Contacts of the helix formed by residues 228 - 243 (chain B) in PDB entry 4IGM
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 ALA 228 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B PRO* 4.0 4.9 + - + +
197B ALA* 5.7 1.6 - - - +
200B THR* 2.9 17.2 + - + +
227B GLY* 1.3 73.1 - - - -
229B PHE* 1.3 68.9 + - - +
230B PRO* 3.4 3.6 - - - -
231B PHE* 2.8 17.1 + - - +
232B THR* 2.9 23.7 + - + +
193C VAL* 6.5 0.2 - - + -
196C PRO* 6.3 0.9 - - + -
228C ALA* 3.7 29.8 - - + -
231C PHE* 4.4 6.1 - - - -
232C THR* 5.0 1.1 - - + -
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Residues in contact with PHE 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B THR* 3.4 11.5 + - + -
203B ILE* 3.7 33.2 - - + -
204B CYS* 4.7 6.3 - - - -
207B ILE* 4.2 16.6 - - + -
226B GLY 3.2 15.7 + - - +
228B ALA* 1.3 77.8 - - - +
230B PRO* 1.3 73.1 - - + +
231B PHE 2.8 0.3 + - - -
232B THR* 3.9 5.4 + - - -
233B VAL* 2.8 50.2 + - + +
236B ILE* 3.9 30.5 - - + -
255B PRO* 5.0 5.8 - - + -
259B LEU* 3.6 28.0 - - + -
262B PHE* 4.0 19.1 - + - -
281B ILE* 4.7 4.3 - - + -
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Residues in contact with PRO 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B GLY 3.0 29.2 - - - +
226B GLY* 3.7 4.9 - - - +
228B ALA 3.5 4.5 - - - -
229B PHE* 1.3 98.3 - - + +
231B PHE* 1.3 57.5 + - - +
233B VAL* 3.5 13.7 - - - +
276B LEU* 4.2 6.2 - - + +
277B LEU* 3.7 22.4 - - + -
280B VAL* 3.8 31.3 - - + +
281B ILE* 4.8 5.6 - - + -
231C PHE* 3.5 26.5 - - + -
273C SER* 4.3 3.3 + - - -
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Residues in contact with PHE 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ALA* 2.8 8.9 + - - +
229B PHE 2.8 1.0 + - - -
230B PRO* 1.3 78.9 - - - +
232B THR* 1.3 67.8 + - + +
233B VAL 3.3 1.3 + - - -
234B GLY 4.5 2.4 + - - -
276B LEU* 4.0 17.0 - - + -
224C HIS 5.1 0.2 - - - -
225C GLY 4.1 4.5 - - - -
227C GLY 3.3 27.4 - - - -
228C ALA* 4.4 6.3 - - - -
230C PRO* 3.9 28.0 - - + -
231C PHE* 3.6 22.7 - - + -
268C VAL* 3.8 31.7 - - + +
273C SER* 2.8 54.7 + - - -
276C LEU* 4.0 15.5 - - + -
277C LEU* 4.5 4.0 - - + -
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Residues in contact with THR 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B THR* 4.4 2.8 - - - +
228B ALA* 2.9 33.7 + - + +
229B PHE* 3.6 0.7 + - - -
231B PHE* 1.3 85.8 - - + +
233B VAL* 1.3 64.9 + - - +
234B GLY 3.2 2.5 - - - -
235B ARG* 3.1 22.3 + - + +
236B ILE* 3.1 29.3 + - - +
192C LEU 5.2 1.6 + - - -
196C PRO* 4.5 17.0 - - + -
227C GLY 3.5 26.2 - - - +
228C ALA* 4.6 0.2 - - - -
268C VAL 6.0 0.2 - - - -
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Residues in contact with VAL 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B PHE* 2.8 42.3 + - + +
230B PRO 3.5 20.0 - - - +
231B PHE 3.3 1.1 - - - +
232B THR* 1.3 76.7 - - - +
234B GLY* 1.3 65.5 + - - +
236B ILE* 3.3 9.5 + - + +
237B SER* 2.9 31.7 + - - -
255B PRO* 5.3 1.3 - - + -
256B LYS* 4.8 12.8 - - - +
259B LEU* 4.4 16.8 - - + -
280B VAL* 4.3 17.3 - - + -
270C ASP* 4.3 8.5 - - - +
273C SER* 5.4 1.3 - - - +
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Residues in contact with GLY 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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231B PHE 4.5 3.0 + - - -
232B THR* 3.2 1.4 - - - +
233B VAL* 1.3 82.9 - - - +
235B ARG* 1.3 56.4 + - - +
237B SER* 3.7 4.2 + - - -
238B HIS* 2.9 31.9 + - - +
256B LYS* 4.9 0.9 + - - -
268C VAL 4.1 3.6 - - - -
269C HIS* 3.6 11.3 - - - +
270C ASP* 3.3 32.7 + - - +
273C SER* 5.3 0.2 + - - -
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Residues in contact with ARG 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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232B THR* 3.1 16.1 + - - +
234B GLY* 1.3 73.9 - - - +
236B ILE* 1.3 62.7 + - + +
239B GLY* 2.8 26.2 + - - -
191C TRP 2.6 30.5 + - - -
192C LEU* 3.7 22.3 + - - +
195C MET* 3.8 23.4 - - - +
196C PRO* 3.9 16.1 - - - +
224C HIS* 3.0 42.8 + - - +
267C LEU* 5.3 2.3 + - - +
268C VAL* 4.2 3.6 + - - +
269C HIS* 3.4 27.5 + - + +
296C LEU* 3.3 37.4 + - + +
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Residues in contact with ILE 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B THR* 4.1 9.0 - - + -
204B CYS* 3.6 34.5 - - - -
208B MET* 5.0 4.9 - - + -
229B PHE* 3.9 22.0 - - + -
232B THR* 3.1 30.0 + - - +
233B VAL* 3.8 4.7 - - - +
235B ARG* 1.3 76.7 - - - +
237B SER* 1.3 58.7 + - - +
239B GLY* 3.4 1.6 + - - -
240B PHE* 2.9 26.2 + - - +
255B PRO* 4.2 21.5 - - + -
192C LEU* 4.1 40.7 - - + +
193C VAL* 4.5 2.7 - - + -
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Residues in contact with SER 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B VAL* 2.9 15.3 + - - -
234B GLY 3.7 0.5 + - - -
236B ILE* 1.3 75.7 - - - +
238B HIS* 1.3 67.5 + - - +
239B GLY 3.1 0.9 - - - -
240B PHE* 3.2 5.2 + - - -
241B SER* 3.2 25.1 + - - -
254B ASN* 3.2 28.7 + - - -
255B PRO* 4.5 5.4 - - - -
256B LYS* 3.3 44.1 + - - +
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Residues in contact with HIS 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 GLY 2.9 19.5 + - - +
235B ARG 4.1 1.6 - - - +
237B SER* 1.3 76.3 + - - +
239B GLY* 1.3 63.7 + - - +
241B SER* 3.2 9.2 + - - -
242B MET* 3.2 49.8 + - + +
269C HIS* 3.5 24.6 - + + -
295C PRO 3.0 21.7 + - - -
296C LEU* 3.4 25.6 - - + -
297C GLY 3.3 11.9 + - - -
298C GLU* 5.9 0.4 - - - -
299C LEU* 4.9 11.4 - - + -
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Residues in contact with GLY 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 ARG 2.8 19.6 + - - -
236B ILE 3.6 2.2 - - - -
237B SER 3.1 0.4 - - - -
238B HIS* 1.3 77.9 - - - +
240B PHE* 1.3 60.5 + - - +
242B MET* 3.3 3.1 + - - -
243B ARG* 3.1 20.6 + - - +
247B CYS* 4.2 2.2 - - - -
188C TRP* 3.6 21.7 - - - -
192C LEU* 3.7 16.4 - - - -
296C LEU* 4.2 5.6 - - - +
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Residues in contact with PHE 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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208B MET* 4.0 17.0 - - + -
236B ILE 2.9 17.5 + - - +
237B SER 3.2 6.0 + - - +
239B GLY* 1.3 72.3 - - - +
241B SER* 1.3 65.8 + - - +
243B ARG 4.0 0.5 - - - -
244B PRO* 3.7 20.3 - - + +
247B CYS* 3.4 43.7 - - + -
248B ALA* 3.5 17.3 - - + -
251B ASN* 3.4 22.4 - - - -
252B PRO 3.8 9.0 - - - -
253B MET 3.6 12.8 - - - -
254B ASN* 3.5 34.3 - - + -
255B PRO* 3.4 17.5 - - + -
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Residues in contact with SER 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 SER 3.2 6.1 + - - -
238B HIS* 3.3 14.2 - - - -
239B GLY 3.2 0.2 - - - -
240B PHE* 1.3 79.3 - - - +
242B MET* 1.3 79.4 + - - +
244B PRO* 3.3 13.5 - - - +
254B ASN* 3.3 20.6 + - - +
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Residues in contact with MET 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 HIS* 3.2 39.4 + - + +
239B GLY 3.3 4.0 + - - +
241B SER* 1.3 94.5 - - - +
243B ARG* 1.3 70.8 + - + +
244B PRO* 3.3 5.6 - - - +
188C TRP* 4.7 4.3 - - + -
295C PRO* 3.4 44.6 - - + +
296C LEU* 4.6 0.7 - - - +
299C LEU* 5.0 15.5 - - + -
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Residues in contact with ARG 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 GLY 3.1 6.8 + - - +
240B PHE 4.0 3.6 - - - -
242B MET* 1.3 87.0 - - + +
244B PRO* 1.4 58.1 - - - +
245B ASP* 2.5 44.1 + - - +
246B LEU* 3.0 48.2 + - + +
247B CYS* 3.2 13.6 + - - +
47C ARG* 6.3 0.8 - - - +
188C TRP* 3.4 49.8 - - + +
295C PRO* 5.2 10.3 - - - -
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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
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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