Contacts of the helix formed by residues 309 - 333 (chain F) in PDB entry 4NFI
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 ASP 309 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306F GLU 3.1 15.2 + - - +
307F GLU 3.3 2.8 - - - +
308F LEU* 1.3 78.5 - - - +
310F LEU* 1.3 66.8 + - - +
311F PRO* 3.3 5.6 - - - -
312F ALA* 3.2 28.6 + - - +
313F VAL* 3.0 24.7 + - + +
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Residues in contact with LEU 310 (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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245F TYR* 5.1 1.1 - - - -
249F PHE* 5.2 0.2 - - + -
269F TRP* 4.6 2.9 - - + -
270F LEU* 3.5 42.6 - - + +
273F GLN* 3.9 18.2 - - + -
274F CYS* 3.9 9.0 - - + +
277F ARG* 3.9 23.1 - - - +
305F TYR* 3.1 43.1 + - + +
308F LEU* 3.7 16.4 - - + +
309F ASP* 1.3 78.1 - - - +
311F PRO* 1.4 63.9 - - + +
313F VAL* 3.2 7.5 + - + +
314F PHE* 2.8 30.5 + - - +
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Residues in contact with PRO 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245F TYR* 3.9 23.2 + - + +
249F PHE* 4.1 34.1 - - + -
305F TYR 4.0 7.6 - - - +
306F GLU* 4.5 8.7 - - + -
309F ASP* 3.5 5.2 - - - +
310F LEU* 1.4 92.7 - - + +
312F ALA* 1.3 55.8 + - - +
314F PHE* 3.4 3.5 + - - +
315F LEU* 3.0 35.7 + - + +
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Residues in contact with ALA 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309F ASP* 3.2 35.4 + - - +
311F PRO* 1.3 75.0 - - - +
313F VAL* 1.3 65.8 + - + +
315F LEU* 3.3 12.1 + - - +
316F GLN* 3.1 23.2 + - - +
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Residues in contact with VAL 313 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269F TRP* 3.8 18.4 - - + -
273F GLN* 4.3 7.4 - - + +
277F ARG* 3.6 43.5 - - - +
308F LEU 4.6 1.6 - - - +
309F ASP* 3.0 24.5 + - + +
310F LEU* 3.5 12.8 - - + +
312F ALA* 1.3 77.7 - - + +
314F PHE* 1.3 57.1 + - - +
316F GLN* 3.4 6.7 + - - +
317F TYR* 2.9 27.9 + - + +
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Residues in contact with PHE 314 (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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238F PHE* 4.2 9.4 - + - -
241F ILE* 4.0 15.3 - - + -
242F GLN* 3.8 39.7 - - + -
245F TYR* 3.7 50.9 - + + -
269F TRP* 3.7 22.4 - + + -
310F LEU 2.8 16.7 + - - +
311F PRO 3.5 7.2 - - - +
313F VAL* 1.3 74.1 - - - +
315F LEU* 1.3 68.9 + - + +
317F TYR* 3.1 3.7 + + - -
318F GLU* 2.8 57.4 + - + +
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Residues in contact with LEU 315 (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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245F TYR* 5.0 8.1 - - + +
311F PRO* 3.0 21.5 + - + +
312F ALA* 3.3 14.3 + - - +
314F PHE* 1.3 91.0 - - + +
316F GLN* 1.3 60.5 + - - +
318F GLU* 3.4 17.9 + - - +
319F GLU* 3.3 20.3 + - - +
350F LYS* 5.4 7.7 + - - +
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Residues in contact with GLN 316 (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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312F ALA 3.1 16.4 + - - +
313F VAL* 3.6 7.2 - - - +
315F LEU* 1.3 74.3 - - - +
317F TYR* 1.3 66.4 + - - +
319F GLU* 3.3 25.3 + - - +
320F ASP* 3.0 58.3 + - - +
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Residues in contact with TYR 317 (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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234F GLU 5.5 0.2 + - - -
237F GLU* 4.3 8.9 + - - +
238F PHE* 3.2 42.0 + + - -
241F ILE* 2.9 48.2 - - + +
269F TRP* 4.1 22.0 - + + -
313F VAL* 2.9 18.2 + - + +
314F PHE* 3.1 6.9 + + - +
316F GLN* 1.3 77.6 - - - +
318F GLU* 1.3 59.8 + - - +
320F ASP* 3.4 8.6 + - + +
321F SER* 2.8 42.6 + - - -
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Residues in contact with GLU 318 (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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238F PHE* 3.6 37.7 - - + -
242F GLN* 3.8 8.7 + - - -
314F PHE* 2.8 34.9 + - + +
315F LEU* 3.7 15.7 - - - +
316F GLN 3.2 0.2 - - - -
317F TYR* 1.3 77.2 - - - +
319F GLU* 1.3 55.5 + - - +
322F TYR* 3.0 29.8 + - - +
349F TYR* 3.7 8.9 - - + -
350F LYS* 3.2 54.4 + - + +
351F ARG 4.5 1.6 - - - +
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Residues in contact with GLU 319 (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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315F LEU 3.3 9.3 + - - +
316F GLN* 3.3 31.1 + - - +
318F GLU* 1.3 79.1 - - - +
320F ASP* 1.3 66.5 + - - +
322F TYR* 3.4 6.1 + - - +
323F SER* 3.1 29.3 + - - +
350F LYS* 5.9 4.1 - - - +
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Residues in contact with ASP 320 (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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316F GLN* 3.0 44.1 + - - +
317F TYR* 4.0 7.3 - - + +
319F GLU* 1.3 76.9 - - - +
321F SER* 1.3 65.9 + - - +
323F SER* 3.4 7.7 + - - -
324F HIS* 3.0 23.1 + - - +
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Residues in contact with SER 321 (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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234F GLU 5.2 0.3 + - - -
238F PHE* 3.5 25.5 - - - +
317F TYR* 2.8 35.3 + - - -
318F GLU 3.9 0.4 - - - -
320F ASP* 1.3 74.1 - - - +
322F TYR* 1.3 67.2 + - - +
324F HIS* 3.1 8.3 + - - +
325F ILE* 2.9 29.1 + - - +
349F TYR* 2.7 23.5 + - - -
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Residues in contact with TYR 322 (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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318F GLU 3.0 19.7 + - - +
319F GLU* 3.5 7.6 - - - +
321F SER* 1.3 77.4 + - - +
323F SER* 1.3 67.4 + - - +
325F ILE* 3.3 1.7 + - - +
326F MET* 3.0 67.6 + - + +
345F ALA* 4.7 3.8 - - + -
346F ARG* 5.4 3.2 - - - -
349F TYR* 3.5 47.2 - + + -
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Residues in contact with SER 323 (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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319F GLU* 3.1 15.4 + - - +
320F ASP* 3.5 11.9 - - - -
322F TYR* 1.3 83.8 - - - +
324F HIS* 1.3 57.9 + - - +
326F MET* 3.4 7.2 + - - +
327F ALA* 2.9 27.9 + - - +
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Residues in contact with HIS 324 (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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234F GLU* 3.5 26.5 + - - -
320F ASP 3.0 13.9 + - - +
321F SER* 3.4 11.0 - - - +
323F SER* 1.3 72.5 - - - +
325F ILE* 1.3 73.3 + - + +
327F ALA* 3.2 10.8 + - + +
328F LEU* 3.0 51.3 + - + +
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Residues in contact with ILE 325 (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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231F ILE* 4.7 4.0 - - + +
234F GLU* 3.5 44.4 - - + +
235F MET* 3.7 35.9 - - + +
321F SER* 2.9 15.9 + - - +
322F TYR* 3.6 5.4 - - - +
324F HIS* 1.3 83.9 - - + +
326F MET* 1.3 60.2 + - + +
328F LEU* 3.1 11.7 + - + +
329F ILE* 2.9 33.7 + - + +
345F ALA* 4.7 7.6 - - + -
349F TYR* 3.1 29.2 - - + +
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Residues in contact with MET 326 (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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322F TYR* 3.0 68.3 + - + +
323F SER* 3.7 5.6 - - - +
324F HIS 3.2 0.2 - - - -
325F ILE* 1.3 76.3 - - + +
327F ALA* 1.3 62.3 - - - +
329F ILE* 3.3 13.0 + - + +
330F GLU* 3.1 31.0 + - - +
342F LEU* 3.6 31.4 - - + +
345F ALA* 3.3 28.7 - - + -
346F ARG 5.2 0.2 - - - +
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Residues in contact with ALA 327 (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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323F SER 2.9 14.9 + - - +
324F HIS* 3.2 15.0 + - - +
326F MET* 1.3 76.6 - - - +
328F LEU* 1.3 57.1 + - + +
330F GLU* 3.3 17.9 + - - +
331F GLN* 2.9 28.2 + - - +
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Residues in contact with LEU 328 (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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230F LYS* 3.6 10.3 - - + +
231F ILE* 3.7 16.1 - - + +
234F GLU* 3.5 37.5 - - + -
324F HIS* 3.0 42.1 + - + +
325F ILE* 3.1 11.4 + - + +
327F ALA* 1.3 76.8 - - + +
329F ILE* 1.3 52.6 + - - +
331F GLN* 3.0 9.4 + - - +
332F TYR* 2.7 62.4 + - + +
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Residues in contact with ILE 329 (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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231F ILE* 3.9 16.2 - - + -
235F MET* 4.3 2.2 - - + -
325F ILE* 2.9 28.1 + - + +
326F MET* 3.3 30.0 + - + +
328F LEU* 1.3 72.4 - - - +
330F GLU* 1.3 67.1 + - + +
333F ALA* 3.0 42.2 + - + +
338F PRO* 4.3 18.2 - - + +
341F PHE* 3.6 42.4 - - + +
342F LEU* 4.1 9.6 - - + -
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Residues in contact with GLU 330 (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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326F MET* 3.1 24.1 + - - +
327F ALA* 3.3 16.2 + - - +
329F ILE* 1.3 76.9 - - + +
331F GLN* 1.3 63.3 + - - +
333F ALA 4.7 0.9 + - - -
334F ALA 5.6 0.9 + - - -
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Residues in contact with GLN 331 (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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327F ALA 2.9 17.6 + - - +
328F LEU* 3.0 13.7 + - - +
330F GLU* 1.3 79.5 - - - +
332F TYR* 1.3 102.8 + - + +
333F ALA 3.8 0.2 - - - -
334F ALA* 5.3 2.0 + - - +
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Residues in contact with TYR 332 (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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227F ASN* 3.4 60.4 - - + +
228F ALA 4.9 0.3 + - - -
230F LYS* 3.7 47.1 - - + -
231F ILE* 3.7 10.1 - - + +
328F LEU* 2.7 38.0 + - + +
331F GLN* 1.3 118.4 + - + +
333F ALA* 1.3 65.5 + - - +
334F ALA 3.4 7.6 + - - +
341F PHE* 5.2 1.0 - - - -
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Residues in contact with ALA 333 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231F ILE* 3.9 1.4 - - - +
329F ILE* 3.0 28.4 + - + +
330F GLU 4.7 0.4 + - - -
331F GLN 3.8 0.6 - - - -
332F TYR* 1.3 77.6 - - - +
334F ALA* 1.3 62.5 + - - +
336F LEU* 2.8 40.9 + - - +
338F PRO* 4.3 14.4 - - + -
341F PHE* 3.9 29.9 - - + -
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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
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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