Contacts of the helix formed by residues 187 - 198 (chain B) in PDB entry 1XAI
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 GLY 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183B ALA 3.3 1.1 + - - +
184B LEU 3.7 2.0 + - - -
185B LEU 3.2 6.0 + - - -
186B ASN* 1.3 80.4 - - - +
188B GLU* 1.3 65.3 + - - -
189B SER* 3.1 5.4 + - - -
190B ALA 3.5 1.1 + - - -
191B THR* 3.1 25.3 + - - -
329B PHE* 3.5 20.2 - - - -
330B GLY* 5.1 1.6 - - - -
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Residues in contact with GLU 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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187B GLY* 1.3 71.0 - - - -
189B SER* 1.3 61.6 + - - +
191B THR* 4.0 0.4 - - - -
192B GLN* 3.2 52.6 + - - +
329B PHE* 3.3 46.9 - - + +
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Residues in contact with SER 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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186B ASN 5.7 0.7 - - - -
187B GLY* 3.1 1.9 - - - -
188B GLU* 1.3 77.5 - - - +
190B ALA* 1.3 56.3 + - - +
191B THR 3.2 0.2 + - - -
192B GLN* 3.4 3.4 + - - +
193B ASP* 2.8 39.9 + - - +
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Residues in contact with ALA 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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183B ALA* 4.0 9.6 - - + +
186B ASN* 3.5 41.0 + - + +
187B GLY 3.5 3.3 + - - +
189B SER* 1.3 80.3 + - - +
191B THR* 1.3 56.1 + - - +
193B ASP* 3.6 9.3 - - - +
194B ILE* 2.9 31.2 + - - +
213B TYR* 5.1 1.2 - - - -
216B LYS* 4.0 16.2 - - - +
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Residues in contact with THR 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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180B TYR* 3.7 18.8 - - + +
183B ALA* 4.4 2.7 - - - -
184B LEU* 3.2 25.7 - - + -
187B GLY 3.1 16.3 + - - -
188B GLU 4.0 2.5 - - - -
189B SER 3.2 0.4 - - - -
190B ALA* 1.3 74.5 - - - +
192B GLN* 1.3 56.9 + - + +
193B ASP 2.9 3.8 - - - -
194B ILE* 3.0 10.0 - - - +
195B GLU* 2.6 59.7 + - + +
284B TYR* 4.5 1.1 - - - +
329B PHE* 3.2 24.3 - - + -
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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
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188B GLU* 3.2 50.2 + - + +
189B SER* 4.1 2.7 - - - +
191B THR* 1.3 81.9 - - + +
193B ASP* 1.3 56.2 + - - +
195B GLU* 3.6 19.5 - - - +
196B GLN* 2.9 31.1 + - - +
283B HIS* 6.0 0.7 - - + +
329B PHE* 5.4 3.1 - - + -
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Residues in contact with ASP 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 SER* 2.8 23.6 + - - +
190B ALA* 3.6 9.5 - - - +
191B THR 2.9 0.2 - - - -
192B GLN* 1.3 76.5 - - - +
194B ILE* 1.3 59.5 + - - +
196B GLN* 3.4 16.2 + - - +
197B HIS* 3.1 20.4 + - - +
212B LYS* 3.8 10.4 + - - -
213B TYR* 3.2 25.7 + - - -
216B LYS* 5.8 2.4 - - - -
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Residues in contact with ILE 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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176B TYR* 3.3 27.8 - - + +
179B VAL* 3.7 40.4 - - + +
180B TYR* 4.0 16.2 - - + -
183B ALA* 4.0 7.2 - - + -
190B ALA 2.9 17.1 + - - +
191B THR* 3.0 18.2 - - - +
193B ASP* 1.3 73.1 - - - +
195B GLU* 1.3 62.4 + - - +
196B GLN 3.1 0.2 - - - -
198B PHE* 2.8 43.3 + - + +
213B TYR* 3.6 32.8 - - + -
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Residues in contact with GLU 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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180B TYR* 3.0 34.5 + - + -
191B THR* 2.6 31.7 + - - +
192B GLN* 3.6 24.0 - - - +
194B ILE* 1.3 74.2 - - - +
196B GLN* 1.3 58.8 + - - +
198B PHE 3.4 14.2 - - - +
199B LYS* 3.7 8.0 - - - +
283B HIS* 2.7 39.2 + - + -
284B TYR* 3.6 5.0 - - - -
287B TYR* 3.7 29.4 - - + -
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Residues in contact with GLN 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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192B GLN 2.9 21.8 + - - +
193B ASP* 3.4 17.8 + - - +
194B ILE 3.1 0.2 - - - -
195B GLU* 1.3 76.7 - - - +
197B HIS* 1.3 60.0 + - - +
199B LYS* 2.9 29.3 - - + +
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Residues in contact with HIS 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 ASP 3.1 7.8 + - - +
194B ILE 3.2 2.7 + - - +
196B GLN* 1.3 75.9 - - - +
198B PHE* 1.3 88.9 + + - +
199B LYS* 3.0 15.1 + - - +
203B ILE* 3.4 19.4 - - + +
208B ASN* 2.5 37.6 + - + -
209B GLY* 3.6 11.9 - - - -
213B TYR* 3.7 30.8 + + + +
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Residues in contact with PHE 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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176B TYR* 3.5 25.1 - + + +
194B ILE* 2.8 23.9 + - + +
195B GLU 3.4 3.2 - - - +
197B HIS* 1.3 91.8 - + - +
199B LYS* 1.3 60.6 + - - +
200B ASP 3.6 2.0 - - - -
203B ILE* 3.8 24.9 - - + -
204B LEU* 3.8 18.8 - - + -
207B LEU 4.7 0.7 - - - -
208B ASN 3.3 26.0 - - - -
210B MET* 3.7 40.4 - - + -
213B TYR* 3.6 18.2 - + - -
287B TYR* 2.8 32.7 + - - +
291B LEU* 3.6 9.1 - - + +
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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