Contacts of the helix formed by residues 280 - 301 (chain F) in PDB entry 6VVT
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 LYS 280 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179F LEU 4.9 3.7 + - - -
180F ASN* 4.3 4.4 - - - +
181F ALA* 3.7 41.1 - - + +
184F GLU* 3.9 15.5 - - - +
273F PHE* 4.4 1.2 - - - -
278F GLY 3.9 1.0 + - - -
279F TYR* 1.3 74.7 - - - +
281F PHE* 1.3 68.0 - - - +
282F SER* 4.1 2.5 - - - +
283F THR* 3.0 19.1 + - - +
284F TYR* 3.9 1.7 + - - +
29O A 2.7 38.4 + - - +
30O C 2.7 47.6 + - - +
31O T 4.9 4.4 - - + +
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Residues in contact with PHE 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184F GLU* 3.2 35.2 + - + +
233F LEU* 4.4 11.2 - - + -
237F ASN* 3.4 45.5 - - + -
266F LEU* 4.1 5.2 - - + -
269F ALA* 4.4 5.4 - - + -
270F VAL* 3.8 31.4 - - + -
273F PHE* 3.4 51.4 - + + -
279F TYR 3.5 1.2 + - - -
280F LYS* 1.3 71.7 - - - +
282F SER* 1.3 65.7 + - - +
283F THR 2.9 1.2 + - - -
284F TYR* 3.0 4.9 + + - +
285F ALA* 3.0 43.4 + - + -
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Residues in contact with SER 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240F LEU* 4.0 20.0 - - - -
280F LYS* 4.1 1.2 - - - +
281F PHE* 1.3 80.3 - - - +
283F THR* 1.3 61.6 + - - +
285F ALA* 4.4 0.2 - - - -
286F THR* 2.9 30.8 + - - -
29O A 3.5 6.2 - - - +
30O C 2.6 42.4 + - - -
31O T 3.5 30.5 + - - -
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Residues in contact with THR 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279F TYR* 4.7 2.0 - - + -
280F LYS 3.0 11.5 + - - -
281F PHE 2.9 0.8 + - - -
282F SER* 1.3 82.5 + - - +
284F TYR* 1.3 60.8 + - - +
286F THR* 3.9 8.0 + - - -
287F TRP* 3.9 14.7 - - - -
27O A 3.8 19.3 - - - +
28O T 3.8 30.3 - - - +
29O A 2.9 50.4 + - + +
30O C 4.0 12.5 + - - -
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Residues in contact with TYR 284 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269F ALA* 3.8 21.8 - - + -
272F LYS* 2.9 22.9 - - + +
273F PHE* 3.9 22.0 - + + -
280F LYS 3.9 0.6 + - - -
281F PHE* 3.0 6.4 + + - +
283F THR* 1.3 78.2 - - - +
285F ALA* 1.3 65.1 + - - +
286F THR 3.6 0.2 + - - -
287F TRP* 3.7 18.6 + + + +
288F TRP* 2.7 40.6 + + - -
26O T 2.8 27.6 + + + -
27O A 3.2 73.4 - + + +
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Residues in contact with ALA 285 (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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240F LEU* 4.0 15.0 - - + -
266F LEU* 4.7 0.7 - - + -
269F ALA* 3.9 14.8 - - + -
281F PHE* 3.0 46.4 + - + +
284F TYR* 1.3 77.8 - - - +
286F THR* 1.3 65.1 + - - +
287F TRP 3.2 0.2 + - - -
288F TRP* 3.2 2.1 + - - +
289F ILE* 2.9 36.4 + - + +
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Residues in contact with THR 286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240F LEU* 4.1 14.8 - - - +
244F LEU* 3.9 29.7 - - + +
282F SER 2.9 21.9 + - - -
283F THR 4.1 2.2 - - - -
284F TYR 3.4 0.4 - - - -
285F ALA* 1.3 77.6 - - - +
287F TRP* 1.3 58.0 + - + +
290F ARG* 2.8 40.1 + - + +
30O C 3.3 38.0 - - + +
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Residues in contact with TRP 287 (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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283F THR 3.9 15.3 - - - -
284F TYR* 3.7 12.9 + + + +
285F ALA 3.2 0.8 - - - -
286F THR* 1.3 80.0 - - + +
288F TRP* 1.3 59.6 + - + +
290F ARG* 3.6 26.3 + - - +
291F GLN* 2.8 30.8 + - - +
26O T 3.3 73.0 - + + +
27O A 3.5 30.0 - - - -
28O T 4.8 4.0 + - - -
30O C 5.7 4.0 - - - +
1P A 4.6 5.6 - + - -
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Residues in contact with TRP 288 (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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265F GLY* 3.6 19.0 - - - +
268F ARG* 3.4 27.8 - - + -
269F ALA* 3.8 16.2 - - + +
272F LYS* 4.3 4.1 - - + +
284F TYR* 2.7 49.3 + + - -
285F ALA 3.2 6.0 + - - +
287F TRP* 1.3 79.5 - - + +
289F ILE* 1.3 54.0 + - - +
291F GLN* 3.3 16.7 + - + +
292F ALA* 2.7 38.3 + - - +
24O G 3.7 4.9 - + + -
25O C 3.2 81.4 - + + -
26O T 3.5 17.7 + - + +
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Residues in contact with ILE 289 (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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240F LEU* 4.1 28.0 - - + -
241F VAL* 3.6 35.7 - - + -
244F LEU* 3.5 24.2 - - + -
262F GLY* 4.0 20.6 - - - +
265F GLY* 4.5 0.2 - - - -
266F LEU* 3.7 34.3 - - + +
285F ALA* 2.9 22.3 + - + +
288F TRP* 1.3 75.4 - - - +
290F ARG* 1.3 63.1 + - - +
292F ALA* 3.4 2.3 + - - +
293F ILE* 3.2 26.2 + - + +
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Residues in contact with ARG 290 (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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244F LEU* 4.3 8.7 - - + +
248F TYR* 3.6 23.7 + - + +
286F THR* 2.8 32.2 + - + +
287F TRP* 4.1 19.0 - - - +
289F ILE* 1.3 74.4 - - - +
291F GLN* 1.3 68.8 + - - +
293F ILE* 3.2 8.1 + - - +
294F THR* 3.1 45.6 + - - +
26O T 3.7 12.1 + - - +
1P A 3.2 57.7 + - - +
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Residues in contact with GLN 291 (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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287F TRP 2.8 15.6 + - - +
288F TRP* 3.5 21.3 - - + +
290F ARG* 1.3 82.3 - - - +
292F ALA* 1.3 67.7 + - - +
294F THR* 3.6 7.9 + - - -
295F ARG* 2.9 51.3 + - - +
24O G 5.2 1.8 + - - -
25O C 2.6 36.0 + - - +
26O T 3.0 35.7 - - + +
1P A 4.0 2.2 + - - +
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Residues in contact with ALA 292 (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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261F GLU* 3.4 20.7 - - - +
264F LEU* 5.3 0.9 - - + -
265F GLY* 3.4 26.7 - - - +
288F TRP* 2.7 22.7 + - + +
289F ILE* 3.7 5.6 - - - +
290F ARG 3.2 0.4 - - - -
291F GLN* 1.3 85.1 - - - +
293F ILE* 1.3 60.0 + - - +
295F ARG* 4.2 1.3 - - - +
296F ALA* 3.1 23.4 + - - +
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Residues in contact with ILE 293 (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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241F VAL 4.8 0.7 - - - +
244F LEU* 4.3 7.9 - - + +
245F ALA* 3.9 31.2 - - + +
248F TYR* 3.9 26.2 - - + -
258F LEU* 3.5 49.4 - - + +
261F GLU* 4.7 2.0 - - - -
262F GLY* 3.9 13.5 - - - +
289F ILE* 3.2 20.1 + - + +
290F ARG* 3.2 8.2 + - - +
292F ALA* 1.3 73.6 - - - +
294F THR* 1.3 66.4 + - - +
296F ALA* 3.0 8.3 + - - +
297F MET* 3.0 26.1 + - + +
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Residues in contact with THR 294 (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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248F TYR* 3.9 27.6 - - + +
290F ARG* 3.1 34.9 + - - +
291F GLN* 3.1 14.9 + - - -
293F ILE* 1.3 75.8 - - - +
295F ARG* 1.3 72.2 + - - +
297F MET* 3.0 22.1 + - - +
298F ALA* 3.2 12.5 + - - +
1P A 4.3 12.9 + - + +
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Residues in contact with ARG 295 (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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291F GLN* 2.9 35.0 + - - +
292F ALA* 4.2 2.5 - - - +
294F THR* 1.3 79.7 + - - +
296F ALA* 1.3 62.5 + - - +
298F ALA* 3.5 4.4 + - - +
299F ASP* 3.3 31.0 + - - +
308F VAL* 3.6 30.1 - - - +
23O T 3.3 29.5 + - - +
24O G 2.5 49.1 + - - -
25O C 3.0 11.0 - - - +
2P G 3.0 17.0 + - - -
3P C 4.5 0.6 - - - +
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Residues in contact with ALA 296 (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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253F MET* 3.4 16.4 - - + +
258F LEU* 5.9 0.2 - - + -
261F GLU* 3.5 36.3 - - + +
292F ALA 3.1 16.4 + - - +
293F ILE* 3.0 11.5 + - - +
295F ARG* 1.3 78.4 - - - +
297F MET* 1.3 63.8 + - - +
299F ASP* 2.9 7.2 + - - -
300F GLN* 2.9 24.7 + - - +
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Residues in contact with MET 297 (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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248F TYR* 4.0 38.1 - - - +
251F ARG* 3.2 50.3 - - + +
253F MET* 3.7 29.8 - - + -
258F LEU* 4.2 3.8 - - + -
293F ILE 3.0 15.2 + - - +
294F THR* 3.0 10.0 + - - +
296F ALA* 1.3 75.0 - - - +
298F ALA* 1.3 60.0 + - - +
301F ALA* 2.9 37.4 + - + +
302F ARG* 4.5 1.6 + - - +
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Residues in contact with ALA 298 (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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294F THR 3.2 10.9 + - - +
295F ARG* 3.9 10.1 - - - +
296F ALA 3.3 0.2 - - - -
297F MET* 1.3 76.2 - - - +
299F ASP* 1.3 61.0 + - - +
302F ARG* 5.9 2.7 - - - +
305F ARG* 4.5 2.6 - - - +
306F ILE 3.1 23.2 + - - +
308F VAL* 4.2 18.6 - - + -
311F VAL* 3.8 37.6 - - + +
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Residues in contact with ASP 299 (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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31D PRO* 5.9 2.8 - - - +
345D ARG* 5.4 0.9 + - - -
295F ARG* 3.3 31.4 + - - +
296F ALA* 2.9 7.3 + - - +
298F ALA* 1.3 80.2 - - - +
300F GLN* 1.3 68.6 + - + +
305F ARG* 3.6 39.4 + - - +
306F ILE 4.9 0.2 - - - +
308F VAL* 3.3 22.2 + - - +
23O T 4.8 9.8 + - - +
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Residues in contact with GLN 300 (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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31D PRO* 6.1 0.7 - - + -
345D ARG* 2.7 40.4 + - - +
349D ASN* 3.5 36.5 + - - +
353D ARG* 3.6 14.2 + - - +
356D ARG* 6.2 0.2 - - - +
253F MET* 3.3 28.2 - - + +
257F ASP* 5.4 1.0 - - - +
261F GLU* 3.3 27.5 + - - -
296F ALA* 2.9 11.3 + - - +
297F MET 3.4 0.2 + - - -
298F ALA 3.6 0.2 - - - -
299F ASP* 1.3 90.4 - - + +
301F ALA* 1.3 55.7 + - - +
302F ARG 3.2 4.5 - - - +
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Residues in contact with ALA 301 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345D ARG* 3.8 5.7 + - - -
251F ARG 4.3 14.8 - - - +
252F GLY* 3.9 27.9 - - - +
253F MET* 4.5 3.8 - - + +
297F MET* 2.9 32.7 + - + +
300F GLN* 1.3 78.5 - - - +
302F ARG* 1.3 63.2 + - + +
303F THR 3.9 1.0 + - - -
357F GLU* 4.7 4.8 - - - +
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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