Contacts of the helix formed by residues 181 - 192 (chain B) in PDB entry 1Z19
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180B LEU* 1.3 80.1 - - - +
182B ALA* 1.3 64.6 + - - +
183B ASP* 3.6 6.6 + - - +
184B GLU* 2.9 32.4 + - - +
185B TYR* 3.0 18.0 + - - +
313B LEU* 4.0 2.9 - - - -
316B ARG* 4.7 4.0 - - - +
348B ARG* 3.7 37.0 + - + +
349B GLU* 3.0 42.1 + - + +
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Residues in contact with ALA 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B THR* 1.3 72.5 - - - +
183B ASP* 1.3 64.6 + - - +
185B TYR* 3.1 11.4 + - - +
186B LEU* 3.0 25.5 + - + +
250B ALA* 5.4 5.2 - - + +
251B LEU* 3.8 18.9 - - + +
313B LEU* 3.8 11.0 - - + +
317B LEU* 4.6 20.4 - - + -
349B GLU* 4.8 1.6 + - - -
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Residues in contact with ASP 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B THR* 3.2 7.7 + - - +
182B ALA* 1.3 76.0 - - - +
184B GLU* 1.3 68.6 + - + +
186B LEU* 2.8 27.3 + - - +
187B LYS* 3.0 32.2 + - - +
349B GLU* 5.4 3.8 + - - +
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Residues in contact with GLU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B ARG 3.8 0.2 - - - +
180B LEU* 3.3 21.9 - - + +
181B THR* 2.9 25.9 + - - +
183B ASP* 1.3 76.0 - - + +
185B TYR* 1.3 63.9 + - - +
187B LYS* 3.1 8.2 + - - +
188B ILE* 3.0 29.7 + - - +
298B LEU* 3.8 22.2 - - + +
299B SER 5.0 2.3 - - - +
300B PHE* 3.7 17.2 - - - -
348B ARG* 2.5 48.8 + - - +
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Residues in contact with TYR 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B LEU* 4.2 11.5 - - + +
181B THR 3.0 12.2 + - - +
182B ALA 3.1 7.8 + - - +
184B GLU* 1.3 78.6 - - - +
186B LEU* 1.3 73.0 + - + +
188B ILE* 3.4 4.8 + - - +
189B TYR* 2.8 51.5 + + + +
203B MSE 3.7 20.0 - - + -
204B GLU* 3.5 17.8 + - - +
207B VAL* 3.6 22.7 - - + -
251B LEU* 3.6 23.1 - - + -
253B ILE* 3.1 27.4 - - + +
310B LEU* 3.6 21.8 - - + -
313B LEU* 4.0 16.8 - - + -
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Residues in contact with LEU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B ALA* 3.0 16.0 + - + +
183B ASP* 2.8 22.3 + - - +
185B TYR* 1.3 93.2 - - + +
187B LYS* 1.3 64.1 + - + +
189B TYR* 3.5 9.9 + - + +
190B GLN* 3.0 24.8 + - - +
250B ALA 5.1 5.6 - - - +
251B LEU* 3.8 26.0 - - + +
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Residues in contact with LYS 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B ASP* 3.0 36.8 + - - +
184B GLU* 3.7 9.7 - - - +
186B LEU* 1.3 76.0 - - + +
188B ILE* 1.3 59.9 + - - +
190B GLN* 3.1 14.7 + - - +
191B ALA* 2.8 28.3 + - - +
296B SER* 4.5 5.6 - - - +
298B LEU* 3.3 38.5 - - + +
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Residues in contact with ILE 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B LEU* 4.0 21.5 - - + -
184B GLU 3.0 16.7 + - - +
185B TYR* 3.8 3.4 - - - +
187B LYS* 1.3 71.9 - - - +
189B TYR* 1.3 67.5 + - - +
190B GLN 2.9 1.6 - - - -
191B ALA* 2.7 18.8 + - - +
192B ALA* 2.7 12.3 + - - +
203B MSE 4.3 6.5 - - + -
289B PHE* 3.8 36.8 - - + -
292B ALA* 4.0 9.6 - - + -
293B ARG* 3.9 41.3 - - + +
296B SER* 4.4 7.0 - - - -
298B LEU* 4.4 13.7 - - + -
300B PHE* 5.4 0.9 - - + -
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Residues in contact with TYR 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B TYR* 2.8 48.7 + + + +
186B LEU* 3.7 11.9 - - + +
188B ILE* 1.3 73.2 - - - +
190B GLN* 1.3 62.7 + - + +
192B ALA* 3.5 5.6 + - - +
200B ARG* 2.8 82.4 + - + +
203B MSE 3.8 17.4 - - + +
204B GLU* 2.6 37.4 + - + -
261B LYS* 4.3 8.1 + - - -
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Residues in contact with GLN 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B LEU 3.0 16.0 + - - +
187B LYS* 3.3 12.9 - - - +
188B ILE 2.9 0.4 - - - -
189B TYR* 1.3 77.6 - - + +
191B ALA* 1.3 65.0 + - - +
192B ALA 3.0 2.0 - - - -
193B GLU* 3.1 27.1 + - - +
200B ARG* 3.2 15.1 + - - +
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Residues in contact with ALA 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B LYS 2.8 13.7 + - - +
188B ILE 2.7 11.1 + - - +
190B GLN* 1.3 70.2 - - - +
192B ALA* 1.3 56.9 + - - +
193B GLU* 2.9 12.1 + - - +
194B SER* 4.1 10.6 + - - -
195B SER* 4.5 1.6 + - - -
292B ALA* 3.5 23.4 - - - +
295B ALA* 4.1 15.1 - - + +
296B SER* 3.9 20.6 - - - +
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Residues in contact with ALA 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B ILE 2.7 13.0 + - - +
189B TYR* 3.6 13.9 - - - +
190B GLN 3.0 1.2 - - - -
191B ALA* 1.3 75.5 - - - +
193B GLU* 1.3 62.2 + - - +
194B SER 3.5 1.3 - - - -
195B SER* 3.4 22.5 + - - +
196B PRO 5.3 0.2 - - - +
199B LEU* 3.7 28.2 - - + +
200B ARG* 3.8 21.0 + - + +
203B MSE 4.5 3.8 - - - -
292B ALA* 3.7 7.8 - - + +
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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