Contacts of the helix formed by residues 176 - 189 (chain B) in PDB entry 2BKU
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 SER 176 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136B MET* 3.4 40.3 - - - +
140B VAL* 4.9 1.2 - - - +
172B ALA* 2.6 21.4 + - - -
173B LEU 3.6 4.9 - - - -
175B SER* 1.3 74.0 - - - +
177B SER* 1.3 61.9 + - - +
178B ASN 3.3 2.7 - - - -
179B ASN* 3.1 21.9 + - - +
180B ILE* 2.9 25.2 + - - +
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Residues in contact with SER 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B LEU 3.1 11.7 + - - -
174B VAL* 2.8 24.3 + - - +
175B SER 3.4 0.6 - - - -
176B SER* 1.3 76.9 - - - +
178B ASN* 1.3 63.6 + - - +
180B ILE* 3.1 9.9 + - - +
181B LEU* 2.8 35.9 + - - +
211B PHE 5.5 3.4 - - - -
212B ILE* 5.2 5.0 - - - +
215B ASN* 3.6 23.7 + - - +
218B ARG* 5.9 0.3 + - - -
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Residues in contact with ASN 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B SER 5.1 3.9 + - - +
176B SER 3.3 1.0 - - - -
177B SER* 1.3 78.7 + - - +
179B ASN* 1.3 59.4 + - - +
181B LEU* 3.1 4.1 + - - +
182B ILE* 2.8 46.4 + - + +
215B ASN* 3.4 14.3 - - - +
218B ARG* 4.5 10.3 + - - +
221B GLU* 3.7 26.0 + - - +
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Residues in contact with ASN 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B VAL* 4.0 29.0 - - + +
176B SER* 3.1 22.0 + - - +
178B ASN* 1.3 82.5 - - - +
180B ILE* 1.3 58.3 + - - +
182B ILE* 4.1 5.1 - - - +
183B ALA* 2.9 31.5 + - - +
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Residues in contact with ILE 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B MET* 3.7 23.1 - - - -
140B VAL* 4.3 9.0 - - + -
159B LEU* 3.7 28.3 - - + -
163B CYS* 3.9 28.9 - - - -
173B LEU* 4.7 7.9 - - + +
176B SER* 2.9 31.4 + - - +
177B SER* 3.1 10.1 + - - +
179B ASN* 1.3 74.6 - - - +
181B LEU* 1.3 57.2 + - - +
183B ALA* 3.1 5.9 + - - +
184B ILE* 2.7 57.2 + - + +
208B SER* 5.5 0.7 - - - +
212B ILE* 5.7 5.6 - - + -
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Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B SER 2.8 20.2 + - - +
178B ASN* 3.6 6.5 - - - +
180B ILE* 1.3 72.5 - - - +
182B ILE* 1.3 73.9 + - + +
184B ILE* 3.2 5.6 + - + +
185B VAL* 2.8 47.9 + - + +
205B LEU* 3.9 11.9 - - + -
212B ILE* 3.4 39.2 - - + +
215B ASN* 4.5 17.0 - - + +
221B GLU* 4.7 13.0 - - + +
224B TYR* 4.6 4.9 - - + -
225B LEU* 3.7 22.7 - - + -
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Residues in contact with ILE 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ASN* 2.8 32.6 + - + +
179B ASN* 4.1 5.6 - - - +
181B LEU* 1.3 88.1 - - + +
183B ALA* 1.3 54.9 + - - +
185B VAL* 4.0 0.2 - - - +
186B GLN* 2.6 61.7 + - + +
221B GLU* 4.8 13.2 - - + -
224B TYR* 4.4 22.9 - - + +
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Residues in contact with ALA 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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140B VAL* 4.6 13.5 - - + -
143B THR* 3.1 43.3 - - + +
156B LEU* 3.4 4.2 - - - +
159B LEU* 4.3 11.7 - - + -
179B ASN 2.9 21.6 + - - +
180B ILE 3.5 4.3 - - - +
182B ILE* 1.3 75.1 - - - +
184B ILE* 1.3 63.9 + - - +
186B GLN* 3.8 5.7 - - - +
187B GLY 3.4 10.0 + - - -
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Residues in contact with ILE 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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156B LEU* 3.9 8.5 - - + +
159B LEU* 4.0 19.5 - - + -
180B ILE* 2.7 51.9 + - + +
181B LEU* 3.6 6.3 - - + +
183B ALA* 1.3 69.4 - - - +
185B VAL* 1.3 68.1 + - + +
187B GLY 3.1 12.0 + - - -
188B ALA* 4.2 0.5 - - - +
201B ALA* 3.3 43.0 - - - +
204B ALA* 3.8 27.4 - - + +
205B LEU* 3.5 24.9 - - + +
208B SER* 4.3 9.0 - - - +
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Residues in contact with VAL 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B LEU* 2.8 48.1 + - + +
184B ILE* 1.3 74.9 - - - +
186B GLN* 1.3 61.7 + - - +
188B ALA* 3.0 8.2 + - - +
189B GLN* 3.0 19.4 + - - +
205B LEU* 4.4 13.9 - - + -
224B TYR* 3.3 28.7 - - + -
225B LEU* 4.1 19.1 - - + +
228B VAL* 3.3 31.0 - - + -
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Residues in contact with GLN 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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143B THR* 4.6 13.2 - - + +
144B GLY* 5.5 1.4 - - - -
145B ALA* 5.3 7.8 + - - +
182B ILE* 2.6 40.5 + - + +
183B ALA* 3.8 8.3 - - - +
185B VAL* 1.3 72.1 - - - +
187B GLY* 1.3 58.7 + - - +
188B ALA 3.0 5.7 + - - -
189B GLN* 3.2 34.7 + - - +
190B SER* 5.2 0.3 - - - -
193B THR* 5.0 1.7 - - - +
224B TYR* 3.7 16.2 + - - +
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Residues in contact with GLY 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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143B THR* 5.3 3.8 - - - -
156B LEU* 4.5 10.3 - - - -
183B ALA 3.4 6.8 + - - -
184B ILE 3.1 9.2 + - - -
186B GLN* 1.3 78.2 - - - +
188B ALA* 1.3 56.6 + - - +
189B GLN 4.2 1.1 - - - -
193B THR* 3.7 15.3 + - - +
197B VAL* 3.9 7.7 - - - +
198B ARG* 3.5 20.1 + - - -
201B ALA* 3.6 11.7 - - - +
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Residues in contact with ALA 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 ILE 3.5 3.2 + - - +
185B VAL* 3.0 10.7 + - - +
186B GLN 3.0 0.6 - - - -
187B GLY* 1.3 77.8 - - - +
189B GLN* 1.3 62.1 + - - +
198B ARG* 2.8 37.5 + - - +
201B ALA* 3.8 14.8 - - + -
202B LEU* 3.8 28.4 - - + +
205B LEU* 6.4 1.1 - - + -
228B VAL* 3.8 14.6 - - + +
232B ALA* 5.4 2.9 - - + +
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Residues in contact with GLN 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 VAL 3.0 5.9 + - - -
186B GLN* 3.2 34.3 + - - +
188B ALA* 1.3 79.3 - - - +
190B SER* 1.3 79.1 + - - +
193B THR* 3.5 7.3 - - - +
198B ARG* 5.1 2.5 - - - +
224B TYR* 3.3 33.9 + - - -
228B VAL* 3.5 26.0 - - + +
231B GLU* 6.5 0.9 - - - -
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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