Contacts of the helix formed by residues 235 - 256 (chain C) in PDB entry 6XAV
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 PRO 235 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B ASN* 5.7 5.2 - - - +
295B HIS* 3.9 19.9 - - + +
233C ASP 4.5 0.4 - - - +
234C GLU* 1.3 100.6 - - + +
236C ALA* 1.3 66.2 + - - +
237C SER* 3.2 10.5 - - - +
238C ARG* 3.2 22.0 + - + +
239C HIS* 3.4 11.4 + - - -
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Residues in contact with ALA 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ASN* 5.9 1.7 + - - +
235C PRO* 1.3 72.4 - - - +
237C SER* 1.3 64.7 + - - +
239C HIS* 3.2 14.1 + - + +
240C VAL* 3.0 26.7 + - - +
273C ALA* 3.8 17.7 - - - +
276C THR* 4.1 19.7 - - + +
277C VAL* 3.7 20.2 - - + -
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Residues in contact with SER 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C PRO* 3.2 11.5 - - - +
236C ALA* 1.3 79.4 - - - +
238C ARG* 1.3 61.1 + - - +
240C VAL* 3.3 6.2 + - - +
241C GLN* 3.0 23.9 + - - +
277C VAL* 4.1 13.5 - - - +
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Residues in contact with ARG 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C SER 3.1 18.0 + - - -
71C SER* 3.0 30.5 + - - -
72C TYR 4.0 7.6 + - - -
73C LEU* 3.3 30.7 - - - +
229C ALA 4.6 3.4 + - - -
230C SER* 3.5 18.6 - - - +
234C GLU* 2.5 50.6 + - + +
235C PRO* 3.2 18.3 + - + +
237C SER* 1.3 79.2 - - - +
239C HIS* 1.3 56.3 + - - +
241C GLN* 3.3 8.0 + - - +
242C VAL* 2.9 51.3 + - - +
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Residues in contact with HIS 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C ILE* 3.5 32.7 - - + +
210C ASP* 3.8 24.6 + - + +
230C SER* 3.1 25.8 + - - -
231C THR 3.2 26.5 + - - -
234C GLU* 3.5 20.5 + - + -
235C PRO 3.4 8.2 + - - -
236C ALA* 3.2 16.0 + - + +
238C ARG* 1.3 76.1 - - - +
240C VAL* 1.3 63.3 + - - +
242C VAL* 4.2 1.2 - - - +
243C ALA* 3.2 23.7 + - - +
269C ARG 5.7 1.1 - - - -
270C LEU* 4.1 5.4 - - + +
273C ALA* 3.9 15.7 - - + -
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Residues in contact with VAL 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C ALA 3.0 15.0 + - - +
237C SER* 3.7 8.1 - - - +
238C ARG 3.2 0.2 - - - -
239C HIS* 1.3 75.3 - - - +
241C GLN* 1.3 64.9 - - - +
243C ALA* 3.3 6.3 + - - +
244C GLU* 3.0 30.5 + - + +
270C LEU* 5.1 0.7 - - - -
273C ALA* 4.1 11.9 - - + +
274C TYR* 3.6 33.4 - - + +
277C VAL* 3.8 28.7 - - + -
296C ARG* 4.6 6.1 - - - +
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Residues in contact with GLN 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C GLU* 3.0 40.3 + - - +
58C LEU* 6.0 1.4 - - - +
72C TYR 5.0 9.0 - - - +
237C SER 3.0 16.6 + - - +
238C ARG* 3.3 9.2 + - - +
240C VAL* 1.3 79.3 - - - +
242C VAL* 1.3 64.1 + - + +
244C GLU* 3.2 9.6 + - - +
245C MET* 3.0 50.7 + - + +
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Residues in contact with VAL 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C SER 3.7 12.6 - - - +
72C TYR* 4.5 5.6 - - + +
207C LEU* 3.8 17.5 - - + -
209C ILE* 4.0 10.8 - - + -
228C VAL* 3.8 28.3 - - + +
229C ALA 5.1 0.7 - - - +
230C SER* 4.4 9.0 - - - -
238C ARG* 2.9 48.9 + - + +
239C HIS 4.2 3.1 - - - +
241C GLN* 1.3 76.2 - - + +
243C ALA* 1.3 62.6 + - - +
245C MET* 3.3 6.8 + - - +
246C VAL* 3.1 23.0 + - - +
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Residues in contact with ALA 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C LEU* 4.5 15.3 - - + -
209C ILE* 5.0 2.2 - - + +
239C HIS 3.2 19.5 + - - +
240C VAL 3.7 3.8 - - - +
241C GLN 3.3 0.2 - - - -
242C VAL* 1.3 77.2 - - - +
244C GLU* 1.3 63.4 + - - +
246C VAL* 3.5 0.7 + - - +
247C ILE* 3.2 25.2 + - - +
270C LEU* 3.7 30.3 - - + -
274C TYR* 4.0 9.4 - - - +
300C PHE* 3.7 10.7 - - + -
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Residues in contact with GLU 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C THR* 6.3 0.9 - - + -
240C VAL* 3.0 25.7 + - + +
241C GLN* 3.7 13.7 - - - +
243C ALA* 1.3 76.1 - - - +
245C MET* 1.3 61.2 + - - +
247C ILE* 3.2 14.2 - - - +
248C GLU* 2.9 42.3 + - + +
274C TYR* 3.9 10.8 + - - +
296C ARG* 2.5 34.0 + - - +
300C PHE* 5.6 2.1 - - - +
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Residues in contact with MET 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C VAL* 3.7 27.7 - - + +
55C LEU 3.4 23.8 - - - +
56C GLU* 3.7 26.9 - - + +
66C ARG* 4.5 5.6 - - + -
72C TYR* 3.6 36.3 - - + -
93C THR* 4.4 11.9 - - + -
94C GLY* 5.3 0.9 - - - +
241C GLN* 3.0 43.7 + - + +
242C VAL 3.3 2.4 + - - +
244C GLU* 1.3 77.9 - - - +
246C VAL* 1.3 62.4 + - - +
248C GLU* 4.2 2.7 - - - +
249C LYS* 3.2 24.3 + - - +
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Residues in contact with VAL 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C TYR* 4.5 8.3 - - + -
205C MET* 4.6 17.6 - - + +
207C LEU* 3.8 38.8 - - + -
228C VAL* 4.4 16.6 - - + -
242C VAL* 3.1 21.3 + - + +
243C ALA 3.9 4.7 - - - +
244C GLU 3.2 0.2 - - - -
245C MET* 1.3 75.3 - - - +
247C ILE* 1.3 60.8 + - - +
249C LYS* 3.3 5.3 + - - +
250C ALA* 2.9 27.9 + - - +
262C ILE* 4.2 24.0 - - + -
300C PHE* 5.0 1.8 - - + -
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Residues in contact with ILE 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243C ALA 3.2 11.0 + - - +
244C GLU* 3.2 28.5 - - - +
246C VAL* 1.3 80.6 - - - +
248C GLU* 1.3 67.5 + - + +
250C ALA* 3.4 5.6 + - + -
251C LYS* 3.0 47.8 + - + +
262C ILE* 4.9 1.8 - - + -
299C ARG 5.6 0.2 - - - +
300C PHE* 3.5 37.2 - - + +
303C ALA* 3.7 26.7 - - + -
313C LEU* 4.5 13.2 - - + -
315C ILE* 4.5 5.2 - - + -
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Residues in contact with GLU 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C THR* 2.9 49.3 - - + +
94C GLY* 4.1 2.9 - - - -
244C GLU* 2.9 27.8 + - + +
245C MET* 4.2 4.3 - - - +
247C ILE* 1.3 81.0 - - + +
249C LYS* 1.3 63.9 + - - +
251C LYS* 3.4 16.6 + - - +
252C ARG* 3.1 48.6 + - - +
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Residues in contact with LYS 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C VAL* 4.5 18.7 - - + +
68C ALA* 5.9 2.2 - - - +
72C TYR* 3.2 28.3 + - + +
94C GLY* 4.4 15.4 - - - +
96C THR* 5.0 9.0 - - - +
121C PHE* 5.3 12.2 - - - -
205C MET* 3.9 23.7 - - + +
226C GLU* 3.0 30.6 + - - +
245C MET 3.2 19.5 + - - +
246C VAL* 3.8 4.7 - - - +
248C GLU* 1.3 76.1 - - - +
250C ALA* 1.3 62.5 + - - +
252C ARG* 3.4 2.5 + - - +
253C LEU* 3.2 35.5 + - + +
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Residues in contact with ALA 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C MET* 5.0 4.4 - - - +
246C VAL 2.9 17.6 + - - +
247C ILE* 3.7 9.6 - - + +
249C LYS* 1.3 76.8 - - - +
251C LYS* 1.3 62.2 + - - +
253C LEU* 3.3 4.7 + - - +
254C VAL* 3.1 28.7 + - - +
260C VAL* 4.0 14.8 - - + +
262C ILE* 3.8 25.4 - - + -
313C LEU* 4.0 13.9 - - + -
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Residues in contact with LYS 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C PHE* 4.4 33.2 - - + -
134C GLU* 5.1 9.3 + - - +
247C ILE* 3.0 46.1 + - + +
248C GLU* 3.9 16.9 + - - +
249C LYS 3.3 0.2 - - - -
250C ALA* 1.3 74.9 - - - +
252C ARG* 1.3 78.5 + - - +
254C VAL* 3.3 8.2 + - - +
255C GLU* 3.0 31.9 + - - +
299C ARG* 5.2 11.1 + - - +
303C ALA* 4.1 17.7 - - - +
313C LEU* 5.1 3.8 - - + -
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Residues in contact with ARG 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ARG* 3.5 32.1 - - - +
93C THR 3.2 11.9 + - - -
94C GLY 3.7 25.1 - - - +
95C ASP* 3.3 21.1 - - - +
120C ASN* 4.5 12.1 - - - +
130C LYS* 4.7 3.4 - - - +
133C PHE* 4.8 2.2 - - - +
134C GLU* 5.1 5.9 + - - -
248C GLU* 3.1 43.4 + - - +
249C LYS* 3.8 4.9 - - + +
250C ALA 3.3 0.2 - - - -
251C LYS* 1.3 95.7 - - - +
253C LEU* 1.3 63.5 + - + +
255C GLU* 3.0 42.1 + - - +
256C HIS* 3.0 30.5 + - - -
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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
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96C THR* 6.1 0.7 - - - +
120C ASN* 5.3 10.1 - - + +
121C PHE* 5.1 17.0 - - + -
203C VAL* 4.1 15.0 - - + -
205C MET* 3.8 28.9 - - + -
249C LYS* 3.2 26.0 + - + +
250C ALA 3.8 0.2 - - - +
251C LYS 3.3 0.2 - - - -
252C ARG* 1.3 75.9 - - + +
254C VAL* 1.3 64.8 + - - +
256C HIS* 3.0 17.8 + - + +
257C LYS 3.2 0.7 + - - -
258C LYS* 3.0 36.5 + - + +
260C VAL* 3.6 24.0 - - + -
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Residues in contact with VAL 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C PHE* 3.6 27.1 - - + -
136C LEU* 4.2 3.1 - - + +
250C ALA 3.1 16.6 + - - +
251C LYS* 3.7 7.0 - - - +
252C ARG 3.3 0.2 - - - -
253C LEU* 1.3 74.8 - - - +
255C GLU* 1.3 63.6 + - - +
257C LYS* 3.0 14.2 + - - +
258C LYS 3.9 8.3 - - - +
260C VAL* 4.3 5.4 - - + -
307C VAL* 3.7 22.2 - - + -
310C GLY 3.6 7.6 - - - +
312C SER 3.7 31.2 - - - +
313C LEU* 3.8 20.0 - - + -
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Residues in contact with GLU 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C ARG* 3.3 12.9 + - - -
130C LYS* 3.1 37.7 + - - +
131C ILE* 3.9 18.1 - - - +
132C LEU* 3.6 1.1 - - - +
133C PHE* 2.8 40.9 + - + +
134C GLU* 4.8 0.3 - - - +
136C LEU* 4.8 6.7 - - + -
251C LYS 3.0 13.4 + - - +
252C ARG* 3.0 44.9 + - - +
253C LEU 3.2 0.2 - - - -
254C VAL* 1.3 76.6 - - - +
256C HIS* 1.3 58.5 + - - +
257C LYS* 3.2 14.6 + - - +
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Residues in contact with HIS 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C ASN* 3.1 40.5 + - + +
122C ASP* 4.0 24.9 + - + +
126C ASN 4.7 3.3 + - - -
127C ALA* 3.8 29.0 - - + +
130C LYS* 3.1 25.5 + - - -
252C ARG 3.0 24.5 + - - +
253C LEU* 3.0 15.9 + - + +
255C GLU* 1.3 74.7 - - - +
257C LYS* 1.3 72.0 + - - +
258C LYS* 3.7 16.7 + - + +
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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
------------------------------------------------------------
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