Contacts of the helix formed by residues 178 - 190 (chain B) in PDB entry 2OB2
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 178 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175B ASP* 2.9 16.5 + - - +
176B LEU 4.6 0.2 - - - -
177B ASN* 1.3 76.0 - - - +
179B ILE* 1.3 53.5 + - - +
180B THR* 3.2 12.5 + - - -
181B GLU* 2.8 46.6 + - - +
182B THR* 2.6 35.4 + - - -
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Residues in contact with ILE 179 (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 LEU 5.2 1.3 - - - +
177B ASN 3.7 4.8 + - - -
178B ASP* 1.3 73.6 + - - +
180B THR* 1.3 66.5 + - - +
182B THR* 4.0 6.3 - - + -
183B THR* 2.9 32.1 + - + -
214B LEU* 3.5 30.7 - - + +
215B LEU* 4.0 32.3 - - + +
218B THR* 3.7 42.6 - - + +
219B ILE* 5.8 0.4 - - + -
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Residues in contact with THR 180 (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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178B ASP* 3.2 9.0 + - - -
179B ILE* 1.3 80.0 - - - +
181B GLU* 1.3 67.7 + - - +
183B THR* 3.4 6.6 + - - +
184B ARG* 3.0 65.5 + - + +
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Residues in contact with GLU 181 (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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173B ALA 4.5 2.0 - - - +
174B CYS* 3.2 15.3 - - - -
175B ASP* 3.0 37.5 + - - +
178B ASP* 2.8 42.7 + - - +
180B THR* 1.3 73.3 - - - +
182B THR* 1.3 63.8 + - - +
184B ARG* 3.6 9.8 - - - +
185B LEU* 3.1 24.4 + - - +
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Residues in contact with THR 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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104B LEU* 5.5 0.9 - - + -
127B ILE* 5.8 2.0 - - + -
174B CYS* 3.6 8.7 - - - -
175B ASP 3.6 1.7 + - - -
176B LEU* 3.5 42.9 - - + -
178B ASP 2.6 23.6 + - - -
179B ILE* 3.6 13.4 - - + -
181B GLU* 1.3 76.7 - - - +
183B THR* 1.3 57.4 + - + +
185B LEU* 3.2 5.0 + - - +
186B LEU* 2.9 47.0 + - + +
215B LEU* 3.8 15.7 - - + -
219B ILE* 4.5 3.4 - - + -
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Residues in contact with THR 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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179B ILE* 2.9 27.6 + - + +
180B THR* 3.4 8.3 + - - +
182B THR* 1.3 69.9 - - - +
184B ARG* 1.3 61.4 + - - +
186B LEU* 3.4 8.4 + - + +
187B ASP* 2.9 38.9 + - - +
218B THR* 3.3 34.3 - - + -
222B LYS* 4.0 17.9 - - + -
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Residues in contact with ARG 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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180B THR* 3.0 52.7 + - + +
181B GLU* 3.6 8.3 - - - +
183B THR* 1.3 77.2 + - - +
185B LEU* 1.3 61.6 + - - +
187B ASP* 3.3 17.3 + - - +
188B VAL* 3.5 16.8 + - - +
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Residues in contact with LEU 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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127B ILE* 3.9 24.2 - - + -
161B PRO* 4.1 24.5 - - + +
162B PHE* 4.2 11.0 - - + -
172B ALA* 3.6 27.8 - - + -
173B ALA 3.9 7.6 - - - +
174B CYS* 3.6 32.1 - - + -
181B GLU 3.1 14.5 + - - +
182B THR* 3.2 8.0 + - + +
184B ARG* 1.3 72.3 - - - +
186B LEU* 1.3 68.8 + - - +
188B VAL* 2.9 23.4 + - + +
189B CYS* 3.2 16.2 - - - -
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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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102B VAL* 4.0 28.7 - - + -
104B LEU* 5.6 0.2 - - + -
127B ILE* 4.1 13.9 - - + -
182B THR* 2.9 28.1 + - + +
183B THR* 3.9 1.6 - - + +
184B ARG 3.4 0.2 - - - -
185B LEU* 1.3 77.4 - - - +
187B ASP* 1.3 62.0 + - - +
188B VAL 3.1 0.7 + - - -
189B CYS* 4.0 5.6 - - - -
190B THR* 2.8 48.3 + - + +
219B ILE* 3.6 35.0 - - + -
222B LYS* 3.7 30.3 - - + -
223B PHE* 4.8 7.0 - - + -
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Residues in contact with ASP 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 THR* 2.9 25.2 + - - +
184B ARG* 3.6 10.4 - - - +
185B LEU 3.1 0.4 - - - -
186B LEU* 1.3 75.6 - - - +
188B VAL* 1.3 64.1 + - + +
189B CYS 3.9 0.3 + - - -
190B THR 3.9 9.3 - - - +
222B LYS* 2.8 28.5 + - - -
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Residues in contact with VAL 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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161B PRO* 3.9 28.3 - - + -
162B PHE* 3.7 17.7 - - + -
170B LYS* 4.5 3.3 - - - -
184B ARG 3.7 11.7 - - - +
185B LEU* 2.9 22.2 + - - +
187B ASP* 1.3 84.3 - - + +
189B CYS* 1.3 56.7 + - - +
190B THR 3.9 0.4 - - - -
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Residues in contact with CYS 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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100B GLN* 4.7 2.4 - - - +
123B ALA* 5.9 2.9 - - - +
125B VAL* 3.8 32.4 - - + +
162B PHE* 3.7 11.7 - - + -
170B LYS* 3.5 30.8 - - + +
185B LEU* 3.2 26.9 - - - -
186B LEU* 3.3 9.8 + - - -
188B VAL* 1.3 79.5 - - - +
190B THR* 1.3 73.5 + - - +
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Residues in contact with THR 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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100B GLN* 3.4 25.8 - - + -
102B VAL* 3.9 27.8 - - + -
125B VAL* 4.3 5.2 - - + -
186B LEU* 2.8 27.0 + - + +
187B ASP* 3.9 10.4 - - - +
188B VAL 3.9 0.4 - - - -
189B CYS* 1.3 96.0 - - - +
191B LYS* 1.3 65.2 + - - +
192B ARG 4.6 0.2 + - - -
222B LYS* 5.4 0.9 - - - -
223B PHE* 3.2 21.6 - - + -
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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