Contacts of the helix formed by residues 221 - 242 (chain B) in PDB entry 5YL4
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 221 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B THR* 4.3 8.7 - - + +
220B PRO* 1.3 77.8 - - - +
222B TYR* 1.3 64.2 + - - +
223B GLY* 3.3 13.6 + - - -
224B ASP* 3.2 28.3 + - - +
225B LEU* 3.3 15.8 + - - +
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Residues in contact with TYR 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLN* 6.6 0.2 - - - -
15B GLN* 5.9 1.1 - - + +
175B VAL* 3.4 30.3 + - + +
176B SER 4.8 0.3 + - - -
177B ASP* 3.0 26.0 + - - -
204B ASN* 4.3 0.2 - - - -
221B THR* 1.3 74.0 - - - +
223B GLY* 1.3 53.1 + - - +
225B LEU* 3.3 10.2 + - + +
226B ASN* 2.7 43.6 + - - +
501B GDP 3.2 75.7 + + - +
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Residues in contact with GLY 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LYS* 6.0 5.9 - - - -
221B THR* 3.2 9.9 + - - -
222B TYR* 1.3 77.4 - - - +
224B ASP* 1.3 57.2 + - - +
226B ASN* 3.7 6.3 - - - +
227B HIS* 2.9 30.3 + - - +
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Residues in contact with ASP 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B CYS* 3.5 26.5 - - - -
215B LEU* 5.7 0.3 - - - +
217B LEU* 3.7 26.3 - - + +
219B THR 4.3 2.6 - - - +
220B PRO* 3.5 9.5 - - + +
221B THR* 3.2 35.2 + - - +
223B GLY* 1.3 74.6 - - - +
225B LEU* 1.3 65.7 + - - +
227B HIS* 3.7 15.5 + - - +
228B LEU* 3.7 7.4 + - - +
275B SER* 5.7 2.6 - - - -
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Residues in contact with LEU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B VAL* 4.0 22.0 - - + -
204B ASN* 3.8 21.3 - - + +
207B LEU* 3.4 47.1 - - + +
208B TYR* 3.7 10.8 - - + +
211B CYS* 3.9 10.1 - - + -
220B PRO* 4.5 7.0 - - + +
221B THR 3.3 14.3 + - - +
222B TYR* 3.3 27.3 + - + +
224B ASP* 1.3 77.6 - - - +
226B ASN* 1.3 59.1 + - - +
228B LEU* 3.1 20.4 + - - +
229B VAL* 3.2 14.2 + - - +
501B GDP 4.1 4.7 - - - +
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Residues in contact with ASN 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLN* 3.7 22.8 + - - +
16B ILE* 3.4 17.8 - - + +
19B LYS* 4.5 19.6 - - + +
222B TYR* 2.7 26.6 + - - +
223B GLY* 3.9 6.8 - - - +
225B LEU* 1.3 69.5 - - - +
227B HIS* 1.3 60.4 + - - +
228B LEU 3.2 0.2 - - - -
229B VAL* 3.7 7.3 - - - +
230B SER* 2.9 32.1 + - - -
501B GDP 2.7 49.3 + - - -
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Residues in contact with HIS 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LYS* 5.9 1.8 - - - +
223B GLY 2.9 18.8 + - - +
224B ASP* 3.7 9.6 - - - +
225B LEU 3.3 0.4 - - - -
226B ASN* 1.3 75.5 - - - +
228B LEU* 1.3 65.2 + - + +
230B SER* 3.1 22.2 + - - -
231B ALA* 3.3 13.9 + - + +
274B THR* 2.9 46.8 + - - -
275B SER* 4.0 15.1 + - - -
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Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B LEU* 3.9 20.4 - - + +
210B ILE* 3.6 33.0 - - + -
211B CYS* 3.9 21.8 - - - -
215B LEU* 4.1 6.3 - - + -
224B ASP 3.7 8.9 + - - +
225B LEU 3.1 7.9 + - - +
227B HIS* 1.3 76.8 - - + +
229B VAL* 1.3 62.9 + - - +
231B ALA* 3.7 7.1 + - + +
232B THR* 3.0 25.8 + - - -
270B PHE* 6.4 0.7 - - + -
273B LEU* 4.1 21.1 - - + -
274B THR 3.9 26.0 - - - +
300B MET* 3.8 10.9 - - + +
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Residues in contact with VAL 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 4.0 26.9 - - + -
167B PHE* 4.6 1.5 - - + -
202B ILE* 3.7 27.8 - - + -
207B LEU* 3.4 33.7 - - + -
225B LEU 3.2 4.8 + - - +
226B ASN* 3.3 15.0 + - - +
228B LEU* 1.3 78.2 - - - +
230B SER* 1.3 57.7 + - - +
232B THR* 3.2 6.9 + - - -
233B MET* 2.9 48.5 + - + +
300B MET* 5.2 1.6 - - - -
501B GDP 5.0 1.3 - - - +
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Residues in contact with SER 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LYS* 3.9 25.0 - - - +
20B PHE* 5.5 1.3 - - - +
23B VAL* 3.8 29.0 - - - +
226B ASN 2.9 15.2 + - - -
227B HIS* 3.1 17.8 + - - -
228B LEU 3.4 0.2 - - - -
229B VAL* 1.3 73.6 - - - +
231B ALA* 1.3 62.3 + - - +
233B MET* 3.9 11.3 - - - +
234B SER* 3.0 30.1 + - - -
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Residues in contact with ALA 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B VAL* 5.9 1.3 - - - -
227B HIS* 3.3 17.3 + - + +
228B LEU* 3.9 8.5 - - + +
229B VAL 3.3 0.2 - - - -
230B SER* 1.3 81.9 + - - +
232B THR* 1.3 57.5 + - - +
234B SER* 3.6 7.2 - - - -
235B GLY 3.0 19.4 + - - -
270B PHE* 3.5 46.3 - - + -
274B THR* 6.1 0.7 - - - +
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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
----------------------------------------------------------
167B PHE* 4.3 14.6 - - + -
202B ILE* 5.6 1.6 - - + -
228B LEU 3.0 14.2 + - - -
229B VAL* 3.2 10.4 + - - -
230B SER 3.2 0.4 - - - -
231B ALA* 1.3 75.6 - - - +
233B MET* 1.3 59.3 + - - +
234B SER 3.3 0.2 - - - -
235B GLY* 3.1 0.7 + - - +
236B VAL* 3.0 32.7 + - + +
268B PRO* 3.7 30.7 - - + -
269B GLY 4.4 3.6 - - - +
270B PHE* 4.0 4.8 - - - +
300B MET* 3.3 22.1 - - + +
366B THR* 4.2 18.6 - - + -
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Residues in contact with MET 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 4.0 19.5 - - + +
20B PHE* 3.5 35.8 - - + -
136B THR* 3.4 33.2 - - + -
167B PHE* 3.4 29.6 - - + -
229B VAL* 2.9 39.3 + - - +
230B SER* 3.4 8.0 + - - +
232B THR* 1.3 72.3 - - - +
234B SER* 1.3 62.5 + - - +
236B VAL* 3.6 1.2 - - - +
237B THR* 2.9 33.1 + - - +
506B 8WR 3.4 17.3 - - + -
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Residues in contact with SER 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PHE* 4.6 1.2 - - - -
23B VAL* 3.9 15.0 - - - -
24B ILE* 4.7 5.8 - - - -
27B GLU* 2.7 28.5 + - - -
230B SER 3.0 18.7 + - - -
231B ALA* 3.6 7.6 - - - -
233B MET* 1.3 76.8 - - - +
235B GLY* 1.3 59.7 + - - +
237B THR* 3.2 9.5 + - - -
238B THR* 2.9 9.5 + - - -
241B ARG* 2.9 24.9 + - - +
318B ARG* 3.2 8.8 + - - -
358B PRO* 4.9 3.4 - - - +
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Residues in contact with GLY 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 ALA 3.0 12.9 + - - -
232B THR 3.1 3.9 + - - -
234B SER* 1.3 77.0 - - - +
236B VAL* 1.3 60.3 + - - +
238B THR* 3.3 17.0 + - - -
239B CYS 4.9 0.2 + - - -
270B PHE* 5.1 1.1 - - - -
316B ILE* 3.4 20.7 - - - +
318B ARG* 5.2 4.0 - - - -
366B THR* 3.0 30.0 - - - -
506B 8WR 4.4 0.5 - - - +
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Residues in contact with VAL 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B PHE* 3.6 29.2 - - + -
200B TYR* 3.8 14.1 - - + +
232B THR* 3.0 21.1 + - + +
233B MET 3.6 6.7 - - - +
235B GLY* 1.3 74.4 - - - +
237B THR* 1.3 61.8 + - - +
238B THR 3.5 0.4 - - - -
239B CYS* 4.7 3.3 - - - -
316B ILE* 5.6 0.2 - - - -
366B THR* 4.0 9.0 - - + -
367B PHE 5.6 0.2 - - - +
368B ILE* 3.6 28.9 - - + -
506B 8WR 2.9 62.8 + - + +
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Residues in contact with THR 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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20B PHE* 3.8 15.0 - - + -
50B TYR* 3.3 27.8 - - - +
233B MET 2.9 21.1 + - - +
234B SER* 3.2 5.5 + - - -
235B GLY 3.3 0.2 - - - -
236B VAL* 1.3 74.5 - - - +
238B THR* 1.3 58.2 + - - +
239B CYS 3.4 2.7 - - - -
240B LEU* 3.4 6.0 + - - +
241B ARG* 2.7 59.8 + - - +
506B 8WR 3.3 27.4 - - + -
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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
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234B SER 2.9 19.4 + - - -
235B GLY* 3.3 6.6 + - - -
236B VAL 3.5 1.2 - - - -
237B THR* 1.3 77.9 - - - +
239B CYS* 1.3 58.4 + - - +
241B ARG* 3.9 8.5 - - - +
242B PHE* 2.9 36.0 + - + +
316B ILE* 3.4 30.3 - - + -
318B ARG* 3.1 27.8 + - - +
354B CYS* 3.6 30.5 - - + -
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Residues in contact with CYS 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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46B ARG* 3.8 5.4 + - - -
235B GLY 4.9 0.4 + - - -
236B VAL 4.7 1.8 + - - -
238B THR* 1.3 80.1 - - - +
240B LEU* 1.3 64.7 + - - +
242B PHE* 3.3 14.5 - - - +
243B PRO 3.7 9.4 - - - +
246B LEU* 4.0 23.9 - - + +
248B ALA 4.8 3.1 - - - +
253B LEU* 3.9 27.8 - - - -
316B ILE* 4.8 8.7 - - + +
352B ALA* 5.3 4.3 - - + -
506B 8WR 3.9 36.6 - - + +
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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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4B ILE* 3.8 13.5 - - + -
46B ARG* 3.2 32.1 + - - +
49B VAL* 3.8 20.4 - - + +
50B TYR* 4.8 2.2 - - + +
131B GLN* 4.1 11.0 - - - +
236B VAL 5.0 0.4 - - - +
237B THR* 3.4 6.6 + - - +
238B THR 3.2 0.6 - - - -
239B CYS* 1.3 84.6 - - - +
241B ARG* 1.3 61.9 + - + +
242B PHE 3.4 2.0 - - - -
248B ALA 3.3 26.7 - - - +
249B ASP* 3.9 16.6 - - - -
250B LEU* 3.6 16.6 - - + -
253B LEU* 4.5 5.6 - - + -
506B 8WR 3.6 35.4 - - + -
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Residues in contact with ARG 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 3.4 25.2 - - - +
27B GLU* 2.9 30.7 + - - +
28B HIS* 3.5 44.0 + - + +
42B LEU 4.6 3.3 - - - +
46B ARG* 4.0 19.1 - - - +
49B VAL* 5.3 0.7 - - + -
50B TYR* 3.6 35.7 - - + -
234B SER* 2.9 34.4 + - - +
237B THR* 2.7 32.7 + - - +
238B THR* 3.7 11.7 + - - +
240B LEU* 1.3 77.2 - - - +
242B PHE* 1.3 73.0 + - + +
318B ARG* 3.7 0.4 - - - +
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Residues in contact with PHE 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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27B GLU* 4.2 17.3 - - + -
28B HIS* 4.1 15.7 - + - -
42B LEU 3.6 24.0 - - - -
43B GLN* 4.5 4.9 - - + -
46B ARG* 3.8 14.5 + - - +
238B THR* 2.9 20.8 + - + +
239B CYS 3.3 14.0 - - - +
241B ARG* 1.3 105.8 - - + +
243B PRO* 1.4 81.1 - - + +
318B ARG* 3.6 21.1 - - - -
354B CYS* 4.0 27.4 - - - -
356B ILE* 4.1 32.5 - - + -
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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