Contacts of the helix formed by residues 223 - 237 (chain B) in PDB entry 1JEH
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 ASP 223 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B GLN* 5.1 0.2 - - - -
222B MET* 1.3 78.3 - - - +
224B GLY* 1.3 60.9 + - - +
225B GLU* 3.2 25.2 + - - +
226B VAL* 3.5 9.7 + - + +
227B ALA* 2.9 28.8 + - - +
375B THR* 3.6 11.5 + - - +
376B GLU* 3.0 39.1 + - - +
410B LYS* 3.2 25.8 + - - -
424B HIS* 3.5 28.6 - - + +
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Residues in contact with GLY 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B GLN* 4.6 14.0 - - - +
222B MET 4.0 0.4 + - - -
223B ASP* 1.3 73.1 - - - +
225B GLU* 1.3 55.5 + - - +
227B ALA* 3.5 2.1 + - - +
228B LYS* 3.1 42.0 + - - +
377B GLU* 3.0 29.4 + - - -
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Residues in contact with GLU 225 (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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223B ASP* 3.2 12.1 + - - +
224B GLY* 1.3 73.4 - - - +
226B VAL* 1.3 65.7 + - - +
228B LYS* 3.4 9.4 + - + +
229B ALA* 3.0 26.6 + - + +
376B GLU* 3.9 12.5 + - - +
388B ILE* 5.5 2.6 - - - +
390B LYS* 2.9 38.3 + - - +
408B PHE* 3.4 20.6 - - + -
410B LYS* 3.5 17.4 - - - +
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Residues in contact with VAL 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B MET* 4.0 11.7 - - + -
223B ASP* 3.4 22.8 + - + +
224B GLY 3.4 0.4 - - - -
225B GLU* 1.3 77.9 - - - +
227B ALA* 1.3 56.2 + - - +
229B ALA 3.5 0.2 + - - -
230B THR* 2.8 35.6 + - - +
369B VAL* 3.6 31.0 - - + -
371B TRP* 5.1 4.0 - - + -
408B PHE* 4.3 15.5 - - + -
424B HIS* 3.6 33.2 - - + -
425B ILE 5.7 0.7 - - - +
426B ILE* 3.6 17.3 - - + +
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Residues in contact with ALA 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B GLN* 3.6 37.2 - - + +
218B ILE* 3.9 17.1 + - - +
222B MET* 4.1 13.7 - - + -
223B ASP 2.9 18.4 + - - +
224B GLY 3.8 2.9 - - - +
226B VAL* 1.3 75.3 - - - +
228B LYS* 1.3 63.1 + - + +
230B THR* 4.4 0.9 - - - -
231B GLN* 3.4 24.9 + - - +
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Residues in contact with LYS 228 (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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224B GLY* 3.1 26.6 + - - +
225B GLU* 3.4 8.6 + - + +
227B ALA* 1.3 75.4 - - - +
229B ALA* 1.3 58.5 + - - +
231B GLN* 3.7 9.5 + - - +
232B LYS* 3.3 29.3 + - - +
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Residues in contact with ALA 229 (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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225B GLU* 3.0 17.7 + - + +
228B LYS* 1.3 77.5 - - - +
230B THR* 1.3 58.1 + - - +
231B GLN 3.3 0.4 - - - -
232B LYS* 3.4 10.4 + - + +
233B PHE* 3.2 31.8 + - - +
408B PHE* 3.9 14.1 - - + -
426B ILE* 3.7 19.7 - - + -
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Residues in contact with THR 230 (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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196B LEU* 4.6 0.7 - - + -
218B ILE* 4.1 9.4 - - + -
222B MET* 4.0 17.3 - - + -
226B VAL 2.8 22.7 + - - -
227B ALA 4.2 4.3 - - - -
229B ALA* 1.3 73.2 - - - +
231B GLN* 1.3 65.1 + - - +
233B PHE* 3.5 13.1 + - + -
234B LEU* 3.1 38.4 + - + +
363B MET* 3.7 30.1 - - + -
369B VAL* 3.5 20.9 - - + +
426B ILE* 3.8 4.7 - - - +
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Residues in contact with GLN 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B PRO 5.0 1.4 + - - -
217B GLN* 5.2 1.4 - - - +
218B ILE* 3.6 22.6 - - + +
227B ALA 3.4 17.5 + - - +
228B LYS* 3.8 8.1 - - - +
229B ALA 3.3 0.4 - - - -
230B THR* 1.3 80.2 - - - +
232B LYS* 1.3 56.4 + - - +
235B LYS* 3.0 34.8 + - + +
241B PHE* 3.5 33.5 - - + +
243B LEU* 3.3 32.9 - - - +
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Residues in contact with LYS 232 (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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228B LYS* 3.3 18.1 + - - +
229B ALA* 3.6 9.6 - - - +
230B THR 3.3 0.4 - - - -
231B GLN* 1.3 79.6 - - - +
233B PHE* 1.3 57.1 + - - +
235B LYS* 3.4 11.0 + - + +
236B LYS* 3.0 29.1 + - + +
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Residues in contact with PHE 233 (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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229B ALA 3.2 26.7 + - - +
230B THR* 3.5 25.8 - - + -
232B LYS* 1.3 74.2 - - - +
234B LEU* 1.3 72.9 + - + +
236B LYS* 3.3 12.5 - - + +
237B GLN* 3.0 60.4 + - - +
363B MET* 4.3 0.2 - - + -
365B SER* 3.7 11.7 - - - -
367B PRO* 3.2 40.8 - - + -
369B VAL* 3.7 12.3 - - + -
406B GLU* 4.0 25.6 - - + +
426B ILE* 3.7 24.5 - - + -
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Residues in contact with LEU 234 (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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196B LEU* 3.7 30.5 - - + +
200B SER* 3.7 24.0 - - - +
218B ILE* 4.2 1.3 - - + -
230B THR* 3.1 34.5 + - + +
233B PHE* 1.3 95.3 - - + +
235B LYS* 1.3 63.4 + - - +
237B GLN* 3.1 16.4 + - - +
238B GLY 3.2 0.9 + - - -
239B LEU* 3.1 41.5 + - + +
241B PHE* 3.7 22.2 - - + -
363B MET* 4.0 7.0 - - + -
365B SER* 4.7 0.7 - - - -
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Residues in contact with LYS 235 (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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231B GLN* 3.0 24.2 + - + +
232B LYS* 3.6 9.9 - - + +
234B LEU* 1.3 73.2 - - - +
236B LYS* 1.3 64.3 + - - +
238B GLY* 3.2 13.7 + - - -
239B LEU 3.3 18.6 + - - +
240B ASP* 5.8 0.9 - - - -
241B PHE* 3.8 8.2 - - + +
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Residues in contact with LYS 236 (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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232B LYS* 3.0 16.3 + - + +
233B PHE* 3.3 14.6 - - - +
235B LYS* 1.3 77.9 - - - +
237B GLN* 1.3 60.7 + - + +
238B GLY* 3.4 0.7 + - - -
406B GLU* 2.9 37.0 + - - +
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Residues in contact with GLN 237 (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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63B HIS* 4.8 16.2 + - + +
200B SER* 5.2 3.1 + - - -
203B SER* 4.6 14.9 + - - +
204B ARG* 3.4 25.0 + - + +
233B PHE* 3.0 41.0 + - - +
234B LEU* 3.1 20.4 + - - +
236B LYS* 1.3 78.8 - - + +
238B GLY* 1.3 55.7 + - - +
239B LEU* 4.2 7.9 - - + -
366B HIS 3.0 29.3 + - - +
367B PRO* 4.4 0.8 - - - +
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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