Contacts of the helix formed by residues 181 - 198 (chain F) in PDB entry 2BWJ
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 THR 181 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180F GLY* 1.3 73.2 - - - -
182F PRO* 1.3 72.2 - - + +
183F GLU* 3.0 18.8 + - - +
184F ASP* 3.0 28.2 + - - +
185F VAL* 2.8 24.2 + - - +
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Residues in contact with PRO 182 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26F THR* 5.2 6.7 - - - +
27F GLN* 2.8 33.2 + - - +
30F LYS* 4.2 14.2 + - - +
180F GLY 3.9 2.2 - - - +
181F THR* 1.3 86.6 - - + +
183F GLU* 1.3 71.7 + - - +
185F VAL* 4.4 2.9 - - + -
186F PHE* 2.9 16.6 + - - +
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Residues in contact with GLU 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F LYS* 4.4 13.9 + - - +
181F THR* 3.0 21.2 + - - +
182F PRO* 1.3 91.5 - - - +
184F ASP* 1.3 64.5 + - - +
186F PHE* 4.0 6.2 - - - +
187F LEU* 3.3 30.3 + - + +
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Residues in contact with ASP 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180F GLY* 4.3 10.4 - - - -
181F THR* 3.0 27.1 + - - +
183F GLU* 1.3 73.0 - - - +
185F VAL* 1.3 66.3 + - - +
187F LEU* 3.4 13.5 + - - +
188F GLN* 3.1 42.1 + - - +
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Residues in contact with VAL 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F SER 6.0 0.2 - - - +
27F GLN* 3.8 24.2 - - + +
121F MET* 4.0 12.3 - - + -
176F ILE* 3.6 20.0 - - + -
177F ASN 3.6 20.2 - - - +
178F ALA* 3.9 11.9 - - + +
180F GLY* 4.0 11.9 - - - +
181F THR 2.8 22.2 + - - +
182F PRO* 3.8 4.9 - - + +
184F ASP* 1.3 77.7 - - - +
186F PHE* 1.3 62.7 + - - +
188F GLN* 3.1 10.8 + - - +
189F LEU* 2.9 22.8 + - + +
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Residues in contact with PHE 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F GLN* 3.1 22.3 + - - +
30F LYS* 3.5 53.6 - - + +
31F LEU* 3.7 17.3 - - + -
34F LYS* 3.6 20.4 - - + -
182F PRO 2.9 17.5 + - - +
183F GLU* 4.0 7.9 - - - +
184F ASP 3.3 0.2 - - - -
185F VAL* 1.3 75.7 - - - +
187F LEU* 1.3 63.6 + - + +
189F LEU* 3.1 3.3 + - - +
190F CYS* 2.9 58.7 + - - -
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Residues in contact with LEU 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F GLU* 3.3 19.9 + - + +
184F ASP* 3.6 14.8 - - - +
186F PHE* 1.3 82.4 - - + +
188F GLN* 1.3 63.1 + - - +
190F CYS* 3.6 9.0 + - + +
191F THR* 3.1 26.9 + - - -
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Residues in contact with GLN 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175F LYS 4.9 0.9 - - - +
176F ILE* 3.9 18.4 - - + +
177F ASN* 3.1 48.9 + - - +
184F ASP* 3.1 41.4 + - - +
185F VAL* 3.1 12.5 + - - +
187F LEU* 1.3 76.1 - - + +
189F LEU* 1.3 63.5 + - - +
191F THR* 3.2 9.2 + - - +
192F ALA* 3.1 21.0 + - - +
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Residues in contact with LEU 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F ILE* 4.4 6.1 - - + -
27F GLN* 3.2 47.8 - - + +
31F LEU* 4.2 22.4 - - + -
119F ILE* 3.3 45.1 - - + -
121F MET* 4.7 3.4 - - + -
176F ILE* 3.8 16.4 - - + -
185F VAL* 2.9 16.3 + - + +
186F PHE* 3.1 6.9 + - - +
188F GLN* 1.3 76.1 - - - +
190F CYS* 1.3 56.6 + - - +
192F ALA* 3.3 5.3 + - - +
193F ILE* 3.0 34.8 + - + +
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Residues in contact with CYS 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F LEU* 4.6 0.2 - - - -
34F LYS* 3.6 14.4 - - - -
35F TYR* 3.2 23.6 - - - +
186F PHE* 2.9 56.7 + - - +
187F LEU* 3.9 9.6 - - + +
189F LEU* 1.3 72.7 - - - +
191F THR* 1.3 60.6 + - - +
194F ASP* 2.8 44.1 + - - +
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Residues in contact with THR 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174F HIS* 6.0 2.2 - - + +
187F LEU 3.1 15.2 + - - -
188F GLN* 3.4 11.6 - - - -
190F CYS* 1.3 76.1 - - - +
192F ALA* 1.3 63.6 + - - +
194F ASP* 4.0 4.9 - - - +
195F SER* 3.1 26.3 + - - -
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Residues in contact with ALA 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F LEU* 3.8 11.6 - - + +
119F ILE* 5.0 2.7 - - + -
174F HIS* 3.5 40.5 + - + -
176F ILE* 4.5 8.1 - - + -
188F GLN 3.1 11.4 + - - +
189F LEU* 3.6 9.2 - - - +
190F CYS 3.3 0.4 - - - -
191F THR* 1.3 77.7 - - - +
193F ILE* 1.3 61.1 + - + +
195F SER* 2.5 23.4 + - - -
196F ILE* 3.6 12.5 + - - +
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Residues in contact with ILE 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F ILE* 4.4 9.4 - - + -
31F LEU* 3.5 39.0 - - + -
35F TYR* 3.7 30.7 - - + +
37F PHE* 4.0 26.5 - - + -
94F LEU* 5.9 0.2 - - + -
117F LEU* 3.9 20.4 - - + -
119F ILE* 4.2 11.7 - - + -
189F LEU 3.0 18.2 + - - +
191F THR 3.3 0.2 - - - -
192F ALA* 1.3 74.1 - - - +
194F ASP* 1.3 56.3 + - - +
196F ILE* 3.1 5.9 + - + +
197F PHE* 2.7 41.0 + - + +
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Residues in contact with ASP 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F LYS* 4.9 4.6 - - - -
35F TYR* 2.8 30.5 + - - -
190F CYS* 2.8 34.1 + - - +
191F THR* 4.0 4.7 + - - +
193F ILE* 1.3 72.4 - - - +
195F SER* 1.3 54.9 + - - +
197F PHE* 4.3 6.4 - - - +
198F LEU* 2.6 40.0 + - + +
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Residues in contact with SER 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174F HIS* 3.9 9.9 + - - -
191F THR* 3.1 15.8 + - - -
192F ALA* 2.5 27.2 + - - -
194F ASP* 1.3 74.8 - - - +
196F ILE* 1.3 69.0 + - - +
198F LEU* 4.4 9.7 - - - +
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Residues in contact with ILE 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F LYS* 6.0 5.8 - - + -
14F ILE* 5.9 5.2 - - + -
116F GLN* 3.9 37.7 - - + +
117F LEU* 4.3 18.6 - - + -
172F GLN* 3.6 28.3 - - + -
174F HIS* 4.5 2.0 - - + -
192F ALA 3.7 7.2 - - - +
193F ILE* 3.1 8.6 + - + +
194F ASP 3.0 0.2 - - - -
195F SER* 1.3 94.2 + - - +
197F PHE* 1.3 69.9 + - + +
198F LEU* 3.1 12.1 - - - +
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Residues in contact with PHE 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F TYR* 5.6 4.3 - - + -
37F PHE* 6.3 0.9 - - + -
193F ILE* 2.7 31.9 + - + +
194F ASP* 4.2 6.7 - - - +
196F ILE* 1.3 76.1 - - + +
198F LEU* 1.3 59.4 + - - +
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Residues in contact with LEU 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194F ASP* 2.6 26.4 + - + +
195F SER* 4.6 9.3 - - - +
196F ILE 3.1 13.4 - - - +
197F PHE* 1.3 76.8 - - - +
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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