Contacts of the helix formed by residues 208 - 220 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A LEU* 4.8 4.5 - - - +
204B PRO* 3.0 27.3 + - - -
207B THR* 1.3 82.1 + - - +
209B GLU* 1.3 58.2 + - - +
210B THR* 2.8 23.6 + - - -
211B GLY 2.8 13.0 + - - -
212B LYS* 2.8 30.4 + - - +
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Residues in contact with GLU 209 (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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207B THR 3.7 1.2 + - - -
208B SER* 1.3 72.5 + - - +
210B THR* 1.3 66.2 + - - +
212B LYS* 3.1 34.0 + - - +
213B ALA* 3.0 23.8 + - + +
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Residues in contact with THR 210 (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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210A THR* 4.7 20.4 - - + +
214A LEU* 4.1 22.4 - - + -
208B SER* 2.8 9.7 + - - +
209B GLU* 1.3 82.4 - - - +
211B GLY* 1.3 67.5 + - - +
213B ALA* 2.9 12.7 + - - +
214B LEU* 3.1 12.1 + - + +
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Residues in contact with GLY 211 (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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205A MET* 6.0 0.7 - - - -
214A LEU* 3.7 16.1 - - - +
205B MET 3.4 21.5 - - - -
208B SER* 2.8 8.8 + - - -
210B THR* 1.3 77.0 - - - +
212B LYS* 1.3 67.2 + - - +
214B LEU* 2.8 19.9 + - - +
215B ILE* 3.0 18.0 + - - +
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Residues in contact with LYS 212 (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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205B MET 4.2 1.4 + - - -
206B ILE 4.1 19.7 + - - +
207B THR* 3.4 17.1 + - - +
208B SER 2.8 24.4 + - - +
209B GLU* 3.1 39.2 + - - +
211B GLY* 1.3 77.7 - - - +
213B ALA* 1.3 60.8 + - - +
215B ILE* 3.5 9.3 + - - +
216B GLN* 3.3 17.8 + - - +
150G PHE* 6.1 2.9 - - + -
155G LEU* 4.0 28.3 - - + +
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Residues in contact with ALA 213 (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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209B GLU* 3.0 14.3 + - - +
210B THR* 2.9 11.3 + - - +
212B LYS* 1.3 75.8 - - - +
214B LEU* 1.3 59.3 + - - +
215B ILE 3.3 0.2 - - - -
216B GLN* 3.4 17.5 + - - +
217B THR* 2.9 32.6 + - - -
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Residues in contact with LEU 214 (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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204A PRO* 4.9 4.9 - - + +
205A MET* 3.5 28.7 - - + +
208A SER* 4.2 15.7 - - - +
210A THR* 4.6 13.7 - - + +
211A GLY* 3.7 29.2 - - - +
214A LEU* 4.4 17.3 - - + -
205B MET* 5.7 0.9 - - - -
210B THR* 3.1 7.1 + - + +
211B GLY* 2.8 14.8 + - - +
213B ALA* 1.3 77.1 - - - +
215B ILE* 1.3 62.2 + - - +
217B THR* 3.4 12.3 - - + +
218B CYS* 3.1 34.9 + - - -
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Residues in contact with ILE 215 (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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202A LEU* 5.3 2.0 - - + -
205A MET* 3.6 24.7 - - + -
186B LEU* 3.7 28.7 - - + -
194B VAL* 4.7 8.1 - - + -
205B MET 4.2 2.0 - - - +
206B ILE* 4.0 32.5 - - + +
211B GLY 3.0 17.9 + - - +
212B LYS* 3.6 9.9 - - - +
214B LEU* 1.3 75.5 - - - +
216B GLN* 1.3 65.9 + - - +
218B CYS* 3.3 3.4 + - - +
219B LEU* 3.0 44.1 + - + +
150G PHE* 5.4 8.5 - - + -
152G LEU* 5.1 0.4 - - + -
155G LEU* 4.7 10.1 - - + -
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Residues in contact with GLN 216 (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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212B LYS 3.3 11.7 + - - +
213B ALA* 3.4 19.7 + - - +
214B LEU 3.3 0.2 - - - -
215B ILE* 1.3 82.0 - - - +
217B THR* 1.3 70.1 + - - +
219B LEU 3.9 0.3 - - - -
220B ASN* 2.9 42.7 + - - +
152G LEU* 4.5 1.7 - - - +
155G LEU* 2.7 52.1 + - + +
156G ASN* 4.0 12.3 + - - +
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Residues in contact with THR 217 (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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204A PRO* 6.1 2.2 - - + -
213B ALA* 2.9 15.5 + - - +
214B LEU* 3.4 17.4 - - + +
216B GLN* 1.3 80.4 + - - +
218B CYS* 1.3 70.3 + - - +
220B ASN* 3.4 3.9 + - - +
221B SER* 3.4 15.6 + - - -
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Residues in contact with CYS 218 (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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201A LYS* 2.9 21.5 - - - +
202A LEU* 4.1 16.2 - - + -
204A PRO* 3.1 39.3 - - - -
205A MET* 4.1 15.0 - - - -
214B LEU* 3.1 17.6 + - - +
215B ILE 3.6 6.5 - - - +
216B GLN 3.2 0.2 - - - -
217B THR* 1.3 77.0 - - - +
219B LEU* 1.3 59.6 + - - +
220B ASN 2.7 10.3 + - - -
221B SER* 2.7 30.4 + - - -
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Residues in contact with LEU 219 (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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182A GLN* 3.8 21.5 - - + -
201A LYS* 2.9 24.7 + - + +
202A LEU* 3.7 32.3 - - + -
186B LEU* 4.5 5.2 - - + -
188B ALA* 3.4 27.1 - - + -
194B VAL* 3.7 21.3 - - + -
215B ILE* 3.0 31.7 + - + +
218B CYS* 1.3 77.3 - - - +
220B ASN* 1.3 58.3 + - - +
221B SER 3.5 0.2 - - - -
152G LEU* 3.6 26.2 - - + +
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Residues in contact with ASN 220 (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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201A LYS* 4.7 0.2 - - - -
216B GLN* 2.9 46.1 + - - +
217B THR* 3.9 4.5 - - - +
218B CYS 2.7 4.2 + - - -
219B LEU* 1.3 75.5 - - - +
221B SER* 1.3 67.0 + - - +
222B PRO* 3.5 2.4 - - - +
152G LEU* 3.8 24.2 + - - +
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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