Contacts of the helix formed by residues 233 - 253 (chain B) in PDB entry 5ICN
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 233 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B GLY 4.1 2.3 - - - +
232B ILE* 1.3 78.2 - - - +
234B ASP* 1.3 60.3 + - - +
235B GLU* 3.4 26.1 - - + +
236B SER* 2.9 12.3 + - - +
237B TYR* 3.0 27.9 + - - +
275B ASN* 4.1 12.7 + - - -
276B LEU* 3.2 3.8 - - - +
347B PRO* 6.2 0.6 - - - +
350B MET 5.7 0.9 - - - +
352B ASN* 2.5 35.3 + - - +
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Residues in contact with ASP 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ASP* 1.3 72.3 - - - +
235B GLU* 1.3 65.1 + - + +
237B TYR* 3.8 0.8 - - - +
238B GLU* 2.8 37.9 + - - +
275B ASN 4.3 2.5 + - - -
276B LEU* 3.2 18.6 - - - +
277B THR* 2.6 57.9 + - - +
280B GLY* 3.6 20.6 + - - -
347B PRO* 5.3 2.8 - - - +
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Residues in contact with GLU 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ASP* 3.2 20.6 - - + +
234B ASP* 1.3 82.3 + - + +
236B SER* 1.3 65.8 + - - +
238B GLU* 3.9 5.9 - - - +
239B ALA* 3.0 26.3 + - - +
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Residues in contact with SER 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ILE* 3.8 19.3 - - - -
233B ASP* 2.9 22.2 + - - +
235B GLU* 1.3 75.9 - - - +
237B TYR* 1.3 64.2 + - - +
239B ALA* 3.3 6.8 + - - +
240B ILE* 3.2 28.1 + - - +
352B ASN* 3.1 10.9 + - - -
354B ASN 4.8 0.7 + - - -
356B ASN* 5.3 3.5 + - - -
359B LEU* 4.1 19.3 - - - +
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Residues in contact with TYR 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ILE* 3.2 33.9 + - + +
198B PHE* 3.3 37.2 - + + +
228B LEU* 4.4 10.1 - - + -
232B ILE* 3.9 22.5 - - + +
233B ASP 3.0 21.1 + - - +
234B ASP* 3.8 3.1 - - - +
236B SER* 1.3 73.1 - - - +
238B GLU* 1.3 68.2 + - - +
240B ILE* 3.1 11.4 + - + +
241B PHE* 2.9 37.2 + + + +
274B PHE* 4.8 8.1 - + - -
276B LEU* 3.8 27.6 - - + -
280B GLY 5.6 1.8 - - - -
281B HIS* 6.3 0.2 - - - -
284B CYS* 3.5 32.8 - - - -
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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
----------------------------------------------------------
234B ASP 2.8 22.8 + - - +
235B GLU* 3.9 5.8 - - - +
237B TYR* 1.3 73.2 - - - +
239B ALA* 1.3 63.3 + - - +
240B ILE 3.1 1.6 + - - -
241B PHE* 3.1 14.9 + - - +
242B LYS* 3.3 45.0 + - + +
243B PRO* 3.9 1.7 - - - +
280B GLY* 6.1 0.9 - - - +
283B LYS* 3.2 40.1 - - + +
284B CYS* 5.9 2.5 - - - -
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Residues in contact with ALA 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 GLU 3.0 19.3 + - - +
236B SER* 3.7 6.7 - - - +
237B TYR 3.2 0.2 - - - -
238B GLU* 1.3 76.6 + - - +
240B ILE* 1.3 62.1 + - + +
243B PRO* 3.2 20.9 - - - +
363B LYS* 4.2 6.4 + - - -
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Residues in contact with ILE 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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198B PHE* 3.6 28.7 - - + -
226B TYR* 3.6 39.9 - - + +
228B LEU* 4.8 6.5 - - + -
232B ILE* 4.9 4.9 - - + -
236B SER 3.2 13.6 + - - +
237B TYR* 3.3 22.9 - - + +
238B GLU 3.1 0.2 - - - -
239B ALA* 1.3 84.4 - - + +
241B PHE* 1.3 60.8 + - + +
243B PRO* 3.7 6.1 - - - -
244B VAL* 3.5 24.4 + - - +
359B LEU* 4.1 22.2 - - + -
363B LYS* 4.5 12.3 - - + -
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Residues in contact with PHE 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ILE* 4.0 14.4 - - + -
175B ILE* 5.1 5.8 - - + -
198B PHE* 3.5 36.6 - + + -
237B TYR* 2.9 35.4 + + + +
238B GLU* 3.1 4.5 + - - +
240B ILE* 1.3 79.3 - - + +
242B LYS* 1.3 67.2 + - + +
244B VAL* 3.4 2.1 + - - +
245B MET* 2.9 58.2 + - + +
259B LEU* 5.5 0.7 - - + -
284B CYS* 3.7 46.0 - - + -
287B PHE* 3.9 16.6 - + - -
288B VAL* 4.1 14.8 - - + -
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Residues in contact with LYS 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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238B GLU* 3.3 39.5 + - + +
241B PHE* 1.3 79.8 - - + +
243B PRO* 1.4 72.5 - - + +
246B SER* 3.0 30.8 + - - +
283B LYS* 3.5 31.5 - - - +
287B PHE* 3.7 52.2 - - + -
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Residues in contact with PRO 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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238B GLU 3.9 0.2 - - - +
239B ALA* 3.2 30.3 - - - +
240B ILE* 3.7 5.6 - - - -
241B PHE 3.5 3.8 - - - +
242B LYS* 1.4 96.9 - - + +
244B VAL* 1.3 60.4 + - - +
246B SER* 3.4 4.9 + - - -
247B LYS* 3.2 19.9 + - - +
363B LYS* 4.2 23.8 - - + +
367B PHE* 4.0 16.4 - - + -
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Residues in contact with VAL 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B VAL* 4.6 6.1 - - + -
198B PHE* 4.1 19.3 - - + -
224B VAL* 4.7 10.1 - - + -
226B TYR* 4.2 21.1 - - + -
240B ILE 3.5 20.0 - - - +
241B PHE 3.4 2.2 + - - +
242B LYS 3.3 0.2 - - - -
243B PRO* 1.3 79.9 - - - +
245B MET* 1.3 61.6 + - - +
247B LYS* 3.3 7.2 + - - +
248B VAL* 2.8 38.6 + - + +
363B LYS* 4.6 7.2 - - + -
366B LEU* 4.5 10.8 - - + -
367B PHE* 4.5 16.6 - - + -
370B LEU* 4.1 6.3 - - + +
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Residues in contact with MET 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B LEU* 4.1 5.2 - - + -
173B ILE* 3.5 35.4 - - + -
196B VAL* 3.9 25.8 - - + -
198B PHE* 4.0 12.8 - - - -
241B PHE* 2.9 48.5 + - + +
244B VAL* 1.3 77.4 - - - +
246B SER* 1.3 60.3 + - - +
248B VAL* 3.3 25.1 + - + +
249B MET* 2.8 37.0 + - + +
287B PHE* 3.7 16.8 - - + -
288B VAL* 5.6 1.3 - - + -
291B PHE* 5.2 2.0 - - + -
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Residues in contact with SER 246 (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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242B LYS 3.0 19.4 + - - -
243B PRO* 3.6 5.6 - - - -
245B MET* 1.3 73.0 - - - +
247B LYS* 1.3 60.8 + - - +
249B MET* 3.9 1.4 - - - +
250B GLU* 2.9 28.8 + - - +
287B PHE* 3.2 19.1 - - - -
291B PHE* 4.0 13.8 - - - -
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Residues in contact with LYS 247 (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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243B PRO 3.2 10.2 + - - +
244B VAL* 3.5 8.5 - - - +
245B MET 3.2 0.2 - - - -
246B SER* 1.3 76.2 - - - +
248B VAL* 1.3 56.7 + - - +
250B GLU* 2.9 32.8 + - - +
251B MET* 2.7 52.9 + - - +
367B PHE* 3.9 29.8 - - + -
370B LEU* 3.5 26.0 - - + -
371B ARG* 3.4 42.6 - - - +
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Residues in contact with VAL 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B LEU* 4.0 26.5 - - + -
194B MET* 3.7 20.6 - - - -
196B VAL* 4.2 14.8 - - + -
224B VAL* 4.7 2.2 - - + -
244B VAL* 2.8 30.7 + - + +
245B MET* 3.4 18.4 - - + +
247B LYS* 1.3 75.8 - - - +
249B MET* 1.3 57.6 + - - +
252B PHE* 2.7 35.9 + - + +
254B PRO* 5.8 0.2 - - + -
370B LEU* 3.9 28.3 - - + -
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Residues in contact with MET 249 (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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171B LEU* 3.9 21.3 - - + -
173B ILE* 5.1 6.3 - - + -
245B MET* 2.8 26.5 + - + +
246B SER 3.9 4.3 - - - +
248B VAL* 1.3 71.9 - - - +
250B GLU* 1.3 66.4 + - - +
253B GLN* 2.9 26.7 + - - -
254B PRO* 3.7 27.6 - - + -
257B VAL* 4.1 16.2 - - + -
288B VAL* 5.0 5.4 - - + +
291B PHE* 3.6 58.3 - - + -
293B LEU* 4.2 6.5 - - + -
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Residues in contact with GLU 250 (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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246B SER 2.9 18.6 + - - +
247B LYS* 2.9 44.5 + - - +
249B MET* 1.3 75.5 - - - +
251B MET* 1.3 75.6 + - + +
253B GLN* 2.8 29.6 + - - +
375B HIS* 5.8 0.2 - - - +
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Residues in contact with MET 251 (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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247B LYS* 2.7 40.2 + - - +
248B VAL* 4.0 1.3 - - - +
250B GLU* 1.3 106.2 - - + +
252B PHE* 1.3 63.7 + - - +
253B GLN* 3.3 12.0 - - - +
370B LEU* 3.2 31.2 - - + +
371B ARG* 4.7 3.4 - - - -
373B LEU* 3.9 23.0 - - + +
374B PRO 4.2 12.5 - - - +
375B HIS* 3.5 41.0 - - + +
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Residues in contact with PHE 252 (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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169B ARG* 3.2 39.3 - - + +
170B VAL 3.5 23.8 - - - -
171B LEU* 3.8 7.6 - - + -
191B ASP 3.5 21.5 - - - -
192B ARG 3.4 18.6 - - - -
194B MET* 3.3 58.8 - - + -
222B TYR* 3.7 22.7 - + - -
248B VAL* 2.7 19.0 + - + +
251B MET* 1.3 71.2 - - - +
253B GLN* 1.3 67.6 + - - +
254B PRO* 3.1 16.2 - - + -
373B LEU* 4.0 4.0 - - - -
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Residues in contact with GLN 253 (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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169B ARG* 3.2 27.1 + - - +
249B MET 2.9 19.4 + - - -
250B GLU* 2.8 24.4 + - - +
251B MET 3.3 15.5 - - - +
252B PHE* 1.3 73.5 - - - +
254B PRO* 1.3 72.9 - - - +
255B SER* 5.2 0.3 - - - -
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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
------------------------------------------------------------
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