Contacts of the helix formed by residues 228 - 245 (chain B) in PDB entry 5J3V
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 GLU 228 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188B PRO* 4.1 24.2 - - + +
189B LYS* 5.2 7.4 + - - -
191B ARG* 5.1 0.2 - - - +
226B ASP* 2.7 24.9 + - - +
227B GLU* 1.3 77.4 - - - +
229B PRO* 1.3 88.4 - - - +
230B GLU* 4.0 11.1 + - + +
231B VAL* 3.7 27.5 - - + +
232B ARG* 3.2 29.8 + - - +
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Residues in contact with PRO 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B GLU 4.8 0.4 - - - +
228B GLU* 1.3 101.3 - - - +
230B GLU* 1.3 58.9 + - + +
232B ARG* 4.0 10.8 - - - +
233B LYS* 3.1 28.8 + - - +
269B ASP* 3.2 27.6 - - - +
272B VAL* 3.3 21.4 - - + +
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Residues in contact with GLU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B SER* 3.2 25.9 + - - +
228B GLU* 3.4 13.6 - - + +
229B PRO* 1.3 79.2 - - + +
231B VAL* 1.3 65.5 + - - +
233B LYS* 3.4 42.1 + - - +
234B ASN* 3.5 12.1 + - - +
271B ASN* 4.9 0.9 - - - +
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Residues in contact with VAL 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B PRO* 3.4 27.6 - - + +
191B ARG* 4.3 19.1 - - + +
192B SER* 3.7 16.8 - - - +
195B VAL* 5.2 4.4 - - + +
223B LEU* 5.1 10.3 - - + +
226B ASP* 3.8 31.9 - - + +
228B GLU* 3.6 19.8 + - + +
229B PRO 3.4 0.2 - - - -
230B GLU* 1.3 74.9 - - - +
232B ARG* 1.3 64.7 - - - +
233B LYS 3.3 0.9 + - - -
234B ASN* 3.3 12.3 + - - +
235B VAL* 3.3 20.8 + - + +
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Residues in contact with ARG 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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223B LEU 5.5 0.7 - - - +
225B GLY* 4.7 2.4 - - - +
226B ASP* 2.5 49.1 + - + +
227B GLU* 4.4 2.0 - - - +
228B GLU 3.2 21.7 + - - +
229B PRO* 4.2 16.5 - - - +
231B VAL* 1.3 76.7 - - - +
233B LYS* 1.3 62.9 + - - +
235B VAL* 3.3 11.0 + - + +
236B CYS* 3.2 25.0 + - - -
260B TYR* 3.7 17.3 - - - +
264B ARG* 3.5 33.0 - - - +
267B ASP* 2.8 42.8 + - - -
268B GLN* 5.6 4.4 + - - +
272B VAL* 4.0 7.2 - - + +
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Residues in contact with LYS 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B PRO 3.1 20.0 + - - +
230B GLU* 3.4 28.4 + - - +
231B VAL 3.1 0.2 - - - -
232B ARG* 1.3 78.6 - - - +
234B ASN* 1.3 62.7 + - - +
236B CYS* 3.3 6.5 + - - +
237B ARG* 3.0 57.0 + - - +
271B ASN* 2.9 45.0 + - - +
272B VAL* 4.3 14.4 - - + +
275B GLU* 4.4 6.3 - - + +
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Residues in contact with ASN 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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192B SER* 3.2 41.8 + - - +
195B VAL* 3.7 23.4 - - + +
196B ALA* 3.8 19.4 - - - +
199B ASN* 3.1 13.0 + - - +
230B GLU* 3.5 9.4 + - - +
231B VAL 3.3 5.8 + - - +
233B LYS* 1.3 79.0 - - - +
235B VAL* 1.3 60.9 + - - +
237B ARG* 3.8 21.6 + - - -
238B ALA* 3.1 24.9 + - - +
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Residues in contact with VAL 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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195B VAL* 4.8 4.3 - - + -
220B LEU* 4.1 36.2 - - + +
223B LEU* 4.1 30.5 - - + +
224B ALA* 5.1 2.0 - - + -
231B VAL* 3.3 20.0 - - + +
232B ARG* 3.5 14.4 - - + +
233B LYS 3.2 0.4 - - - -
234B ASN* 1.3 79.2 - - - +
236B CYS* 1.3 60.7 + - - +
238B ALA* 3.6 4.8 + - - +
239B LEU* 3.2 25.3 + - + +
260B TYR* 4.5 20.4 - - + +
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Residues in contact with CYS 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 ARG* 3.2 18.9 + - - -
233B LYS* 3.3 7.4 + - - +
235B VAL* 1.3 79.1 - - - +
237B ARG* 1.3 63.4 + - - +
239B LEU* 3.1 16.4 + - - +
240B VAL* 3.1 19.8 + - - +
260B TYR* 4.6 5.4 - - - -
261B MET* 4.2 15.4 - - + +
264B ARG* 4.1 33.7 - - - -
272B VAL* 4.7 8.1 - - - +
275B GLU* 3.6 23.8 - - + +
276B ALA* 4.6 3.4 - - - -
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Residues in contact with ARG 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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199B ASN* 3.9 15.0 - - - +
233B LYS* 3.0 47.1 + - - +
234B ASN* 4.0 14.5 + - - +
235B VAL 3.4 0.2 - - - -
236B CYS* 1.3 75.7 - - - +
238B ALA* 1.3 60.8 + - - +
239B LEU 3.4 0.5 + - - -
240B VAL* 3.5 5.0 + - - +
241B MET* 3.4 47.9 + - + +
275B GLU* 2.8 46.8 + - - +
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Residues in contact with ALA 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B VAL* 4.9 0.2 - - + -
199B ASN* 3.3 29.1 - - - +
202B ILE* 3.9 15.3 - - + +
220B LEU* 4.0 24.9 - - + -
234B ASN 3.1 15.5 + - - +
235B VAL 4.0 0.9 - - - +
236B CYS 3.3 0.2 - - - -
237B ARG* 1.3 75.5 - - - +
239B LEU* 1.3 59.0 + - - +
240B VAL 3.4 0.2 - - - -
241B MET* 4.1 2.2 - - - +
242B LEU* 3.2 31.9 + - - +
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Residues in contact with LEU 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B LEU* 6.3 0.2 - - - -
221B PHE* 4.9 6.5 - - + -
235B VAL* 3.2 20.5 + - + +
236B CYS* 3.1 8.8 + - - +
238B ALA* 1.3 78.6 - - - +
240B VAL* 1.3 59.8 + - - +
242B LEU* 4.0 6.9 + - + -
243B LEU* 3.2 24.1 - - - +
250B LEU* 3.9 26.1 - - + +
257B ILE* 3.6 39.3 - - + -
260B TYR* 4.3 9.6 - - + -
261B MET* 3.5 31.4 - - + -
279B PHE* 4.2 6.0 - - + -
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Residues in contact with VAL 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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236B CYS 3.1 16.1 + - - +
237B ARG* 3.9 7.2 - - - +
238B ALA 3.4 0.2 - - - -
239B LEU* 1.3 77.9 - - - +
241B MET* 1.3 67.2 + - + +
242B LEU 3.1 2.5 + - - -
243B LEU* 3.3 11.5 + - - +
244B GLU* 4.1 5.9 + - - +
261B MET* 4.5 1.8 - - + -
275B GLU* 3.5 21.5 - - - +
278B GLU* 4.0 17.3 - - + +
279B PHE* 4.0 26.0 - - + +
282B THR* 3.2 39.1 - - - +
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Residues in contact with MET 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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199B ASN* 3.7 26.5 - - + +
202B ILE* 3.9 23.1 - - + -
203B ILE* 4.1 29.4 - - + +
237B ARG* 3.4 41.4 + - + +
238B ALA 4.1 3.3 + - - +
239B LEU 3.5 0.2 - - - -
240B VAL* 1.3 80.3 - - + +
242B LEU* 1.3 58.0 + - - +
243B LEU 3.1 4.3 + - - -
244B GLU* 3.6 13.5 + - - +
245B VAL* 3.2 26.6 + - - +
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Residues in contact with LEU 242 (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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202B ILE* 4.0 20.9 - - + -
216B PHE* 4.0 24.7 - - + -
217B ILE* 4.1 25.6 - - + -
220B LEU* 5.3 3.8 - - + -
238B ALA 3.2 23.4 + - - +
239B LEU* 4.3 5.8 - - + +
240B VAL 3.1 1.6 - - - -
241B MET* 1.3 76.6 - - - +
243B LEU* 1.3 59.0 + - - +
245B VAL* 3.0 26.4 - - + +
246B ARG* 3.2 26.6 - - + +
247B MET* 4.3 1.2 - - - -
250B LEU* 3.3 30.2 - - + +
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Residues in contact with LEU 243 (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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239B LEU 3.2 25.4 - - - +
240B VAL 3.3 2.0 + - - +
241B MET 3.1 0.6 - - - -
242B LEU* 1.3 76.6 - - - +
244B GLU* 1.3 65.9 + - - +
245B VAL 3.3 2.0 - - - -
247B MET* 3.9 35.5 - - + +
250B LEU* 3.6 21.5 - - + -
254B MET* 6.2 2.9 - - + -
257B ILE* 6.1 0.4 - - + -
279B PHE* 3.6 36.1 - - + +
282B THR* 3.6 16.8 - - + +
283B LEU* 4.0 37.5 - - + +
286B GLN* 3.5 18.2 + - + +
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Residues in contact with GLU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ILE* 5.2 9.9 - - + +
205B ARG* 5.0 1.9 + - - -
240B VAL* 4.4 8.1 - - - +
241B MET* 3.6 12.1 + - - +
243B LEU* 1.3 79.1 - - - +
245B VAL* 1.3 66.3 + - + +
247B MET* 6.0 0.4 - - - -
282B THR* 3.6 29.6 + - + +
285B GLU* 4.6 11.0 - - + +
286B GLN* 4.5 7.0 - - - +
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Residues in contact with VAL 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ILE* 3.6 35.0 - - + +
203B ILE* 5.1 9.2 - - + +
205B ARG* 3.3 37.0 - - + +
241B MET 3.2 15.2 + - - +
242B LEU* 3.0 25.5 - - + +
244B GLU* 1.3 87.3 - - + +
246B ARG* 1.3 75.5 + - + +
247B MET 3.5 2.0 - - - -
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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
------------------------------------------------------------
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