Contacts of the helix formed by residues 181 - 196 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180D GLY* 1.3 72.3 - - - -
182D PRO* 1.4 76.4 - - - +
183D GLU* 3.4 8.1 + - - +
184D ASP* 3.0 38.4 + - - +
185D VAL* 3.1 26.2 + - - +
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Residues in contact with PRO 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D THR* 5.0 9.2 - - - +
27D GLN* 2.9 22.1 + - - +
131D ARG* 6.3 0.9 - - - +
181D THR* 1.4 91.3 - - - +
183D GLU* 1.3 57.5 + - + +
185D VAL* 3.3 1.0 + - + -
186D PHE* 2.8 30.0 + - - +
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Residues in contact with GLU 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D THR* 3.3 7.3 + - - +
182D PRO* 1.3 80.3 - - - +
184D ASP* 1.3 59.3 + - - +
186D PHE* 3.6 8.6 - - - +
187D LEU* 3.0 31.7 + - - +
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Residues in contact with ASP 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D GLY* 4.5 7.6 - - - -
181D THR* 3.0 37.7 + - - +
183D GLU* 1.3 79.3 - - - +
185D VAL* 1.3 61.2 - - + +
187D LEU* 3.7 4.9 + - - +
188D GLN* 3.3 25.7 + - - +
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Residues in contact with VAL 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D GLN* 3.7 24.5 - - + +
121D MET* 4.8 2.9 - - + -
176D ILE* 3.7 22.1 - - + +
177D ASN 4.0 12.6 - - - +
178D ALA* 4.1 20.0 - - + -
180D GLY* 4.0 18.8 - - - +
181D THR 3.1 18.9 + - - +
182D PRO* 4.9 0.2 - - + -
184D ASP* 1.3 76.7 - - + +
186D PHE* 1.3 56.9 + - - +
188D GLN* 3.4 9.8 + - - +
189D LEU* 2.9 30.0 + - + +
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Residues in contact with PHE 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D GLN* 3.4 21.2 - - - +
30D LYS* 3.5 34.5 - - + -
31D LEU* 3.8 23.3 - - + -
34D LYS* 3.5 28.3 - - + -
182D PRO 2.8 18.8 + - - +
183D GLU* 3.6 8.5 - - - +
185D VAL* 1.3 74.0 - - - +
187D LEU* 1.3 61.6 + - - +
188D GLN 3.1 1.3 - - - -
189D LEU* 3.0 4.7 + - + +
190D CYS* 2.8 47.3 + - - -
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Residues in contact with LEU 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D GLU 3.0 17.8 + - - +
184D ASP* 4.1 4.9 - - - +
186D PHE* 1.3 78.2 - - - +
188D GLN* 1.3 55.7 + - - +
190D CYS* 3.9 8.7 - - - +
191D THR* 2.9 31.2 + - - -
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Residues in contact with GLN 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D LYS 4.5 3.8 + - - -
176D ILE* 4.0 18.3 - - + +
177D ASN* 3.2 49.6 - - - +
184D ASP* 3.3 19.1 + - - +
185D VAL* 3.4 8.3 - - - +
186D PHE 3.1 0.4 - - - -
187D LEU* 1.3 75.4 - - - +
189D LEU* 1.3 62.2 + - - +
191D THR* 3.7 8.3 + - - -
192D ALA* 3.5 15.8 + - - +
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Residues in contact with LEU 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ILE* 4.8 1.1 - - + -
27D GLN* 3.1 47.1 - - + +
31D LEU* 4.4 22.2 - - + -
119D ILE* 3.4 40.8 - - + +
121D MET* 4.2 13.5 - - + -
176D ILE* 3.8 15.3 - - + -
185D VAL* 2.9 21.9 + - + +
186D PHE* 3.0 8.0 + - + +
188D GLN* 1.3 75.4 - - - +
190D CYS* 1.3 60.2 + - - +
192D ALA* 3.1 5.9 + - - +
193D ILE* 2.9 31.4 + - + +
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Residues in contact with CYS 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D LEU* 4.8 5.6 - - - -
34D LYS* 5.8 2.0 - - - -
186D PHE* 2.8 52.2 + - - +
187D LEU* 3.9 9.0 - - - +
188D GLN 3.4 0.2 - - - -
189D LEU* 1.3 75.8 - - - +
191D THR* 1.3 52.7 + - - +
193D ILE* 4.1 9.2 - - - -
194D ASP* 2.5 54.1 + - - +
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Residues in contact with THR 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D LEU 2.9 20.2 + - - -
188D GLN* 3.7 9.5 - - - +
189D LEU 3.2 0.2 - - - -
190D CYS* 1.3 79.0 - - - +
192D ALA* 1.3 56.7 + - - +
194D ASP* 4.3 6.3 - - - +
195D SER* 3.2 24.8 + - - -
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Residues in contact with ALA 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D LEU* 5.1 2.6 - - - +
119D ILE* 5.1 8.3 - - + -
174D HIS* 4.0 26.5 - - + -
176D ILE* 4.1 12.1 - - + -
188D GLN 3.5 8.7 + - - +
189D LEU 3.1 9.0 + - - +
191D THR* 1.3 76.9 - - - +
193D ILE* 1.3 64.7 + - - +
195D SER* 3.1 19.1 - - - -
196D ILE* 3.4 14.0 - - - +
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Residues in contact with ILE 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D LEU* 3.3 35.7 - - + -
35D TYR* 5.6 4.0 - - + -
37D PHE* 5.0 25.1 - - + -
94D LEU* 5.9 2.5 - - + -
119D ILE* 3.9 25.6 - - + -
189D LEU 2.9 16.8 + - - +
190D CYS* 3.5 9.4 - - + +
192D ALA* 1.3 73.5 - - - +
194D ASP* 1.3 69.5 + - - +
195D SER 3.1 0.2 - - - -
196D ILE* 2.9 31.2 + - - +
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Residues in contact with ASP 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D CYS* 2.5 41.1 + - - +
191D THR* 4.3 5.8 + - - +
193D ILE* 1.3 78.5 - - - +
195D SER* 1.3 64.2 + - - +
196D ILE 3.3 7.3 + - - -
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Residues in contact with SER 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D THR 3.2 16.4 + - - -
192D ALA* 3.1 18.8 - - - -
194D ASP* 1.3 77.4 - - - +
196D ILE* 1.3 64.3 + - - +
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Residues in contact with ILE 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LYS* 6.0 5.8 - - + -
116D GLN* 3.8 33.0 - - + +
117D LEU* 3.7 22.7 - - + -
172D GLN* 5.7 6.1 - - + -
192D ALA 3.4 17.5 - - - +
193D ILE* 2.9 17.8 + - - +
194D ASP* 3.7 7.6 - - - -
195D SER* 1.3 87.3 - - - +
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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