Contacts of the helix formed by residues 235 - 256 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292E ASN* 4.4 17.7 - - - +
295E HIS* 4.0 19.3 - - + +
234F GLU* 1.3 99.3 - - + +
236F ALA* 1.3 64.8 + - - +
237F SER* 3.2 10.3 - - - +
238F ARG* 3.4 19.5 + - + +
239F HIS* 3.2 19.6 + - - -
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Residues in contact with ALA 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291E ALA 6.0 1.3 - - - +
292E ASN* 5.1 3.4 + - - +
235F PRO* 1.3 72.9 - - - +
237F SER* 1.3 65.1 + - - +
239F HIS* 3.2 15.3 + - + +
240F VAL* 3.0 27.2 + - - +
273F ALA* 4.1 27.5 - - + +
276F THR* 4.3 15.7 - - + +
277F VAL* 4.2 9.4 - - + -
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Residues in contact with SER 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283E LYS* 5.6 1.4 + - - -
235F PRO* 3.2 9.4 - - - +
236F ALA* 1.3 79.4 - - - +
238F ARG* 1.3 59.3 + - - +
240F VAL* 3.4 5.4 + - - +
241F GLN* 3.1 21.7 + - - +
277F VAL* 3.8 19.0 - - - +
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Residues in contact with ARG 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F SER 3.3 17.2 + - - -
71F SER* 2.8 33.7 + - - -
72F TYR 4.3 3.4 + - - +
73F LEU* 3.3 30.7 - - + +
229F ALA 4.5 1.2 + - - -
230F SER* 2.8 40.9 + - - +
234F GLU* 3.2 38.8 + - + +
235F PRO* 3.4 22.4 + - + +
236F ALA 3.3 0.4 - - - -
237F SER* 1.3 74.6 - - - +
239F HIS* 1.3 62.5 + - - +
241F GLN* 4.3 7.2 - - + -
242F VAL* 2.8 44.3 + - + +
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Residues in contact with HIS 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298E LYS* 5.9 0.4 + - - -
209F ILE* 3.5 38.7 - - + +
210F ASP* 4.3 15.7 + - + -
230F SER* 3.0 26.5 + - - -
231F THR 3.1 27.0 + - - -
234F GLU* 3.0 25.6 + - + +
235F PRO 3.2 9.8 + - - -
236F ALA* 3.2 18.7 + - + +
238F ARG* 1.3 77.0 - - - +
240F VAL* 1.3 61.3 + - - +
242F VAL* 4.8 0.4 - - - -
243F ALA* 3.1 24.3 + - - +
269F ARG 5.7 0.4 - - - -
270F LEU* 3.8 4.8 - - + +
273F ALA* 4.1 11.2 - - + -
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Residues in contact with VAL 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236F ALA 3.0 14.4 + - - +
237F SER* 3.7 8.1 - - - +
239F HIS* 1.3 76.1 - - - +
241F GLN* 1.3 64.7 + - - +
243F ALA* 3.4 2.4 + - - +
244F GLU* 3.0 28.9 + - + +
270F LEU* 4.5 5.4 - - - -
273F ALA* 3.9 19.7 - - + +
274F TYR* 3.5 34.9 + - + +
277F VAL* 3.9 26.9 - - + -
296F ARG* 5.2 3.1 - - - +
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Residues in contact with GLN 241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F GLU* 3.0 47.0 + - - +
72F TYR 5.6 4.0 - - - +
93F THR* 5.6 1.8 - - - +
237F SER 3.1 17.0 + - - +
238F ARG* 3.1 8.7 + - + +
240F VAL* 1.3 78.2 - - - +
242F VAL* 1.3 60.2 + - + +
244F GLU* 3.1 12.9 + - - +
245F MET* 2.9 49.6 + - + +
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Residues in contact with VAL 242 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F SER 3.6 19.7 - - - +
72F TYR* 3.9 16.8 - - + +
207F LEU* 3.9 20.9 - - + -
209F ILE* 4.8 6.3 - - + -
228F VAL* 3.9 21.8 - - + +
229F ALA 5.6 0.2 - - - -
230F SER* 4.8 6.3 - - - -
238F ARG* 2.8 42.5 + - + +
239F HIS* 4.2 4.3 - - - +
241F GLN* 1.3 72.4 - - + +
243F ALA* 1.3 64.4 + - - +
245F MET* 3.2 8.6 + - - +
246F VAL* 3.1 22.7 + - + +
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Residues in contact with ALA 243 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207F LEU* 4.1 19.2 - - + +
209F ILE* 5.5 1.6 - - + -
239F HIS 3.1 19.9 + - - +
240F VAL 3.7 4.5 - - - +
241F GLN 3.3 0.2 - - - -
242F VAL* 1.3 76.6 - - - +
244F GLU* 1.3 61.9 + - - +
246F VAL* 3.5 1.6 + - - +
247F ILE* 3.3 16.8 + - - +
270F LEU* 3.7 33.2 - - + -
274F TYR* 4.6 4.7 - - - +
300F PHE* 3.3 18.2 - - + -
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Residues in contact with GLU 244 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F THR* 6.1 0.7 - - + -
240F VAL* 3.0 23.2 + - + +
241F GLN* 3.1 17.5 + - - +
243F ALA* 1.3 75.8 - - - +
245F MET* 1.3 59.4 + - - +
247F ILE* 3.3 16.0 - - - +
248F GLU* 2.9 43.9 + - + +
274F TYR* 3.7 16.0 + - - +
296F ARG* 2.4 37.1 + - - +
300F PHE* 4.7 4.2 - - - +
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Residues in contact with MET 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F VAL* 3.7 30.5 - - + +
55F LEU 3.3 22.7 - - - +
56F GLU* 3.7 23.3 - - + +
66F ARG* 4.1 9.4 - - + -
72F TYR* 3.6 31.5 - - + +
93F THR* 3.9 14.1 - - + -
241F GLN* 2.9 45.7 + - + +
242F VAL* 3.2 4.2 + - - +
244F GLU* 1.3 76.8 - - - +
246F VAL* 1.3 61.6 + - - +
248F GLU* 4.3 2.1 - - - +
249F LYS* 3.1 26.0 + - - +
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Residues in contact with VAL 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F TYR* 4.3 9.6 - - + -
205F MET* 3.8 37.3 - - + +
207F LEU* 3.8 32.1 - - + -
228F VAL* 4.8 3.6 - - + -
242F VAL* 3.1 18.9 + - + +
243F ALA 3.8 4.7 - - - +
244F GLU 3.2 0.4 - - - -
245F MET* 1.3 76.5 - - - +
247F ILE* 1.3 61.0 + - - +
249F LYS* 3.4 2.1 + - - +
250F ALA* 2.9 28.1 + - - +
262F ILE* 4.2 30.1 - - + -
300F PHE* 5.4 0.9 - - + -
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Residues in contact with ILE 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243F ALA 3.3 11.0 + - - +
244F GLU* 3.3 29.6 - - - +
246F VAL* 1.3 79.1 - - - +
248F GLU* 1.3 66.8 + - + +
250F ALA* 4.2 1.6 - - - -
251F LYS* 2.9 47.7 + - - +
262F ILE* 4.0 14.1 - - + -
300F PHE* 3.5 31.4 - - + +
303F ALA* 3.7 26.9 - - + -
313F LEU* 3.9 17.9 - - + -
315F ILE* 4.6 0.9 - - + -
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Residues in contact with GLU 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F THR* 3.2 41.7 - - + +
244F GLU* 2.9 28.2 + - + +
245F MET 4.3 1.6 - - - +
247F ILE* 1.3 78.8 - - + +
249F LYS* 1.3 64.9 + - - +
251F LYS* 3.4 16.8 + - - +
252F ARG* 2.9 59.3 + - - +
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Residues in contact with LYS 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F VAL* 4.0 16.0 - - + +
68F ALA* 5.5 2.8 - - - +
72F TYR* 3.3 27.9 + - - +
94F GLY* 3.9 22.7 - - - +
96F THR* 4.3 13.2 - - - +
121F PHE* 5.5 9.5 - - - -
203F VAL* 5.6 3.0 - - - +
205F MET* 4.6 15.7 - - + +
226F GLU* 3.5 24.5 + - - -
245F MET 3.1 19.9 + - - +
246F VAL 3.8 3.6 - - - +
248F GLU* 1.3 76.3 - - - +
250F ALA* 1.3 62.1 + - - +
252F ARG* 3.5 2.3 + - - +
253F LEU* 3.1 44.1 + - + +
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Residues in contact with ALA 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205F MET* 5.6 2.0 - - - -
246F VAL* 2.9 18.4 + - + +
247F ILE* 3.7 5.4 - - + +
248F GLU 3.2 0.2 - - - -
249F LYS* 1.3 75.4 - - - +
251F LYS* 1.3 64.8 + - - +
253F LEU* 3.3 3.8 + - - +
254F VAL* 3.0 29.2 + - - +
260F VAL* 3.7 26.3 - - + +
262F ILE* 3.7 24.7 - - + -
313F LEU* 3.7 8.5 - - + -
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Residues in contact with LYS 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F PHE* 4.2 30.7 - - + -
134F GLU* 5.4 6.6 + - - +
247F ILE* 2.9 46.1 + - + +
248F GLU* 3.9 15.4 + - - +
249F LYS 3.4 0.2 - - - -
250F ALA* 1.3 75.4 - - - +
252F ARG* 1.3 82.2 + - - +
254F VAL* 3.4 8.6 + - - +
255F GLU* 3.0 32.2 + - - +
299F ARG* 5.2 15.8 + - - +
303F ALA* 3.7 18.7 - - - +
313F LEU* 4.7 4.3 - - + -
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Residues in contact with ARG 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F ARG* 3.1 38.1 - - - +
93F THR 3.4 12.5 + - - +
94F GLY 4.1 9.2 - - - +
95F ASP* 3.3 26.9 - - - +
120F ASN* 4.3 13.0 - - - +
130F LYS* 4.1 5.4 - - - +
133F PHE* 4.5 3.4 - - - +
134F GLU* 5.0 6.1 + - - -
248F GLU* 2.9 44.8 + - - +
249F LYS 3.9 4.5 - - - +
250F ALA 3.3 0.2 - - - -
251F LYS* 1.3 99.2 - - - +
253F LEU* 1.3 58.7 + - + +
255F GLU* 2.8 39.8 + - - +
256F HIS* 2.9 34.8 + - - -
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Residues in contact with LEU 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96F THR* 6.1 1.3 - - - +
120F ASN* 4.8 25.4 - - + +
121F PHE* 5.2 10.5 - - + -
203F VAL* 4.2 24.5 - - + -
205F MET* 5.8 1.1 - - - -
249F LYS* 3.1 37.0 + - + +
250F ALA* 3.3 0.9 + - - +
252F ARG* 1.3 74.3 - - + +
254F VAL* 1.3 61.1 + - - +
256F HIS* 3.0 18.2 + - + +
257F LYS 3.1 0.7 + - - -
258F LYS* 2.9 40.0 + - + +
260F VAL* 3.6 29.8 - - + -
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Residues in contact with VAL 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F PHE* 3.7 26.2 - - + -
136F LEU* 4.2 3.2 - - + +
250F ALA 3.0 17.7 + - - +
251F LYS* 3.7 5.6 - - - +
252F ARG 3.3 0.2 - - - -
253F LEU* 1.3 75.0 - - - +
255F GLU* 1.3 58.3 + - - +
257F LYS* 3.0 14.7 + - - +
258F LYS 3.7 9.0 - - - +
260F VAL* 4.5 5.2 - - + -
307F VAL* 3.7 23.3 - - + -
310F GLY 3.5 12.0 - - - +
311F GLY 4.4 0.2 - - - -
312F SER 3.5 33.4 - - - +
313F LEU* 3.8 17.7 - - + -
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Residues in contact with GLU 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F ARG* 2.9 22.5 + - - -
130F LYS* 3.1 28.9 + - - +
131F ILE* 3.4 23.6 + - - +
132F LEU* 3.3 1.3 - - - +
133F PHE* 2.5 41.6 + - + +
134F GLU* 4.7 0.2 - - - +
136F LEU* 4.6 6.7 - - + -
251F LYS 3.0 15.5 + - - +
252F ARG* 2.8 35.7 + - - +
254F VAL* 1.3 75.9 - - - +
256F HIS* 1.3 59.1 + - - +
257F LYS* 3.2 14.1 + - - +
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Residues in contact with HIS 256 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119F VAL 4.6 3.8 - - - -
120F ASN* 3.1 39.5 + - + +
122F ASP* 4.1 19.8 + - + +
126F ASN 4.4 4.7 + - - -
127F ALA* 3.7 35.1 - - + +
130F LYS* 3.1 26.4 + - + -
252F ARG 2.9 26.0 + - - +
253F LEU* 3.0 14.9 + - + +
255F GLU* 1.3 73.9 - - - +
257F LYS* 1.3 73.7 + - - +
258F LYS* 3.7 15.7 + - + +
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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