Contacts of the helix formed by residues 332 - 355 (chain F) in PDB entry 4E2I
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 ASN 332 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339E GLN* 4.1 0.4 - - - +
270F TRP* 5.1 6.7 - - + -
330F SER* 3.2 9.9 + - - +
331F LYS* 1.3 93.9 - - - +
333F GLN* 1.3 63.2 + - - +
334F LYS 3.2 2.9 - - - +
335F THR* 3.6 28.2 + - + +
336F ILE* 3.0 29.7 + - + +
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Residues in contact with GLN 333 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E THR* 5.3 7.3 + - - +
339E GLN* 3.2 32.1 - - + +
343E THR* 3.5 23.4 + - - +
289F LEU* 3.2 28.5 - - + +
293F LEU* 3.8 25.0 - - - +
327F PHE* 3.3 38.5 - - + +
328F ALA* 3.0 28.8 - - - +
330F SER* 3.6 7.2 - - - +
332F ASN* 1.3 76.9 - - - +
334F LYS* 1.3 59.5 - - - +
337F CYS* 3.6 10.0 + - - -
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Residues in contact with LYS 334 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338E GLN* 5.3 3.0 + - - +
339E GLN* 4.9 5.2 - - + +
342E ASP* 3.9 36.5 + - + +
512E LYS* 4.6 12.3 - - - +
514E LEU* 5.5 4.5 - - - +
516E LYS* 4.5 19.1 - - - +
285F VAL* 4.2 24.6 - - + +
286F LEU* 4.6 7.4 - - + -
289F LEU* 4.6 16.6 - - + -
332F ASN* 3.2 0.6 - - - +
333F GLN* 1.3 78.3 - - - +
335F THR* 1.3 61.0 + - - +
337F CYS* 4.3 2.0 - - - -
338F GLN* 3.0 33.7 + - + +
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Residues in contact with THR 335 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A LYS 5.5 1.6 - - - +
270F TRP* 3.6 22.8 - - + -
332F ASN* 3.1 31.3 + - + +
334F LYS* 1.3 77.9 - - - +
336F ILE* 1.3 64.9 + - - +
338F GLN* 3.1 16.7 + - + +
339F GLN* 3.2 11.4 + - - +
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Residues in contact with ILE 336 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268F VAL* 3.9 20.6 - - + -
269F SER 4.6 0.7 - - - +
270F TRP* 3.6 45.9 - - + +
273F VAL* 3.6 33.3 - - + +
274F THR* 5.3 1.7 + - - -
327F PHE* 3.5 25.8 - - + -
330F SER* 3.3 26.0 - - - +
332F ASN* 3.0 13.3 + - + +
335F THR* 1.3 77.1 - - - +
337F CYS* 1.3 61.4 + - - +
338F GLN 3.4 0.2 + - - -
339F GLN* 3.6 4.9 + - - +
340F ALA* 3.5 16.3 + - - +
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Residues in contact with CYS 337 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273F VAL* 4.2 14.6 - - - -
285F VAL* 4.3 9.9 - - + +
288F LEU* 3.4 16.2 - - + +
289F LEU* 3.6 28.7 - - + -
292F TYR* 4.7 1.8 - - - -
327F PHE* 3.5 29.6 - - - -
333F GLN 3.6 10.1 + - - +
334F LYS* 4.3 3.1 - - - +
335F THR 3.3 0.2 - - - -
336F ILE* 1.3 77.2 - - - +
338F GLN* 1.3 65.9 + - - +
340F ALA* 3.3 9.4 + - - +
341F VAL* 3.0 27.9 + - - +
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Residues in contact with GLN 338 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A LYS* 5.2 4.5 + - - +
514E LEU* 4.9 11.4 - - - +
285F VAL* 3.3 38.1 - - + +
334F LYS* 3.0 27.2 + - + +
335F THR* 3.1 12.3 + - + +
337F CYS* 1.3 77.1 - - - +
339F GLN* 1.3 63.0 + - - +
341F VAL* 3.1 20.4 + - - +
342F ASP* 3.0 38.5 + - - +
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Residues in contact with GLN 339 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LEU* 6.2 0.4 - - + -
330A SER 3.0 21.6 + - - +
331A LYS 3.2 13.1 + - - +
332A ASN* 3.8 0.2 - - - +
333A GLN* 2.8 56.5 - - + +
334A LYS* 5.0 5.6 - - + +
270F TRP* 3.1 29.7 - - + +
274F THR* 4.2 7.5 + - - +
335F THR 3.2 8.6 + - - +
336F ILE 3.9 7.1 - - - +
337F CYS 3.4 0.2 - - - -
338F GLN* 1.3 77.4 - - - +
340F ALA* 1.3 60.5 + - - +
342F ASP* 3.2 14.4 + - + +
343F THR* 2.9 26.1 + - - +
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Residues in contact with ALA 340 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273F VAL* 4.1 4.5 - - + +
274F THR* 3.9 19.7 + - - +
277F ALA* 3.6 15.0 - - + +
288F LEU* 3.4 17.7 - - + -
336F ILE 3.5 10.2 + - - +
337F CYS* 3.3 11.8 + - - +
338F GLN 3.2 0.8 - - - -
339F GLN* 1.3 79.3 - - - +
341F VAL* 1.3 62.5 + - - +
343F THR* 3.0 11.2 + - - -
344F VAL* 2.9 26.2 + - - +
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Residues in contact with VAL 341 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282F CYS 4.3 0.7 - - - +
283F ASP* 3.4 29.8 - - - +
284F ASP 3.1 28.9 - - - +
285F VAL* 3.7 20.4 - - + -
288F LEU* 3.9 5.4 - - + +
337F CYS 3.0 17.3 - - - +
338F GLN* 3.1 10.1 + - - +
340F ALA* 1.3 77.2 - - - +
342F ASP* 1.3 58.5 + - - +
344F VAL* 3.0 12.0 + - - +
345F LEU* 2.9 38.6 + - + +
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Residues in contact with ASP 342 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A LEU* 3.7 25.2 - - + +
289A LEU* 4.0 14.3 - - + +
334A LYS* 3.7 32.8 + - + +
338F GLN* 3.0 35.5 + - - +
339F GLN* 3.2 12.5 + - + +
341F VAL* 1.3 77.1 - - - +
343F THR* 1.3 56.7 + - - +
345F LEU* 3.8 10.6 - - - +
346F ALA* 2.8 30.0 + - - +
516F LYS* 5.9 0.2 - - - -
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Residues in contact with THR 343 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LEU* 4.6 1.6 - - - +
293A LEU* 3.6 25.1 - - + -
333A GLN* 3.3 20.0 + - - +
274F THR* 3.6 23.9 - - + +
278F MET* 3.6 31.1 - - + +
339F GLN 2.9 14.6 + - - -
340F ALA 3.0 8.8 + - - -
342F ASP* 1.3 75.2 - - - +
344F VAL* 1.3 62.7 + - - +
346F ALA* 3.4 7.3 - - - +
347F LYS* 3.1 16.8 + - - +
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Residues in contact with VAL 344 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277F ALA* 3.7 28.7 - - + +
278F MET* 4.3 8.5 - - - +
281F LYS* 3.6 22.4 - - + +
282F CYS 3.2 24.5 - - - +
283F ASP* 3.9 4.5 - - + +
340F ALA 2.9 21.1 + - - +
341F VAL 3.2 7.2 - - - +
343F THR* 1.3 76.0 - - - +
345F LEU* 1.3 65.8 + - - +
347F LYS* 3.1 19.3 + - + +
348F LYS* 3.3 32.5 + - - +
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Residues in contact with LEU 345 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A LEU* 4.2 25.6 - - + -
283F ASP* 3.9 28.7 - - + +
341F VAL* 2.9 31.1 + - + +
342F ASP* 4.0 9.9 - - - +
344F VAL* 1.3 76.7 - - - +
346F ALA* 1.3 52.1 + - - +
348F LYS* 3.4 14.7 + - + +
349F ARG* 2.8 36.3 + - - +
466F ASP* 4.9 1.4 - - - +
511F LYS* 4.3 24.7 - - + +
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Residues in contact with ALA 346 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A LEU* 3.5 25.5 - - - +
289A LEU* 4.3 6.1 - - + -
290A GLY* 3.6 17.9 - - - +
293A LEU* 4.8 1.1 - - + -
342F ASP 2.8 20.6 + - - +
343F THR* 3.4 11.7 - - - +
344F VAL 3.1 0.2 - - - -
345F LEU* 1.3 75.0 - - - +
347F LYS* 1.3 64.9 + - - +
349F ARG* 3.1 5.1 + - - +
350F VAL* 3.0 29.5 + - - +
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Residues in contact with LYS 347 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A GLY* 5.5 1.1 - - - -
294A GLU* 4.3 20.0 + - + +
297A TYR* 5.9 1.8 + - - -
304A LYS* 5.5 5.7 - - - +
278F MET* 3.9 26.5 - - + +
343F THR 3.1 11.5 + - - +
344F VAL* 3.1 12.4 + - + +
346F ALA* 1.3 76.5 - - - +
348F LYS* 1.3 58.0 + - + +
350F VAL* 3.0 9.8 + - + +
351F ASP* 2.7 55.8 + - - +
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Residues in contact with LYS 348 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281F LYS* 3.7 23.7 + - - +
283F ASP* 4.4 12.2 - - + +
344F VAL* 3.3 36.6 + - - +
345F LEU* 3.8 16.8 - - + +
347F LYS* 1.3 78.0 - - + +
349F ARG* 1.3 63.7 + - - +
351F ASP* 4.0 8.5 - - - +
352F SER* 3.1 27.9 + - - -
466F ASP* 4.1 17.3 - - + +
467F GLN* 5.5 8.5 - - - +
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Residues in contact with ARG 349 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ASP* 4.4 1.1 + - - -
286A LEU* 3.1 37.1 - - - +
287A LEU* 3.5 39.3 - - + +
345F LEU* 2.8 15.5 + - - +
346F ALA* 3.1 17.7 + - - +
348F LYS* 1.3 76.6 - - - +
350F VAL* 1.3 57.3 + - - +
352F SER* 3.0 13.9 + - - -
353F LEU* 4.0 6.1 - - - +
465F ILE* 3.1 17.0 - - - +
466F ASP* 3.0 29.7 + - - -
511F LYS* 3.5 16.0 - - - +
516F LYS* 2.9 35.8 + - - +
517F ARG* 3.1 27.8 + - - +
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Residues in contact with VAL 350 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 4.4 8.1 - - + +
290A GLY* 3.8 7.4 - - - +
291A MET* 3.5 42.2 - - + +
294A GLU* 4.3 11.2 - - + +
346F ALA 3.0 15.4 + - - +
347F LYS* 3.0 10.5 + - + +
349F ARG* 1.3 76.8 - - + +
351F ASP* 1.3 64.0 + - - +
352F SER 3.1 1.8 - - - -
353F LEU* 2.9 22.4 + - + +
354F GLN* 3.1 42.9 + - + +
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Residues in contact with ASP 351 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347F LYS* 2.7 53.7 + - - +
348F LYS* 3.9 7.7 + - - +
350F VAL* 1.3 77.8 - - - +
352F SER* 1.3 57.0 + - - +
353F LEU 3.0 5.2 + - - -
354F GLN* 4.5 3.9 - - - +
355F LEU* 3.3 56.5 + - + +
360F MET* 4.0 8.3 - - + +
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Residues in contact with SER 352 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348F LYS 3.1 12.2 + - - -
349F ARG 3.0 19.2 + - - -
351F ASP* 1.3 75.9 - - - +
353F LEU* 1.3 64.6 + - - +
355F LEU 4.9 2.7 - - - -
360F MET* 4.2 19.8 - - - +
466F ASP* 3.1 38.2 + - - -
467F GLN 5.5 1.6 - - - -
517F ARG* 4.1 5.4 + - - -
519F GLN* 5.1 2.9 - - - -
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Residues in contact with LEU 353 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 3.8 31.0 - - + -
291A MET* 6.3 1.3 - - - -
310A GLN* 4.9 7.4 + - - +
349F ARG 4.0 4.0 - - - +
350F VAL* 2.9 6.4 + - + +
352F SER* 1.3 88.0 - - - +
354F GLN* 1.3 67.5 + - + +
355F LEU 4.6 2.1 - - - +
517F ARG* 3.2 33.4 - - - +
519F GLN* 6.0 2.7 - - + -
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Residues in contact with GLN 354 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A MET* 3.8 13.7 - - + +
294A GLU* 3.5 19.8 + - - -
304A LYS* 4.0 22.4 - - - +
309A GLU* 4.8 6.6 - - - +
310A GLN* 3.2 46.3 + - + +
313A HIS* 5.6 2.5 - - - +
350F VAL* 3.1 38.3 + - + +
351F ASP* 4.9 2.0 - - - +
353F LEU* 1.3 81.1 - - + +
355F LEU* 1.3 69.2 + - + +
356F THR* 3.5 5.2 + - - +
359F GLN* 4.7 1.0 - - - +
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Residues in contact with LEU 355 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A GLU* 6.2 0.2 - - - +
351F ASP* 3.3 47.8 + - + +
352F SER 4.9 0.7 - - - -
353F LEU 4.6 2.8 - - - +
354F GLN* 1.3 83.2 + - + +
356F THR* 1.3 71.0 + - - +
357F ARG 3.8 0.2 + - - -
359F GLN* 3.4 30.7 - - + +
360F MET* 3.8 15.8 - - + +
363F ASN* 3.6 26.2 - - - +
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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