Contacts of the helix formed by residues 238 - 260 (chain C) in PDB entry 5H1C
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 LEU 238 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B VAL* 4.9 1.6 - - + -
232C TYR* 4.6 0.8 - - - +
234C GLY* 4.2 6.8 - - - -
235C ARG* 3.5 36.3 - - + +
237C GLU* 1.3 75.1 - - - +
239C SER* 1.3 54.7 + - - +
240C ALA 3.0 0.7 - - - -
241C ARG* 2.7 46.3 + - - +
242C GLN* 2.7 22.3 + - - +
6D T 3.4 50.0 - - + +
7D T 3.7 39.5 - - + +
8D T 4.8 6.1 - - - +
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Residues in contact with SER 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C GLY 5.3 0.3 - - - -
237C GLU 2.2 27.3 + - - -
238C LEU* 1.3 71.2 - - - +
240C ALA* 1.3 56.1 + - - +
242C GLN* 4.5 1.1 - - - +
243C MET* 3.2 23.9 + - - +
5D T 4.0 17.9 - - - -
6D T 3.5 32.6 + - - +
4E A 5.1 1.8 - - - -
5E A 4.5 14.6 + - - -
6E A 5.2 6.5 + - - -
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Residues in contact with ALA 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C TYR* 4.9 14.3 - - + -
237C GLU* 3.4 15.3 + - + +
238C LEU 3.0 0.4 - - - -
239C SER* 1.3 82.7 + - - +
241C ARG* 1.3 59.3 + - - +
243C MET* 3.1 15.8 + - - +
244C HIS* 2.9 28.2 + - - +
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Residues in contact with ARG 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C TYR* 3.3 40.7 - - + +
229C ARG* 5.3 1.7 - - - +
232C TYR* 3.5 37.9 + - + -
238C LEU* 2.7 29.3 + - - +
240C ALA* 1.3 79.6 - - - +
242C GLN* 1.3 85.2 + - - +
244C HIS* 3.1 4.3 + - - +
245C LEU* 2.9 36.6 + - + +
287C ILE* 4.1 11.3 - - - +
288C GLY* 3.8 18.8 - - - +
7D T 3.5 5.1 + - - -
8D T 3.2 36.1 + - - -
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Residues in contact with GLN 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C LEU 2.7 17.8 + - - +
239C SER 4.5 1.1 - - - +
241C ARG* 1.3 103.8 - - - +
243C MET* 1.3 57.1 + - - +
245C LEU* 3.8 7.3 - - - +
246C ALA* 3.0 33.1 + - - +
288C GLY* 2.9 24.5 + - - +
291C ILE* 3.3 26.3 - - + +
6D T 2.8 20.4 - - - +
7D T 2.0 54.2 + - - +
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Residues in contact with MET 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B SER* 3.4 47.4 - - - +
234B GLY 5.3 4.3 - - - +
239C SER 3.2 18.1 + - - +
240C ALA* 3.1 19.5 - - - +
241C ARG 3.1 0.2 - - - -
242C GLN* 1.3 80.7 - - - +
244C HIS* 1.3 58.1 + - - +
246C ALA* 4.0 4.8 + - - +
247C ARG* 3.8 32.5 + - - +
6D T 5.8 2.2 - - - -
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Residues in contact with HIS 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C THR 3.8 15.9 - - - -
198C ASP* 3.6 22.0 + - - -
201C THR* 3.8 24.3 - - + +
228C TYR* 2.7 38.4 + + + -
232C TYR* 4.5 13.2 - - - +
240C ALA 2.9 11.6 + - - +
241C ARG* 3.1 7.8 + - - +
243C MET* 1.3 77.9 - - - +
245C LEU* 1.3 67.0 + - - +
246C ALA 3.2 1.6 - - - -
247C ARG* 3.1 12.5 + - + +
248C PHE* 3.0 22.8 + + + +
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Residues in contact with LEU 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C ALA* 4.8 3.1 - - + +
225C THR* 5.3 9.9 - - + -
228C TYR* 3.4 40.8 - - + +
241C ARG* 2.9 45.3 + - + +
242C GLN* 3.3 12.3 + - - +
244C HIS* 1.3 77.5 - - - +
246C ALA* 1.3 62.8 + - - +
248C PHE* 3.1 13.4 + - + +
249C LEU* 2.9 40.4 + - + +
287C ILE* 5.8 0.2 - - + -
288C GLY* 4.4 13.9 - - - -
291C ILE* 5.1 4.3 - - + -
292C ILE* 4.6 11.7 - - + -
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Residues in contact with ALA 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ARG* 5.1 6.7 - - + +
230B THR* 3.4 36.7 - - + +
242C GLN 3.0 17.0 + - - +
243C MET* 4.2 6.7 - - - +
244C HIS 3.2 0.2 - - - -
245C LEU* 1.3 76.8 - - - +
247C ARG* 1.3 58.7 + - + +
249C LEU* 3.6 3.1 + - - +
250C ARG* 3.0 22.5 + - - +
291C ILE* 4.0 24.6 - - + +
6D T 5.8 1.6 - - - +
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Residues in contact with ARG 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B THR 4.1 18.2 + - - +
231B ASP 5.3 3.0 + - - -
233B SER* 2.3 41.6 + - - +
237B GLU* 5.4 2.2 + - - -
243C MET* 3.8 24.3 + - - +
244C HIS* 3.1 13.2 + - + +
246C ALA* 1.3 74.2 - - + +
248C PHE* 1.3 67.0 + - - +
250C ARG* 3.2 7.7 + - - +
251C MET* 2.9 31.7 + - + +
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Residues in contact with PHE 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C ILE* 6.4 0.4 - - + -
200C GLN* 3.9 39.3 - - + -
201C THR* 5.2 7.0 - - + -
204C LEU* 3.6 32.5 - - + -
221C VAL* 5.0 11.0 - - + -
224C ALA* 3.8 26.7 - - + -
228C TYR* 4.3 11.2 - + - +
244C HIS* 3.0 14.8 + - + +
245C LEU* 3.4 17.7 - - + +
247C ARG* 1.3 76.9 - - - +
249C LEU* 1.3 73.6 + - + +
251C MET* 3.0 9.9 + - - +
252C LEU* 3.0 54.1 + - + +
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Residues in contact with LEU 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C ILE* 4.3 5.5 - - + +
245C LEU* 2.9 25.8 + - + +
246C ALA* 4.0 3.1 - - - +
248C PHE* 1.3 87.8 - - + +
250C ARG* 1.3 67.4 + - - +
252C LEU* 3.1 18.4 + - + +
253C LEU* 2.9 27.3 + - - +
265C ILE* 4.3 18.6 - - + -
291C ILE* 3.8 30.3 - - + +
292C ILE* 3.8 27.4 - - + -
295C ALA* 4.1 18.4 - - + -
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Residues in contact with ARG 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B PHE* 3.1 26.7 + - - +
196B ASN* 4.2 10.5 + - - +
227B LEU* 3.5 23.8 - - - +
230B THR* 3.0 38.7 + - + +
231B ASP* 3.0 28.6 + - - -
54C TYR 4.6 5.3 + - - -
56C PRO* 4.7 6.5 - - - +
246C ALA 3.0 19.1 + - - +
247C ARG* 3.2 6.9 + - - +
249C LEU* 1.3 76.3 - - - +
251C MET* 1.3 63.4 + - + +
253C LEU* 3.1 16.3 + - + +
254C ARG* 2.9 35.1 + - + +
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Residues in contact with MET 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C GLU* 5.8 0.2 - - - +
204C LEU* 3.8 26.9 - - + -
205C TYR* 4.5 30.1 - - + +
208C SER* 6.4 2.2 - - - -
247C ARG* 2.9 21.6 + - + +
248C PHE* 3.4 7.6 - - - +
250C ARG* 1.3 77.4 - - - +
252C LEU* 1.3 62.8 + - - +
254C ARG* 2.8 72.4 + - + +
255C LEU* 3.0 22.9 + - + +
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Residues in contact with LEU 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C ILE* 4.0 11.7 - - + -
204C LEU* 3.8 28.5 - - + -
219C LEU* 4.7 6.7 - - + -
221C VAL* 5.6 9.2 - - + -
248C PHE* 3.0 46.3 + - + +
249C LEU* 3.1 21.5 + - + +
251C MET* 1.3 75.8 - - - +
253C LEU* 1.3 59.8 + - - +
255C LEU* 3.3 11.2 + - + +
256C ALA* 2.9 29.9 + - - +
263C VAL* 4.3 26.1 - - + +
265C ILE* 4.4 11.0 - - + -
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Residues in contact with LEU 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B GLU* 5.4 17.7 - - + +
193B ARG* 5.5 2.7 - - - +
120C GLY 6.0 0.9 - - - +
121C SER* 6.1 1.1 - - - -
122C ILE* 3.9 24.0 - - + -
249C LEU 2.9 18.2 + - - +
250C ARG* 3.1 18.4 + - + +
252C LEU* 1.3 75.0 - - - +
254C ARG* 1.3 58.9 + - - +
256C ALA* 4.4 3.8 - - + +
257C ASP* 2.9 56.1 + - - +
295C ALA* 5.1 17.5 - - + +
297C THR* 5.8 6.1 - - + -
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Residues in contact with ARG 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C GLY 6.1 0.4 - - - -
46C PHE* 3.2 30.6 - - - -
51C ALA* 5.0 14.3 + - + -
54C TYR* 5.2 14.3 + - + -
55C ALA* 5.1 1.5 - - - +
56C PRO* 4.4 12.3 - - - +
59C GLU* 2.9 31.9 + - - -
205C TYR* 5.0 5.1 + - - -
208C SER* 6.6 0.2 - - - -
250C ARG* 2.9 21.3 + - + +
251C MET* 2.8 51.6 + - - +
253C LEU* 1.3 76.9 - - - +
255C LEU* 1.3 61.6 + - + +
257C ASP* 4.6 1.7 - - - +
258C GLU* 3.0 48.4 + - - +
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Residues in contact with LEU 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C LEU* 4.4 22.2 - - + +
207C ALA* 4.7 9.6 - - + -
208C SER* 3.9 31.4 - - - -
211C MET* 4.7 12.8 - - + -
219C LEU* 3.5 32.5 - - + -
251C MET* 3.0 21.7 + - + +
252C LEU* 3.8 8.1 - - + +
254C ARG* 1.3 84.6 - - + +
256C ALA* 1.3 60.2 + - - +
258C GLU* 3.1 13.2 + - - +
259C PHE* 3.0 35.2 + - + +
260C GLY 4.7 0.8 - - - +
263C VAL* 6.1 0.7 - - + -
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Residues in contact with ALA 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C GLY* 3.3 36.7 - - - +
121C SER* 4.2 2.5 - - - +
122C ILE* 5.2 2.2 - - + -
252C LEU 2.9 17.8 + - - +
253C LEU* 4.2 5.6 - - + +
255C LEU* 1.3 78.5 - - - +
257C ASP* 1.3 62.7 + - - +
258C GLU 3.1 1.1 + - - -
260C GLY 3.6 18.9 + - - +
263C VAL* 3.4 26.9 - - + -
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Residues in contact with ASP 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B GLU 5.5 0.3 - - - +
193B ARG* 2.6 31.8 + - - -
195B PHE* 3.5 23.0 - - + -
50C GLU* 5.2 0.3 - - - +
54C TYR* 4.6 11.4 + - + -
120C GLY 4.1 10.0 - - - +
253C LEU* 2.9 44.7 + - - +
254C ARG* 4.6 3.3 - - - +
256C ALA* 1.3 78.6 - - - +
258C GLU* 1.3 63.2 + - + +
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Residues in contact with GLU 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C PRO* 4.7 5.9 - - - +
48C THR* 3.9 4.5 + - - -
50C GLU* 4.2 16.0 - - - +
51C ALA* 3.1 39.3 - - - +
54C TYR* 4.0 21.2 - - + -
254C ARG* 3.0 30.9 - - - +
255C LEU* 3.1 9.0 + - - +
257C ASP* 1.3 83.7 - - - +
259C PHE* 1.3 100.6 + - + +
260C GLY 3.5 2.0 + - - -
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Residues in contact with PHE 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C PRO* 3.6 32.3 - - + -
48C THR* 3.4 31.4 - - + -
50C GLU* 4.7 1.6 - - + -
208C SER* 5.1 3.8 - - - -
211C MET* 3.4 59.9 - - + -
212C VAL* 6.0 0.2 - - - -
215C ARG* 5.7 8.9 + - - +
255C LEU* 3.0 15.9 + - + +
258C GLU* 1.3 113.9 - - + +
260C GLY* 1.3 68.2 + - - +
261C VAL* 2.9 13.9 + - + +
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Residues in contact with GLY 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C THR* 4.2 5.2 - - - -
120C GLY* 3.5 27.6 + - - -
255C LEU 4.7 0.5 - - - +
256C ALA* 3.6 15.6 + - - -
258C GLU 3.5 4.2 + - - -
259C PHE* 1.3 77.7 - - - +
261C VAL* 1.3 69.3 + - - +
262C ALA* 3.1 6.7 + - - -
263C VAL* 5.6 0.2 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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