Contacts of the helix formed by residues 188 - 200 (chain B) in PDB entry 2PZI
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 ASP 188 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187B GLY* 1.3 78.3 - - - +
189B ALA* 1.3 65.4 + - - +
190B GLU* 3.4 10.9 + - - +
191B ALA* 3.1 22.3 + - - +
192B GLN* 3.1 16.7 + - - +
226B PRO* 5.4 1.1 - - - -
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Residues in contact with ALA 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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188B ASP* 1.3 74.5 - - - +
190B GLU* 1.3 61.6 + - - +
192B GLN* 3.5 6.6 + - - +
193B ALA* 3.2 23.2 + - - +
218B GLU* 4.3 4.6 - - - +
226B PRO* 4.1 32.3 - - + +
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Residues in contact with GLU 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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188B ASP* 3.2 11.9 + - - +
189B ALA* 1.3 76.7 - - - +
191B ALA* 1.3 61.2 + - - +
193B ALA* 3.4 6.1 + - + +
194B MET* 2.9 51.1 + - + +
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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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184B VAL* 5.3 5.1 - - + +
186B SER 5.1 1.8 - - - +
187B GLY* 4.0 17.3 - - - -
188B ASP* 3.1 21.4 + - - +
190B GLU* 1.3 73.6 - - - +
192B GLN* 1.3 60.4 + - - +
194B MET* 3.4 9.3 - - - +
195B ALA* 2.9 28.8 + - - +
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Residues in contact with GLN 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LEU* 4.9 1.4 - - - +
184B VAL* 3.9 23.6 + - - +
186B SER* 3.9 3.6 - - - +
187B GLY 3.1 31.0 + - - +
188B ASP 3.1 16.1 + - - +
189B ALA* 3.8 5.4 - - - +
191B ALA* 1.3 78.4 - - - +
193B ALA* 1.3 61.9 + - - +
195B ALA* 3.2 7.8 + - - +
196B MET* 3.2 28.0 + - - +
218B GLU* 4.4 9.2 - - - +
226B PRO 3.4 20.9 + - - +
227B VAL* 3.7 14.0 - - - +
228B GLY* 3.0 32.6 + - - +
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Residues in contact with ALA 193 (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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189B ALA 3.2 17.0 + - - +
190B GLU* 3.6 7.6 - - + +
192B GLN* 1.3 72.3 - - - +
194B MET* 1.3 59.9 + - - +
196B MET* 3.3 19.9 + - + +
197B ALA* 2.9 30.8 + - - +
218B GLU* 4.1 7.7 + - - +
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Residues in contact with MET 194 (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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190B GLU* 2.9 40.9 + - + +
191B ALA* 3.4 10.8 - - - +
193B ALA* 1.3 74.2 - - - +
195B ALA* 1.3 60.3 + - - +
197B ALA* 4.5 5.2 - - - +
198B GLU* 2.9 61.5 + - - +
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Residues in contact with ALA 195 (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 LEU* 4.0 19.4 - - + +
184B VAL* 4.2 15.5 - - + -
191B ALA 2.9 14.2 + - - +
192B GLN* 3.2 11.2 + - - +
194B MET* 1.3 76.2 - - - +
196B MET* 1.3 60.1 + - - +
198B GLU* 4.3 3.6 - - - +
199B ARG* 3.1 53.7 + - - +
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Residues in contact with MET 196 (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 LEU* 3.6 21.8 - - + -
192B GLN 3.2 10.4 + - - +
193B ALA* 3.6 19.7 - - + +
194B MET 3.2 0.4 - - - -
195B ALA* 1.3 73.8 - - - +
197B ALA* 1.3 65.2 + - - +
199B ARG* 3.0 13.7 + - - +
200B GLN* 3.1 20.1 + - - +
216B PHE* 4.1 19.9 - - + +
217B VAL* 3.9 25.1 - - - +
218B GLU* 3.6 44.6 - - + +
228B GLY* 4.2 3.6 - - - -
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Residues in contact with ALA 197 (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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193B ALA 2.9 21.3 + - - +
194B MET* 4.0 5.6 - - - +
196B MET* 1.3 73.2 - - - +
198B GLU* 1.3 62.6 + - + +
200B GLN* 3.5 22.6 - - - +
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Residues in contact with GLU 198 (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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194B MET* 2.9 44.4 + - + +
195B ALA* 4.3 5.0 - - - +
197B ALA* 1.3 78.6 - - + +
199B ARG* 1.3 66.3 + - + +
200B GLN 3.3 0.2 - - - -
201B PHE* 3.2 25.3 - - - -
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Residues in contact with ARG 199 (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 LEU* 3.8 39.3 + - - +
184B VAL* 4.4 6.9 - - - +
195B ALA* 3.1 43.6 + - - +
196B MET 3.0 4.8 + - - +
198B GLU* 1.3 84.0 + - + +
200B GLN* 1.3 63.5 + - - +
201B PHE* 3.2 11.9 - - + -
202B LEU* 3.1 35.3 + - + +
216B PHE* 3.1 28.1 - - + -
295B GLY* 3.3 28.0 + - - -
296B ALA* 5.3 0.8 - - - +
297B VAL 5.6 6.9 + - - +
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Residues in contact with GLN 200 (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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196B MET* 3.1 20.6 + - - +
197B ALA* 3.5 17.7 - - - +
198B GLU 3.3 2.6 - - - -
199B ARG* 1.3 76.8 - - - +
201B PHE* 1.3 61.2 + - - +
202B LEU 3.1 1.6 + - - -
203B ALA* 3.4 21.8 + - - +
204B GLU* 4.7 2.8 - - - +
215B ASN* 5.5 1.6 - - - +
216B PHE* 3.5 32.1 + - - +
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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