 4.9 2.5 - - + -
186A LEU 3.6 15.5 - - - +
187A GLN 3.1 6.5 + - - +
188A GLU 4.8 0.2 - - - -
189A ILE* 1.3 76.4 - - - +
191A THR* 1.3 62.6 + - - +
194A CYS* 4.2 15.3 - - + -
195A LEU* 4.1 12.3 - - + -
201A PRO* 4.8 1.6 - - + -
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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