Contacts of the helix formed by residues 227 - 248 (chain B) in PDB entry 4MCA
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 THR 227 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B LYS 4.7 1.0 + - - -
220B ALA* 3.7 20.0 - - + +
225B VAL* 4.6 7.6 - - + -
226B VAL* 1.3 81.1 - - - +
228B GLU* 1.3 65.9 + - - +
229B ALA* 3.5 15.2 + - - +
230B VAL* 3.1 26.4 + - - +
231B GLU* 3.1 15.8 + - - +
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Residues in contact with GLU 228 (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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227B THR* 1.3 74.2 - - - +
229B ALA* 1.3 64.0 + - - +
231B GLU* 3.2 17.3 + - - +
232B ARG* 2.9 63.6 + - - +
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Residues in contact with ALA 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B GLU* 3.3 31.3 - - - +
216B LYS* 3.7 30.7 - - + +
217B ALA* 3.9 9.0 - - - +
227B THR* 3.2 9.3 + - - +
228B GLU* 1.3 78.7 - - - +
230B VAL* 1.3 58.0 + - - +
232B ARG* 3.3 2.9 + - - +
233B ILE* 3.0 33.4 + - - +
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Residues in contact with VAL 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ILE* 5.8 0.2 - - + -
158B ALA* 4.5 10.1 - - + -
165B LEU* 5.5 2.7 - - + -
217B ALA* 3.8 19.7 - - - +
220B ALA* 3.4 32.8 - - + -
221B VAL* 4.0 16.4 - - + -
225B VAL 3.8 5.4 - - - +
226B VAL* 4.3 11.2 - - + -
227B THR* 3.1 19.4 + - - +
229B ALA* 1.3 73.9 - - - +
231B GLU* 1.3 68.2 + - - +
233B ILE* 3.2 2.0 + - - +
234B ILE* 3.0 41.2 + - + +
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Residues in contact with GLU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLN* 2.7 34.2 + - - +
14B GLY* 4.0 4.9 - - - -
15B ALA* 3.9 8.0 + - - +
154B VAL* 2.6 51.3 - - - +
226B VAL* 3.5 7.2 - - + +
227B THR 3.1 15.5 + - - +
228B GLU* 3.2 22.9 + - - +
230B VAL* 1.3 77.1 - - - +
232B ARG* 1.3 61.8 + - - +
234B ILE* 4.6 1.6 - - - -
235B GLU* 3.0 13.5 + - - +
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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
----------------------------------------------------------
209B THR* 3.7 12.6 - - + +
213B GLU* 3.6 38.3 + - + -
228B GLU* 2.9 50.3 + - - +
229B ALA 3.8 4.7 - - - +
230B VAL 3.1 0.2 - - - -
231B GLU* 1.3 78.4 - - - +
233B ILE* 1.3 57.1 + - - +
235B GLU* 3.4 8.0 + - - +
236B ALA* 2.9 27.4 + - - +
240B LEU* 5.5 0.2 - - - +
1002B GOL 2.8 47.2 + - - -
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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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165B LEU* 4.0 16.8 - - + -
169B MET* 3.9 19.3 - - + -
209B THR* 3.9 11.7 - - + +
210B LEU* 3.8 24.7 - - + -
213B GLU* 3.7 13.7 - - + +
214B GLY* 3.8 21.3 - - - +
217B ALA* 3.6 18.2 - - + -
229B ALA 3.0 20.7 + - - +
230B VAL* 3.9 3.1 - - - +
232B ARG* 1.3 73.3 - - - +
234B ILE* 1.3 56.6 + - - +
236B ALA* 3.5 1.9 - - + +
237B ASN* 2.7 48.5 + - - +
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Residues in contact with ILE 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B TYR* 4.0 4.9 - - - +
13B GLN* 3.6 17.9 - - + +
118B ALA* 4.4 5.6 - - + -
152B MET* 4.1 27.8 - - + -
154B VAL* 3.7 33.4 - - + +
157B ILE* 3.8 31.9 - - + -
165B LEU* 4.7 6.1 - - + -
230B VAL* 3.0 33.9 + - + +
231B GLU 3.9 3.8 - - - +
233B ILE* 1.3 75.5 - - - +
235B GLU* 1.3 64.1 + - - +
237B ASN* 3.3 4.9 + - - -
238B THR* 2.8 30.6 + - - +
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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
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11B TYR* 3.7 9.2 - - + -
13B GLN* 3.4 20.2 + - - +
205B LEU* 5.5 1.2 - - - +
231B GLU 3.0 15.7 + - - +
232B ARG* 3.7 7.3 - - - +
234B ILE* 1.3 77.7 - - - +
236B ALA* 1.3 61.8 + - - +
239B TYR* 2.9 39.7 + - + -
240B LEU* 3.1 34.4 + - + +
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Residues in contact with ALA 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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206B CYS* 3.6 17.0 - - - +
209B THR* 4.1 19.7 - - + -
210B LEU* 4.6 6.7 - - + -
232B ARG 2.9 18.6 + - - +
233B ILE* 3.5 9.2 - - - +
235B GLU* 1.3 75.8 - - - +
237B ASN* 1.3 63.7 + - - +
240B LEU* 3.8 18.1 - - + +
241B SER* 3.0 32.4 + - - -
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Residues in contact with ASN 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ALA* 3.1 28.8 + - + +
120B THR 3.7 5.7 - - - +
121B ASP* 3.5 25.6 + - - +
165B LEU* 3.5 15.4 + - - +
168B GLY* 3.4 29.1 - - - +
169B MET* 3.5 15.4 - - - +
172B ALA* 3.7 12.2 + - - +
210B LEU* 3.8 4.3 - - - +
233B ILE* 2.7 32.8 + - - +
234B ILE* 3.8 5.4 - - - +
236B ALA* 1.3 76.1 - - - +
238B THR* 1.3 60.8 + - - +
241B SER* 3.7 1.6 - - - -
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Residues in contact with THR 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B TYR* 3.6 23.8 - - + -
118B ALA* 4.4 3.5 - - - +
120B THR 4.9 2.9 + - - +
121B ASP* 4.4 5.9 - - - +
123B PRO* 4.6 15.9 - - + -
124B THR* 3.8 15.1 + - + +
150B VAL* 4.7 2.0 - - + -
152B MET* 3.4 32.3 - - + +
234B ILE* 2.8 18.9 + - - +
236B ALA 3.1 0.6 - - - -
237B ASN* 1.3 84.3 - - - +
239B TYR* 1.3 62.4 + - - +
242B GLY* 3.1 25.8 + - - -
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Residues in contact with TYR 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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7B SER* 3.1 28.7 + - - -
8B PRO* 4.2 7.4 - - + -
11B TYR* 3.6 52.7 - + + -
124B THR* 4.2 10.3 + - + -
202B LEU* 4.5 11.9 - - + -
235B GLU* 2.9 21.7 + - + +
238B THR* 1.3 75.1 - - - +
240B LEU* 1.3 79.7 + - + +
242B GLY 3.2 0.3 + - - -
243B ILE* 2.9 54.0 + - + +
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Residues in contact with LEU 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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175B THR* 4.5 0.7 - - - +
202B LEU* 3.7 47.5 - - + +
205B LEU* 3.9 25.1 - - + +
206B CYS* 3.7 25.4 - - + +
209B THR* 4.3 4.9 - - + +
232B ARG 5.5 0.2 - - - +
235B GLU* 3.1 36.2 + - + +
236B ALA* 3.8 23.6 - - + +
239B TYR* 1.3 80.3 - - + +
241B SER* 1.3 64.0 + - - +
243B ILE* 4.1 1.0 - - - +
244B GLY* 2.9 23.0 + - - -
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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
----------------------------------------------------------
121B ASP* 2.6 35.5 + - - +
172B ALA* 3.5 16.0 - - - -
175B THR* 2.8 23.7 + - - +
206B CYS* 4.0 2.9 - - - -
236B ALA 3.0 22.2 + - - -
237B ASN 3.7 6.1 - - - -
240B LEU* 1.3 76.7 - - - +
242B GLY* 1.3 58.7 + - - +
245B PHE* 2.9 32.7 + - - +
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Residues in contact with GLY 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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121B ASP* 3.6 15.4 - - - +
124B THR* 3.4 22.4 - - - -
125B SER* 5.3 0.6 - - - -
238B THR 3.1 15.6 + - - -
239B TYR 3.2 0.2 + - - -
241B SER* 1.3 78.6 - - - +
243B ILE* 1.3 62.7 + - - +
245B PHE* 3.3 8.8 - - - -
246B GLU* 3.1 26.7 + - - +
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Residues in contact with ILE 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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5B ILE* 3.9 27.8 - - + -
6B GLN 3.7 17.7 - - - +
7B SER* 4.1 11.0 - - - -
8B PRO* 4.2 6.1 - - + -
124B THR* 4.7 4.5 - - - +
199B ALA* 4.3 5.0 - - - +
202B LEU* 3.9 23.1 - - + -
239B TYR* 2.9 59.8 + - + +
240B LEU 4.2 0.7 - - - +
242B GLY* 1.3 75.7 - - - +
244B GLY* 1.3 57.4 + - - +
246B GLU* 5.0 4.5 - - - +
247B SER* 2.9 34.8 + - - +
248B SER 3.8 0.5 + - - -
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Residues in contact with GLY 244 (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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175B THR* 3.8 15.0 - - - -
179B ALA* 4.4 1.2 - - - +
199B ALA 3.9 19.3 + - - -
202B LEU* 5.0 0.4 - - - +
203B ALA* 4.1 4.3 - - - -
240B LEU 2.9 19.1 + - - -
241B SER 3.8 0.4 - - - -
243B ILE* 1.3 76.8 - - - +
245B PHE* 1.3 57.2 + - - +
248B SER* 3.0 30.5 + - - -
249B GLY 3.2 3.9 + - - +
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Residues in contact with PHE 245 (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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121B ASP* 3.6 37.5 - - - -
125B SER* 3.7 25.4 - - - -
127B LEU* 3.8 17.0 - - + -
175B THR* 3.7 5.5 - - + +
178B GLU* 5.9 0.2 - - - +
190B MET* 4.1 12.6 + - - +
241B SER 2.9 21.0 + - - +
242B GLY* 3.3 20.2 - - - -
244B GLY* 1.3 73.8 - - - +
246B GLU* 1.3 70.7 + - + +
249B GLY* 3.3 28.9 + - - +
250B LEU* 3.6 31.9 + - + +
1001B GOL 3.6 24.2 - - - -
1004B NA 4.0 12.3 - - - -
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Residues in contact with GLU 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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6B GLN* 3.5 32.4 + - - +
124B THR* 4.4 0.5 + - - +
125B SER* 3.6 8.5 - - - -
126B ALA* 2.8 31.8 + - - +
127B LEU* 4.9 2.1 - - - +
146B ASN* 2.9 22.2 + - - -
189B SER* 3.4 0.9 + - - -
190B MET* 3.2 25.8 + - + +
191B ALA 3.0 26.3 + - - +
242B GLY 3.1 16.1 + - - +
243B ILE* 4.3 3.7 - - - +
245B PHE* 1.3 95.5 - - + +
247B SER* 1.3 62.0 + - - +
248B SER 3.5 0.2 - - - -
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Residues in contact with SER 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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4B ILE 3.9 5.4 - - - +
5B ILE* 3.7 19.2 - - - -
6B GLN* 3.1 34.5 + - - +
189B SER* 3.7 15.3 + - - -
191B ALA* 3.8 7.1 - - - +
195B SER* 3.7 13.3 - - - -
199B ALA* 3.7 18.7 - - - +
243B ILE* 2.9 16.0 + - - -
246B GLU* 1.3 78.1 - - - +
248B SER* 1.3 58.5 + - - +
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Residues in contact with SER 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ALA* 3.5 24.6 + - - +
182B CYS* 3.8 13.3 - - - +
183B PHE* 5.0 0.2 - - - -
187B ALA 4.9 3.1 - - - +
188B THR 5.5 0.2 - - - -
189B SER* 3.8 9.8 + - - -
195B SER* 2.8 31.1 + - - -
199B ALA* 3.6 13.7 - - - -
200B LEU* 3.4 17.2 + - - +
244B GLY 3.0 17.5 + - - -
246B GLU 3.5 0.2 - - - -
247B SER* 1.3 79.2 - - - +
249B GLY* 1.3 56.7 + - - +
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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