Contacts of the helix formed by residues 181 - 192 (chain A) in PDB entry 1Z1G
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 THR 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A LEU* 1.3 74.9 - - - +
182A ALA* 1.3 65.0 + - - +
183A ASP* 3.4 14.3 + - - +
184A GLU* 3.0 42.4 + - - +
185A TYR* 3.2 11.8 + - - +
313A LEU* 4.0 3.8 - - - -
316A ARG* 4.8 3.8 - - - +
348A ARG* 3.5 33.4 + - - +
349A GLU* 4.4 18.4 - - - +
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Residues in contact with ALA 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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181A THR* 1.3 73.6 - - - +
183A ASP* 1.3 64.2 + - - +
185A TYR* 3.4 6.2 + - - +
186A LEU* 3.3 18.5 + - - +
250A ALA* 5.3 7.9 - - + +
251A LEU* 3.7 19.9 - - + +
313A LEU* 3.8 11.1 - - - +
317A LEU* 4.2 26.4 - - + +
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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 THR* 3.2 10.2 + - - +
182A ALA* 1.3 77.3 - - - +
184A GLU* 1.3 59.3 + - + +
186A LEU* 3.2 18.4 + - - +
187A LYS* 3.0 31.7 + - + +
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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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179A ARG 3.8 8.7 - - - +
180A LEU* 4.0 14.6 - - + +
181A THR* 3.0 37.5 + - - +
183A ASP* 1.3 73.4 - - + +
185A TYR* 1.3 55.3 + - - +
187A LYS* 2.8 14.1 + - - +
188A ILE* 2.7 41.5 + - + +
298A LEU* 2.6 36.7 - - + +
300A PHE* 3.7 10.9 - - + -
348A ARG* 3.2 32.8 + - - +
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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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180A LEU* 4.4 5.6 - - + +
181A THR 3.2 3.8 + - - -
182A ALA 3.5 9.2 - - - +
184A GLU* 1.3 77.2 - - - +
186A LEU* 1.3 60.0 + - - +
188A ILE* 2.9 12.8 + - - +
189A TYR* 2.6 60.9 + + + -
203A MSE 4.4 14.9 - - + +
204A GLU* 3.3 32.9 + - - +
207A VAL* 3.5 23.8 - - + -
251A LEU* 3.7 24.2 - - + -
253A ILE* 3.3 17.8 - - + +
310A LEU* 4.0 20.2 - - + -
313A LEU* 3.8 25.8 - - + -
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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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182A ALA 3.3 7.4 + - - +
183A ASP* 3.2 19.4 + - - +
185A TYR* 1.3 89.5 - - + +
187A LYS* 1.3 64.6 + - + +
189A TYR* 3.0 16.2 + - + +
190A GLN* 2.9 36.1 + - + +
251A LEU* 5.0 7.0 - - + -
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Residues in contact with LYS 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 ASP* 3.0 16.2 + - + +
184A GLU* 2.8 17.6 + - - +
186A LEU* 1.3 77.8 - - - +
188A ILE* 1.3 58.4 + - + +
190A GLN* 3.4 15.9 - - - +
191A ALA* 3.4 14.6 + - - +
296A SER* 3.7 29.2 + - - +
298A LEU* 3.1 34.7 - - + +
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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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180A LEU* 4.1 22.2 - - + -
184A GLU* 2.7 32.9 + - + +
185A TYR* 3.6 7.0 - - - +
187A LYS* 1.3 72.5 - - + +
189A TYR* 1.3 67.1 + - - +
190A GLN 2.9 3.1 + - - -
191A ALA* 2.9 12.6 + - - +
192A ALA* 2.9 10.7 + - - +
203A MSE 4.0 7.2 - - + -
289A PHE* 3.8 32.3 - - + -
292A ALA* 3.6 33.2 - - + -
293A ARG* 4.1 9.0 - - + +
296A SER* 4.2 17.3 - - - +
300A PHE* 5.9 5.8 - - + -
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Residues in contact with TYR 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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185A TYR* 2.6 43.4 + + + +
186A LEU* 3.3 21.5 - - + +
188A ILE* 1.3 70.0 - - - +
190A GLN* 1.3 58.1 + - - +
192A ALA* 3.1 13.1 - - - +
200A ARG* 3.1 66.5 + - + -
203A MSE 3.9 11.5 - - + +
204A GLU* 3.2 34.0 + - + -
253A ILE* 6.1 1.3 - - + -
261A LYS* 4.7 6.9 + - - -
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Residues in contact with GLN 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 LEU* 2.9 20.6 + - + +
187A LYS* 3.4 20.8 - - - +
188A ILE 2.9 0.6 - - - -
189A TYR* 1.3 75.2 - - + +
191A ALA* 1.3 62.4 + - - +
192A ALA 3.0 5.4 + - - -
193A GLU* 3.2 36.4 + - - +
200A ARG* 4.7 1.1 - - - +
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Residues in contact with ALA 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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187A LYS 3.4 2.7 + - - +
188A ILE 2.9 8.7 + - - +
190A GLN* 1.3 70.1 - - - +
192A ALA* 1.3 54.8 + - - +
193A GLU* 2.9 13.1 + - - +
194A SER* 3.2 20.6 + - - -
195A SER* 4.0 0.3 + - - -
292A ALA* 3.9 26.1 - - - +
295A ALA* 4.1 11.9 - - + +
296A SER* 4.0 22.9 - - - +
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Residues in contact with ALA 192 (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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188A ILE 2.9 11.4 + - - +
189A TYR* 3.1 22.0 - - + +
190A GLN 3.0 0.6 - - - -
191A ALA* 1.3 73.3 - - - +
193A GLU* 1.3 58.4 + - - +
195A SER* 2.6 36.0 + - - +
199A LEU* 3.7 22.8 - - + +
200A ARG* 3.7 17.7 + - + +
203A MSE 4.5 7.0 - - - -
292A ALA* 4.4 4.9 - - + +
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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