Contacts of the helix formed by residues 182 - 190 (chain B) in PDB entry 1XUO
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 182 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168B PHE 3.8 4.2 - - - +
169B ALA* 4.0 6.3 - - + -
179B THR* 4.2 13.4 - - + +
181B PHE* 1.3 78.1 - - - +
183B PHE* 1.3 65.3 + - + +
184B SER* 3.1 8.7 + - - -
185B ASP* 2.9 49.8 + - - +
186B TYR 3.1 9.7 + - - -
219B VAL* 5.9 2.0 - - + -
224B LEU* 3.6 43.5 - - + +
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Residues in contact with PHE 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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131B ASP* 3.7 17.5 - - + -
132B LEU 3.9 5.4 - - - -
133B VAL* 3.7 22.0 - - + -
167B GLN* 3.6 35.6 - - + +
168B PHE 3.4 31.4 + - - -
169B ALA* 3.9 7.4 - - + +
182B ASP* 1.3 76.9 - - + +
184B SER* 1.3 56.1 + - - +
186B TYR* 3.1 4.2 + - - +
187B VAL* 3.0 34.2 + - - +
219B VAL* 3.8 24.5 - - + -
220B PHE* 3.8 17.3 - + - -
224B LEU 3.4 8.5 + - - +
225B GLY* 3.7 6.7 - - - -
226B ALA* 3.7 27.1 - - + -
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Residues in contact with SER 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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182B ASP* 3.1 10.0 + - - -
183B PHE* 1.3 73.9 - - - +
185B ASP* 1.3 67.2 + - - +
187B VAL* 3.4 17.0 + - - +
188B LYS* 3.5 15.6 + - - +
223B GLU 4.7 2.6 + - - -
224B LEU* 3.2 17.1 + - - -
225B GLY* 3.3 14.1 - - - -
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Residues in contact with ASP 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 GLU 4.8 0.3 - - - +
181B PHE* 3.5 18.7 - - + -
182B ASP* 2.9 44.8 + - - +
184B SER* 1.3 77.3 - - - +
186B TYR* 1.3 65.9 + - - +
187B VAL 3.5 0.3 + - - -
188B LYS* 3.6 12.8 + - - +
189B TRP* 4.4 2.3 + - - -
190B LYS 5.2 0.2 + - - -
195B LEU* 3.7 15.3 - - + +
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Residues in contact with TYR 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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158B MET* 4.3 14.2 + - + -
161B LEU 4.5 0.5 + - - -
162B SER* 4.2 19.6 - - - -
163B ASN 5.0 1.2 + - - -
166B TYR 3.9 20.3 + - - -
167B GLN* 4.1 9.4 - - + -
168B PHE* 3.4 68.0 - + + +
181B PHE* 4.1 4.3 - - + -
182B ASP 3.1 6.4 + - - +
183B PHE 3.4 4.0 - - - +
185B ASP* 1.3 76.3 - - - +
187B VAL* 1.3 63.4 + - + +
188B LYS 3.2 0.2 + - - -
190B LYS* 3.0 66.1 + - + +
192B PRO* 5.3 2.7 - - + -
195B LEU* 3.7 25.5 - - + +
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Residues in contact with VAL 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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167B GLN* 3.2 36.3 - - + +
183B PHE 3.0 19.3 + - - +
184B SER* 3.7 10.1 - - - +
185B ASP 3.3 0.6 - - - -
186B TYR* 1.3 80.9 - - + +
188B LYS* 1.3 65.6 + - + +
190B LYS* 3.9 21.0 + - - +
225B GLY* 5.8 0.7 - - - +
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Residues in contact with LYS 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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184B SER 3.5 9.1 + - - +
185B ASP* 4.1 9.4 - - - +
186B TYR 3.2 1.8 + - - -
187B VAL* 1.3 82.4 - - + +
189B TRP* 1.3 83.3 + - + +
190B LYS* 5.5 1.6 + - - -
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Residues in contact with TRP 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 ASP 4.4 3.1 + - - +
186B TYR 3.7 1.0 + - - -
188B LYS* 1.3 102.1 + - + +
190B LYS* 1.3 76.8 + - - +
191B ASP* 4.1 20.7 - - + +
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Residues in contact with LYS 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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162B SER* 5.6 10.0 - - - -
163B ASN* 4.6 19.0 + - - +
185B ASP 5.2 0.4 + - - -
186B TYR* 3.0 54.1 + - + +
187B VAL* 3.9 18.9 + - - +
188B LYS 5.5 1.3 + - - +
189B TRP* 1.3 79.6 - - - +
191B ASP* 1.3 58.0 + - - +
192B PRO* 3.4 11.2 - - - +
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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