Contacts of the helix formed by residues 176 - 188 (chain D) in PDB entry 2BHT
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 176 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173D MET* 3.6 10.8 - - - -
174D GLY 3.3 4.2 - - - +
175D THR* 1.3 82.7 - - - +
177D GLY* 1.3 52.8 + - - +
178D THR 2.9 3.9 + - - -
179D ILE* 2.9 25.1 + - - +
180D THR* 2.6 55.9 + - - +
218D PRO* 4.6 3.1 - - + -
220D ILE* 3.3 17.5 - - + -
221D PHE* 3.1 35.0 - - + -
320D PLP 2.8 13.8 + - - -
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Residues in contact with GLY 177 (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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146D ASN* 3.6 21.8 - - - -
147D PRO* 3.4 11.3 - - - +
150D HIS* 3.8 8.6 - - - -
175D THR* 3.1 9.3 + - - -
176D THR* 1.3 77.7 - - - +
178D THR* 1.3 56.3 + - - +
180D THR* 4.1 1.1 - - - -
181D GLY* 2.7 26.0 + - - -
220D ILE* 3.5 15.1 - - - +
320D PLP 3.6 2.0 - - - -
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Residues in contact with THR 178 (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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40D VAL* 4.0 7.4 - - + +
150D HIS* 2.9 36.9 - - + +
154D THR* 4.9 1.3 - - + -
169D PHE* 4.2 2.7 - - + -
171D SER* 4.4 6.1 - - - +
176D THR 3.0 0.2 - - - -
177D GLY* 1.3 73.5 - - - +
179D ILE* 1.3 58.7 + - - +
180D THR 3.2 1.3 - - - -
182D VAL* 2.7 50.0 + - + +
278D ILE* 4.2 28.3 - - + -
320D PLP 2.4 33.0 + - - -
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Residues in contact with ILE 179 (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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169D PHE* 4.4 8.5 - - + -
171D SER* 3.6 20.6 + - - +
173D MET* 3.6 15.5 - - + -
176D THR* 2.9 33.6 - - - +
178D THR* 1.3 77.6 - - - +
180D THR* 1.3 57.3 + - - +
182D VAL* 4.9 0.2 - - - +
183D SER* 2.7 38.8 + - - -
195D ILE* 3.6 25.1 - - + -
196D VAL 4.0 3.8 - - - +
197D GLY* 3.4 33.4 - - - +
221D PHE* 4.7 0.4 - - + -
225D LEU* 6.0 0.4 - - - -
226D VAL* 3.4 25.8 - - + -
320D PLP 4.6 0.6 + - - -
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Residues in contact with THR 180 (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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147D PRO* 3.7 18.6 - - + -
176D THR* 2.6 47.9 + - - +
177D GLY* 3.8 5.2 - - - -
179D ILE* 1.3 70.1 - - - +
181D GLY* 1.3 68.0 + - - +
182D VAL 3.0 1.1 - - - -
183D SER* 2.9 4.9 + - - -
184D GLU* 2.8 44.2 + - + +
220D ILE 3.9 19.5 + - - +
221D PHE* 4.4 4.7 - - - -
222D ASN* 5.1 2.1 + - + +
225D LEU* 4.5 12.1 - - + +
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Residues in contact with GLY 181 (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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147D PRO* 3.0 29.4 - - - +
150D HIS* 3.2 8.6 - - - +
151D TYR* 3.0 25.6 - - - +
177D GLY 2.7 18.3 + - - -
180D THR* 1.3 73.6 - - - +
182D VAL* 1.3 59.4 + - - +
184D GLU* 4.0 7.4 + - - -
185D PHE* 3.9 7.4 + - - +
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Residues in contact with VAL 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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150D HIS* 4.1 2.7 - - + +
154D THR* 4.1 12.1 - - + -
155D GLY* 4.1 19.3 - - - +
169D PHE* 3.4 50.7 - - + -
178D THR* 2.7 36.5 + - + +
179D ILE 4.2 0.2 - - - +
181D GLY* 1.3 74.5 - - - +
183D SER* 1.3 65.9 + - - +
185D PHE* 3.0 15.2 + - - +
186D MET* 3.2 32.5 + - + +
195D ILE* 6.0 0.4 - - + -
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Residues in contact with SER 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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179D ILE 2.7 25.7 + - - -
180D THR 2.9 2.2 + - - -
182D VAL* 1.3 75.0 - - - +
184D GLU* 1.3 61.0 + - - +
185D PHE 3.0 1.2 + - - -
186D MET* 3.3 2.9 + - - +
187D ARG* 2.8 40.2 + - - +
195D ILE* 3.4 21.5 - - - +
225D LEU* 2.3 43.1 + - - +
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Residues in contact with GLU 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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147D PRO* 4.4 9.6 - - - +
148D LYS* 5.0 1.7 + - - -
151D TYR* 3.8 29.1 - - + +
180D THR* 2.8 46.3 + - - +
181D GLY* 4.0 4.4 - - - +
183D SER* 1.3 77.0 - - - +
185D PHE* 1.3 56.5 + - - +
187D ARG* 4.1 6.1 - - - +
188D GLU* 3.0 29.8 + - - +
225D LEU* 3.8 18.5 - - + +
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Residues in contact with PHE 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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151D TYR* 3.8 37.6 - + + +
155D GLY* 3.6 30.7 - - - -
156D PRO* 3.9 20.2 - - + -
159D TRP* 3.6 21.1 - + + -
181D GLY 4.1 5.2 - - - +
182D VAL 3.0 9.4 + - - +
183D SER 3.0 0.6 - - - -
184D GLU* 1.3 77.5 - - - +
186D MET* 1.3 67.8 + - + +
187D ARG 3.0 4.3 - - - -
188D GLU* 2.7 26.7 + - - -
189D GLN* 2.8 46.7 + - - -
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Residues in contact with MET 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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155D GLY* 3.3 37.0 - - - +
158D ILE* 3.5 25.6 - - + -
159D TRP* 3.3 33.9 - - + +
166D ILE* 4.5 6.1 - - + -
169D PHE* 5.6 1.1 - - + -
182D VAL* 3.2 26.0 + - + +
183D SER* 3.3 4.9 + - - +
185D PHE* 1.3 78.9 - - + +
187D ARG* 1.3 63.4 + - - +
189D GLN* 3.1 20.3 + - - +
191D LYS 4.5 7.1 - - - +
192D PRO* 5.7 0.2 - - - +
193D VAL* 3.8 34.6 + - + +
195D ILE* 5.1 6.3 - - + -
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Residues in contact with ARG 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 SER* 2.8 28.6 + - - +
184D GLU* 4.1 7.6 - - - +
186D MET* 1.3 74.9 - - - +
188D GLU* 1.3 53.3 - - + +
189D GLN 2.7 25.3 + - - +
193D VAL 3.9 6.5 + - - +
195D ILE* 3.2 28.0 - - - +
224D SER 3.6 7.0 + - - -
225D LEU* 2.8 49.6 + - + +
227D ASP* 3.4 24.4 + - - +
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Residues in contact with GLU 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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151D TYR* 2.5 33.2 + - - -
184D GLU* 3.0 24.2 - - - +
185D PHE* 2.7 16.0 + - - +
187D ARG* 1.3 70.1 - - + +
189D GLN* 1.3 71.2 + - - +
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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