Contacts of the helix formed by residues 208 - 220 (chain D) in PDB entry 1HBX
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 208 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204D PRO* 2.7 31.0 + - - -
207D THR* 1.3 82.3 + - - +
209D GLU* 1.3 58.9 + - - +
210D THR* 4.0 8.1 - - - -
211D GLY* 2.7 27.5 + - - -
212D LYS* 2.9 32.3 + - - +
214E LEU* 4.3 7.0 - - - +
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Residues in contact with GLU 209 (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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207D THR 3.8 4.0 + - - +
208D SER* 1.3 70.9 - - - +
210D THR* 1.3 69.8 + - - +
212D LYS* 3.0 34.4 + - - +
213D ALA* 3.2 24.3 + - - +
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Residues in contact with THR 210 (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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208D SER* 3.2 7.7 + - - -
209D GLU* 1.3 81.2 - - - +
211D GLY* 1.3 67.9 + - - +
213D ALA* 3.3 5.1 - - - +
214D LEU* 2.9 16.5 + - - +
210E THR* 4.2 23.8 - - + -
214E LEU* 4.3 14.8 - - + -
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Residues in contact with GLY 211 (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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205D MET* 3.6 15.9 - - - -
208D SER* 2.7 24.3 + - - -
210D THR* 1.3 69.6 - - - +
212D LYS* 1.3 57.4 + - - +
214D LEU* 2.5 33.8 + - - +
215D ILE* 3.1 14.0 + - - -
214E LEU* 3.6 13.0 - - - +
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Residues in contact with LYS 212 (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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205D MET 4.3 1.4 + - - -
206D ILE 3.1 22.3 + - - +
207D THR* 3.8 10.8 - - - +
208D SER 2.9 22.7 + - - +
209D GLU* 3.0 43.6 + - - +
211D GLY* 1.3 67.2 - - - -
213D ALA* 1.3 63.8 + - - +
215D ILE* 3.0 17.4 + - - +
216D GLN* 2.8 27.2 + - - +
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Residues in contact with ALA 213 (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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209D GLU 3.2 18.8 + - - +
210D THR* 3.3 6.1 - - - +
211D GLY 2.6 3.4 + - - -
212D LYS* 1.3 76.2 - - - +
214D LEU* 1.3 65.1 + - - +
216D GLN* 2.8 9.5 + - - +
217D THR* 2.7 28.5 + - - +
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Residues in contact with LEU 214 (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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205D MET* 4.8 6.5 - - + -
210D THR 2.9 12.1 + - - +
211D GLY* 2.5 16.5 + - - +
213D ALA* 1.3 72.0 - - - +
215D ILE* 1.3 61.9 + - - +
217D THR* 3.1 12.1 + - + -
218D CYS* 2.9 34.0 + - - -
204E PRO* 4.5 5.4 - - + +
205E MET* 3.2 33.0 - - - +
208E SER* 4.5 8.3 - - - +
210E THR* 4.4 13.7 - - + -
211E GLY* 3.7 33.0 - - - +
214E LEU* 5.0 2.7 - - + -
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Residues in contact with ILE 215 (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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186D LEU* 3.9 27.4 - - + -
194D VAL* 5.2 7.2 - - + -
205D MET 3.6 16.2 - - - +
206D ILE* 4.3 9.4 - - + +
211D GLY* 3.1 38.3 + - - +
212D LYS* 3.0 12.2 + - - +
214D LEU* 1.3 77.0 - - - +
216D GLN* 1.3 69.6 + - - +
218D CYS* 2.9 15.5 + - - +
219D LEU* 2.9 40.6 + - + +
202E LEU* 4.9 2.0 - - + -
205E MET* 3.9 20.9 - - + -
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Residues in contact with GLN 216 (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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194D VAL* 6.0 2.2 - - - +
212D LYS* 2.8 15.5 + - - +
213D ALA* 2.8 15.0 + - - +
215D ILE* 1.3 78.3 - - - +
217D THR* 1.3 62.6 + - - +
219D LEU* 4.9 9.5 - - - +
220D ASN* 2.9 57.0 + - - +
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Residues in contact with THR 217 (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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213D ALA* 2.7 19.7 + - - +
214D LEU* 3.5 17.5 - - + +
216D GLN* 1.3 73.2 - - - +
218D CYS* 1.3 69.6 + - - +
220D ASN* 4.0 2.3 - - - +
221D SER* 3.3 17.9 + - - -
204E PRO* 6.3 0.7 - - + -
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Residues in contact with CYS 218 (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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214D LEU* 2.9 30.2 + - - -
215D ILE 2.9 4.1 + - - +
217D THR* 1.3 77.0 - - - +
219D LEU* 1.3 59.2 + - - +
221D SER* 2.7 36.0 + - - -
201E LYS* 3.1 20.1 - - - +
202E LEU* 3.3 15.3 - - + -
204E PRO* 3.3 31.0 - - - -
205E MET* 3.6 25.4 - - - -
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Residues in contact with LEU 219 (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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186D LEU* 4.7 4.0 - - + -
188D ALA* 4.0 11.2 - - + -
194D VAL* 3.5 32.8 - - + -
215D ILE* 2.9 34.5 + - + +
216D GLN* 4.8 8.5 - - - +
218D CYS* 1.3 76.5 - - - +
220D ASN* 1.3 63.0 + - - +
221D SER 3.5 0.3 + - - -
182E GLN* 3.7 35.9 - - + -
201E LYS* 3.7 22.9 + - - +
202E LEU* 3.7 17.9 - - + -
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Residues in contact with ASN 220 (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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216D GLN* 2.9 52.2 + - - +
217D THR* 4.0 3.4 - - - +
218D CYS 2.9 1.8 + - - -
219D LEU* 1.3 75.5 - - - +
221D SER* 1.3 67.9 + - - +
222D PRO* 4.5 0.5 - - - +
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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