Contacts of the helix formed by residues 223 - 237 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A MET* 1.3 77.9 - - - +
224A GLY* 1.3 58.3 + - - +
225A GLU 3.2 15.7 + - - -
226A VAL* 3.2 18.5 + - + +
227A ALA* 2.8 28.1 + - - +
371A TRP* 5.3 0.2 - - - -
375A THR* 3.8 9.5 - - + +
376A GLU* 3.1 30.5 + - - +
377A GLU* 3.4 8.6 - - - +
410A LYS* 2.8 31.6 + - - -
424A HIS* 3.5 31.1 + - + -
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Residues in contact with GLY 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A GLN* 5.9 5.3 - - - +
222A MET 3.7 1.7 + - - -
223A ASP* 1.3 71.1 - - - +
225A GLU* 1.3 60.3 + - - +
227A ALA* 3.5 5.1 + - - +
228A LYS* 3.1 32.0 + - - +
377A GLU* 3.0 28.8 + - - -
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Residues in contact with GLU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ASP* 3.2 10.6 + - - +
224A GLY* 1.3 75.4 - - - +
226A VAL* 1.3 62.0 + - - +
228A LYS* 3.7 7.0 + - - +
229A ALA* 3.3 23.4 + - - +
376A GLU* 3.6 13.2 + - - +
377A GLU* 4.4 2.0 + - - -
388A ILE* 5.2 3.5 - - - +
390A LYS* 3.1 32.1 + - - +
408A PHE* 3.2 22.9 - - + -
410A LYS* 3.3 25.1 + - - +
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Residues in contact with VAL 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A MET* 4.3 9.0 - - + -
223A ASP* 3.2 23.0 + - + +
225A GLU* 1.3 75.3 - - - +
227A ALA* 1.3 54.0 + - - +
229A ALA 3.4 0.2 + - - -
230A THR* 2.6 36.7 + - - +
369A VAL* 3.6 30.5 - - + -
370A ALA 6.0 0.2 - - - +
371A TRP* 5.7 2.2 - - + -
408A PHE* 3.9 23.6 - - + -
410A LYS* 4.7 0.7 - - + -
424A HIS* 3.7 30.5 - - + +
425A ILE 5.7 0.2 - - - +
426A ILE* 3.4 19.4 - - + +
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Residues in contact with ALA 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A GLN* 4.4 16.6 - - + +
218A ILE* 3.6 25.7 - - - +
222A MET* 3.8 20.6 - - + +
223A ASP 2.8 21.2 + - - +
224A GLY* 3.8 5.6 - - - +
226A VAL* 1.3 70.4 - - - +
228A LYS* 1.3 63.1 + - - +
230A THR* 3.2 3.4 + - - -
231A GLN* 3.1 27.8 + - - +
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Residues in contact with LYS 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A GLN* 5.5 2.4 - - + +
224A GLY 3.1 17.5 + - - +
225A GLU* 4.0 6.5 - - - +
227A ALA* 1.3 78.0 - - - +
229A ALA* 1.3 61.4 + - - +
231A GLN* 3.4 25.3 + - - +
232A LYS* 3.4 33.5 + - - +
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Residues in contact with ALA 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A GLU* 3.3 16.6 + - + +
226A VAL 3.6 4.5 - - - +
227A ALA 3.2 0.4 - - - -
228A LYS* 1.3 78.4 - - - +
230A THR* 1.3 57.8 + - - +
232A LYS* 3.4 13.4 + - + +
233A PHE* 3.2 31.6 + - - +
408A PHE* 4.2 11.0 - - + -
426A ILE* 3.7 15.3 - - + -
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Residues in contact with THR 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A LEU* 4.6 0.4 - - + -
218A ILE* 4.1 15.0 - - + -
222A MET* 4.0 11.6 - - + -
226A VAL* 2.6 23.6 + - - +
227A ALA* 3.2 10.3 + - - -
229A ALA* 1.3 73.4 - - - +
231A GLN* 1.3 65.5 + - - +
233A PHE* 3.5 14.1 + - + -
234A LEU* 3.3 25.5 + - + +
363A MET* 3.6 31.6 - - + -
369A VAL* 3.7 10.0 - - + +
426A ILE* 3.7 9.5 - - - +
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Residues in contact with GLN 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A PRO 4.7 2.6 + - - -
217A GLN* 4.5 13.3 - - - +
218A ILE* 3.8 26.8 - - + +
227A ALA 3.1 14.1 + - - +
228A LYS* 3.5 29.6 + - - +
229A ALA 3.3 0.2 - - - -
230A THR* 1.3 77.0 - - - +
232A LYS* 1.3 58.4 + - + +
234A LEU 3.3 1.4 + - - -
235A LYS* 2.9 39.3 + - + +
241A PHE* 3.6 17.5 - - + +
243A LEU* 3.1 33.1 - - - +
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Residues in contact with LYS 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A LYS* 3.4 25.7 + - - +
229A ALA* 3.6 13.7 - - + +
230A THR 3.3 0.2 - - - -
231A GLN* 1.3 82.2 - - + +
233A PHE* 1.3 61.0 + - - +
235A LYS* 3.5 7.0 + - - +
236A LYS* 3.2 28.0 + - + +
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Residues in contact with PHE 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ALA 3.2 26.2 + - - +
230A THR* 3.5 26.7 - - + -
232A LYS* 1.3 75.9 - - - +
234A LEU* 1.3 76.6 + - + +
236A LYS* 3.6 9.3 + - - +
237A GLN* 3.2 45.9 + - - +
363A MET* 4.4 0.2 - - + -
365A SER* 3.8 8.3 - - - -
366A HIS 4.2 0.9 - - - -
367A PRO* 3.3 45.3 - - + -
369A VAL* 3.7 11.0 - - + -
406A GLU* 3.5 28.9 - - + +
426A ILE* 3.6 25.1 - - + -
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Residues in contact with LEU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A LEU* 3.8 31.0 - - + -
200A SER* 3.6 24.7 - - - +
218A ILE* 4.3 0.7 - - + -
230A THR* 3.3 27.1 + - + +
231A GLN 3.3 1.0 + - - -
233A PHE* 1.3 96.0 - - + +
235A LYS* 1.3 60.5 + - - +
236A LYS 3.2 0.2 - - - -
237A GLN* 3.1 16.9 + - + +
238A GLY 3.0 10.2 + - - -
239A LEU* 2.9 38.5 + - + +
241A PHE* 3.8 22.2 - - + -
363A MET* 4.7 2.5 - - + -
365A SER* 4.8 3.6 - - - -
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Residues in contact with LYS 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A GLN* 2.9 24.6 + - + +
232A LYS* 3.8 7.4 - - - +
234A LEU* 1.3 75.3 - - - +
236A LYS* 1.3 61.6 + - + +
238A GLY* 3.4 10.7 + - - -
239A LEU 3.4 16.4 + - - +
240A ASP* 4.9 6.7 - - - +
241A PHE* 3.9 44.0 + - + +
243A LEU* 5.5 2.8 - - - +
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Residues in contact with LYS 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A LYS 3.2 15.6 + - - +
233A PHE* 3.8 10.5 - - - +
234A LEU 3.2 0.2 - - - -
235A LYS* 1.3 77.2 - - + +
237A GLN* 1.3 60.5 + - + +
238A GLY* 3.3 0.8 + - - -
406A GLU* 3.5 31.4 + - - +
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Residues in contact with GLN 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A HIS* 4.8 23.1 + - + +
200A SER* 5.0 3.2 + - - +
203A SER* 4.3 19.6 + - - +
204A ARG* 3.9 29.5 - - - +
233A PHE* 3.2 29.8 + - - +
234A LEU* 3.1 24.0 + - + +
236A LYS* 1.3 78.5 - - + +
238A GLY* 1.3 54.7 + - - +
239A LEU* 3.8 1.3 - - + -
366A HIS* 2.8 29.5 + - - +
367A PRO* 4.3 0.9 - - - +
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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