Contacts of the helix formed by residues 229 - 241 (chain B) in PDB entry 2JI8
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 CYS 229 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224B ALA 4.9 1.2 + - - -
227B ALA* 3.8 18.6 - - - +
228B GLN* 1.3 75.8 - - - +
230B ASP* 1.3 65.4 + - - +
231B ASP 3.2 2.9 - - - -
232B GLU* 3.3 12.1 + - + -
233B ILE* 3.2 30.8 + - - +
326B ILE* 4.0 12.1 - - - -
327B LYS* 3.7 55.9 - - + +
330B VAL* 5.5 0.2 - - - -
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Residues in contact with ASP 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ALA 4.9 0.2 - - - +
225B ALA 4.6 0.7 - - - +
228B GLN* 3.7 1.8 - - - -
229B CYS* 1.3 81.8 + - - +
231B ASP* 1.3 62.0 + - - +
233B ILE* 3.6 2.1 + - - +
234B ARG* 3.0 29.7 + - - +
253B LEU* 2.9 39.0 - - + +
254B LEU* 4.7 3.3 - - - +
416B PRO* 3.3 15.6 - - + +
417B ARG* 3.0 40.8 + - - -
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Residues in contact with ASP 231 (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 CYS 3.2 0.4 - - - -
230B ASP* 1.3 79.9 - - - +
232B GLU* 1.3 59.4 + - - +
234B ARG* 4.1 19.6 + - - +
235B ALA* 2.9 32.1 + - - +
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Residues in contact with GLU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B CYS* 3.3 25.6 + - + +
231B ASP* 1.3 78.0 - - + +
233B ILE* 1.3 58.0 + - - +
235B ALA* 3.4 1.1 + - - -
236B LEU 3.0 23.7 + - - -
327B LYS* 4.4 18.1 - - + +
330B VAL* 3.6 16.3 - - + +
331B SER* 3.5 26.9 - - - -
334B ARG* 2.8 51.3 + - - +
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Residues in contact with ILE 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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220B LEU* 3.7 27.6 - - + -
224B ALA* 3.6 42.4 - - + +
229B CYS* 3.2 28.8 + - - +
230B ASP 3.9 4.0 - - - +
232B GLU* 1.3 74.2 - - - +
234B ARG* 1.3 65.4 + - - +
236B LEU* 3.4 3.8 + - + +
237B VAL* 3.2 24.1 + - + +
253B LEU* 4.0 12.6 - - + -
254B LEU* 4.2 13.9 - - + -
279B ILE* 4.8 5.4 - - + -
326B ILE* 4.3 4.5 - - + -
330B VAL* 4.2 19.3 - - + -
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Residues in contact with ARG 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ASP 3.0 19.4 + - - +
231B ASP* 4.1 17.2 + - - +
233B ILE* 1.3 73.6 - - - +
235B ALA* 1.3 61.0 + - - +
237B VAL* 3.3 1.7 + - - +
238B GLU* 3.0 58.6 + - - +
253B LEU 5.6 1.6 - - - +
254B LEU* 3.6 35.9 - - + +
255B PRO* 5.1 10.1 - - - +
258B HIS* 4.9 5.6 - - - -
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Residues in contact with ALA 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 ASP 2.9 21.0 + - - +
232B GLU 3.7 3.4 - - - +
234B ARG* 1.3 76.4 - - - +
236B LEU* 1.3 61.1 + - - +
238B GLU* 4.6 6.3 - - - +
239B GLU* 3.0 38.0 + - - +
334B ARG* 3.1 28.5 - - - +
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Residues in contact with LEU 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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210B ILE* 6.1 0.9 - - + -
218B ILE* 4.7 11.7 - - + -
232B GLU 3.0 17.6 + - - +
233B ILE* 3.6 8.1 - - + +
235B ALA* 1.3 77.4 - - - +
237B VAL* 1.3 60.3 + - + +
239B GLU* 4.2 0.8 - - + +
240B THR* 2.8 39.0 + - + +
277B VAL* 5.8 1.6 - - + -
279B ILE* 4.0 25.6 - - + -
330B VAL* 3.9 17.7 - - + +
333B LEU* 4.2 29.6 - - + -
334B ARG* 3.6 34.7 - - + +
337B LEU* 4.2 12.6 - - + -
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Residues in contact with VAL 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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218B ILE* 4.1 22.9 - - + -
220B LEU* 5.0 1.8 - - + -
233B ILE* 3.2 22.8 + - + +
234B ARG 3.3 6.5 + - - +
236B LEU* 1.3 77.9 - - + +
238B GLU* 1.3 58.2 + - - +
240B THR* 3.3 5.6 + - - -
241B GLY 3.0 18.9 + - - -
242B ILE 3.6 5.5 + - - +
244B PHE* 3.8 31.2 - - + -
254B LEU* 3.8 20.0 - - + -
258B HIS* 4.6 1.8 - - + -
260B GLN* 3.0 38.0 + - + +
279B ILE* 6.3 0.2 - - + -
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Residues in contact with GLU 238 (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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234B ARG* 3.0 50.2 + - + +
235B ALA* 4.4 5.2 - - - +
237B VAL* 1.3 75.4 - - + +
239B GLU* 1.3 54.3 + - + +
241B GLY 4.1 2.1 + - - -
258B HIS* 2.9 39.9 + - + +
260B GLN* 3.5 10.7 - - - +
342B LYS* 2.7 31.4 + - - -
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Residues in contact with GLU 239 (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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235B ALA* 3.0 26.7 + - - +
236B LEU* 4.2 1.5 - - - +
238B GLU* 1.3 79.4 - - + +
240B THR* 1.3 67.6 + - + +
241B GLY 3.3 0.7 - - - -
334B ARG* 2.7 41.2 + - - +
338B LYS* 3.6 29.7 + - + +
340B ALA 4.7 7.3 - - - +
342B LYS* 3.5 20.7 - - - +
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Residues in contact with THR 240 (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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210B ILE* 5.0 2.5 - - + -
218B ILE* 4.3 2.1 - - - +
236B LEU* 2.8 30.8 + - + +
237B VAL* 3.3 5.7 + - - -
239B GLU* 1.3 80.2 - - + +
241B GLY* 1.3 60.5 + - - +
242B ILE* 3.2 34.9 + - + +
337B LEU* 3.8 35.7 - - + -
340B ALA 6.0 0.2 - - - -
341B PRO 4.4 3.6 - - - +
342B LYS* 3.2 6.9 - - - +
343B ALA 2.9 24.8 + - - -
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Residues in contact with GLY 241 (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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237B VAL 3.0 11.5 + - - -
238B GLU 4.6 1.6 - - - -
239B GLU 3.3 3.0 - - - -
240B THR* 1.3 78.3 - - - +
242B ILE* 1.3 60.9 + - - +
243B PRO 3.7 0.2 - - - -
260B GLN* 3.6 19.2 + - - +
342B LYS* 4.2 16.6 - - - -
343B ALA* 3.4 15.3 + - - +
348B THR* 3.4 14.2 - - - +
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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