Contacts of the helix formed by residues 208 - 220 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214D LEU* 4.5 6.1 - - - +
204E PRO* 2.5 35.0 + - - +
207E THR* 1.3 81.8 - - - +
209E GLU* 1.3 66.3 + - - +
210E THR* 3.9 9.4 + - - -
211E GLY* 3.4 11.1 + - - -
212E LYS* 3.0 20.4 + - - +
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Residues in contact with GLU 209 (chain E).
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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207E THR 3.5 2.7 + - - +
208E SER* 1.3 71.4 - - - +
210E THR* 1.3 64.1 + - - +
212E LYS* 3.0 38.7 + - - +
213E ALA* 2.9 28.0 + - - +
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Residues in contact with THR 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D THR* 4.2 24.7 - - + -
214D LEU* 4.4 15.7 - - + -
208E SER* 3.0 10.1 - - - -
209E GLU* 1.3 79.4 - - - +
211E GLY* 1.3 66.8 + - - +
213E ALA* 3.3 6.3 + - - +
214E LEU* 3.0 21.0 + - + +
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Residues in contact with GLY 211 (chain E).
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* 4.7 1.1 - - - -
214D LEU* 3.7 16.2 - - - -
205E MET 3.4 23.3 - - - -
208E SER* 3.0 11.5 + - - -
210E THR* 1.3 75.6 - - - +
212E LYS* 1.3 67.3 + - - +
214E LEU* 2.9 9.0 + - - +
215E ILE* 2.7 25.7 + - - +
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Residues in contact with LYS 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205E MET 4.3 1.4 + - - -
206E ILE 3.2 20.9 - - - +
207E THR* 3.1 20.8 + - - +
208E SER 3.0 12.4 + - - +
209E GLU* 3.0 36.4 + - - +
211E GLY* 1.3 72.8 - - - +
213E ALA* 1.3 56.1 + - - +
215E ILE* 2.7 34.9 + - - +
216E GLN* 2.9 29.0 + - - +
150H PHE* 6.5 0.9 - - + -
154H SER 6.1 1.3 - - - -
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Residues in contact with ALA 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209E GLU* 2.9 19.1 + - - +
210E THR* 3.5 6.1 - - - +
212E LYS* 1.3 74.5 - - - +
214E LEU* 1.3 53.3 + - - +
216E GLN* 3.1 8.3 + - - +
217E THR* 2.6 42.8 + - - +
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Residues in contact with LEU 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D PRO* 4.8 2.7 - - + -
205D MET* 3.6 33.2 - - + +
208D SER* 4.3 7.2 - - - +
210D THR* 4.3 16.6 - - + -
211D GLY* 3.6 32.5 - - - +
214D LEU* 5.0 7.2 - - + -
210E THR* 3.0 13.1 + - + +
211E GLY 2.9 9.6 + - - +
213E ALA* 1.3 74.9 - - - +
215E ILE* 1.3 64.9 + - - +
217E THR* 3.2 10.0 + - + -
218E CYS* 2.9 38.7 + - - -
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Residues in contact with ILE 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D LEU* 4.9 0.9 - - + -
205D MET* 4.2 20.2 - - + -
186E LEU* 3.8 26.0 - - + -
194E VAL* 5.0 7.0 - - + -
205E MET 3.8 17.0 - - - +
206E ILE* 3.9 26.7 - - + +
211E GLY 2.7 22.1 + - - +
212E LYS* 2.7 13.2 + - + +
214E LEU* 1.3 70.9 - - - +
216E GLN* 1.3 67.8 + - - +
218E CYS* 2.9 7.0 + - - +
219E LEU* 2.8 44.6 + - + +
150H PHE* 5.2 10.1 - - + -
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Residues in contact with GLN 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E VAL* 5.8 0.3 - - - +
212E LYS* 2.9 25.5 + - - +
213E ALA* 3.5 10.3 - - - +
215E ILE* 1.3 81.7 - - - +
217E THR* 1.3 57.2 + - - +
218E CYS 2.7 15.5 + - - -
219E LEU* 3.0 6.4 + - - +
220E ASN* 2.8 46.8 + - - +
150H PHE* 4.7 14.1 - - - -
152H LEU* 3.9 18.4 - - + +
153H ASN 4.4 3.6 - - - +
154H SER 2.9 32.5 + - - +
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Residues in contact with THR 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213E ALA* 2.6 31.0 + - - +
214E LEU* 3.4 12.5 - - + -
216E GLN* 1.3 72.2 - - - +
218E CYS* 1.3 61.7 + - - +
220E ASN* 4.4 3.5 - - - +
221E SER* 3.9 14.4 + - - -
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Residues in contact with CYS 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D LYS* 3.4 20.7 - - - +
202D LEU* 3.8 18.8 - - + -
204D PRO* 3.1 35.4 - - - -
205D MET* 4.1 5.4 - - - -
214E LEU* 2.9 29.4 + - - +
215E ILE 3.2 8.1 - - - +
216E GLN 2.7 5.5 + - - -
217E THR* 1.3 76.9 - - - +
219E LEU* 1.3 65.0 + - - +
220E ASN 3.1 1.6 - - - -
221E SER* 3.1 21.7 + - - -
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Residues in contact with LEU 219 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D GLN* 4.4 14.8 - - + -
201D LYS* 3.6 25.2 + - + +
202D LEU* 3.6 39.9 - - + -
186E LEU* 5.0 2.0 - - + -
188E ALA* 3.8 16.2 - - + -
194E VAL* 3.8 30.5 - - + -
215E ILE* 2.8 32.3 + - + +
216E GLN* 4.2 3.8 - - - +
218E CYS* 1.3 74.0 - - - +
220E ASN* 1.3 61.2 + - - +
221E SER 3.5 0.3 + - - -
152H LEU* 4.2 29.4 - - + +
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Residues in contact with ASN 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216E GLN* 2.8 46.8 + - - +
217E THR* 4.9 3.8 - - - +
219E LEU* 1.3 74.1 - - - +
221E SER* 1.3 70.6 + - - +
222E PRO* 3.4 4.2 - - - +
152H LEU* 3.4 21.3 - - - +
153H ASN 5.9 0.2 + - - -
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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