Contacts of the helix formed by residues 332 - 355 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339D GLN* 3.6 0.4 - - - +
270E TRP* 5.1 6.9 - - + -
330E SER* 3.2 10.4 + - - +
331E LYS* 1.3 94.1 - - - +
333E GLN* 1.3 63.8 + - - +
334E LYS 3.2 3.4 - - - +
335E THR* 3.6 28.2 + - + -
336E ILE* 3.0 29.2 + - + +
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Residues in contact with GLN 333 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D THR* 4.8 9.3 + - - +
339D GLN* 2.8 35.9 + - + +
343D THR* 3.2 26.5 + - - +
289E LEU* 3.2 26.1 - - + +
293E LEU* 3.8 23.0 - - - +
296E GLN* 4.9 0.2 - - - +
327E PHE* 3.3 38.7 - - + +
328E ALA* 3.0 28.6 - - - +
330E SER* 3.6 6.5 - - - +
332E ASN* 1.3 73.0 - - - +
334E LYS* 1.3 59.0 + - - +
337E CYS* 3.6 9.9 + - - -
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Residues in contact with LYS 334 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D GLN* 5.2 3.8 + - - +
339D GLN* 4.5 5.4 - - + +
342D ASP* 3.6 39.5 + - + +
512D LYS* 4.6 12.1 - - - +
514D LEU* 5.7 4.5 - - - +
516D LYS* 4.4 19.7 - - - +
285E VAL* 4.1 24.3 - - + +
286E LEU* 4.6 7.4 - - + -
289E LEU* 4.6 14.3 - - + +
332E ASN* 3.2 0.6 - - - +
333E GLN* 1.3 78.1 - - - +
335E THR* 1.3 60.5 + - - +
337E CYS* 4.0 2.1 - - - -
338E GLN* 3.0 34.0 + - + +
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Residues in contact with THR 335 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270E TRP* 3.6 23.2 - - + -
332E ASN* 3.1 31.7 + - + +
334E LYS* 1.3 77.5 - - - +
336E ILE* 1.3 64.2 + - - +
338E GLN* 3.1 15.9 + - + +
339E GLN* 3.2 11.6 + - - +
331F LYS 5.9 0.2 - - - +
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Residues in contact with ILE 336 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268E VAL* 3.9 21.1 - - + -
269E SER 4.6 0.9 - - - +
270E TRP* 3.6 46.2 - - + +
273E VAL* 3.6 34.0 - - + +
274E THR* 5.3 1.7 + - - -
327E PHE* 3.5 25.4 - - + -
330E SER* 3.3 26.0 - - - +
332E ASN* 3.0 13.7 + - + +
335E THR* 1.3 77.4 - - - +
337E CYS* 1.3 61.2 + - - +
338E GLN 3.4 0.2 + - - -
339E GLN* 3.6 4.7 + - - +
340E ALA* 3.5 16.6 + - - +
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Residues in contact with CYS 337 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273E VAL* 4.2 14.4 - - - -
285E VAL* 4.3 9.4 - - + +
288E LEU* 3.4 15.5 - - + +
289E LEU* 3.6 29.6 - - + -
292E TYR* 4.7 2.0 - - - -
327E PHE* 3.5 30.3 - - - -
333E GLN 3.6 9.0 + - - +
334E LYS* 4.3 3.1 - - - +
335E THR 3.3 0.4 - - - -
336E ILE* 1.3 77.3 - - - +
338E GLN* 1.3 64.9 + - - +
340E ALA* 3.3 9.0 + - - +
341E VAL* 3.0 27.6 + - - +
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Residues in contact with GLN 338 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514D LEU* 4.9 12.0 - - - +
285E VAL* 3.3 37.7 - - + +
334E LYS* 3.0 27.4 + - + +
335E THR* 3.1 13.0 + - + +
337E CYS* 1.3 77.6 - - - +
339E GLN* 1.3 62.9 + - - +
341E VAL* 3.1 20.0 + - - +
342E ASP* 3.0 38.6 + - - +
334F LYS* 5.3 3.8 + - - +
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Residues in contact with GLN 339 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270E TRP* 3.2 30.1 - - + +
274E THR* 4.2 9.8 + - - +
335E THR 3.2 8.2 + - - +
336E ILE 4.0 6.7 - - - +
338E GLN* 1.3 78.6 - - - +
340E ALA* 1.3 63.6 + - - +
342E ASP* 3.2 14.2 + - + +
343E THR* 2.9 24.2 + - - +
289F LEU* 5.8 0.8 - - + +
328F ALA 5.6 0.3 - - - +
330F SER 3.1 25.7 + - - +
331F LYS 3.3 14.6 + - - -
332F ASN* 4.1 0.2 - - - +
333F GLN* 3.2 44.6 - - + +
334F LYS* 5.4 5.2 - - + +
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Residues in contact with ALA 340 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273E VAL* 4.1 4.7 - - + +
274E THR* 4.0 19.9 + - - +
277E ALA* 3.6 14.7 - - + +
288E LEU* 3.4 16.8 - - + -
336E ILE 3.5 10.4 + - - +
337E CYS* 3.4 11.7 - - - +
338E GLN 3.1 0.4 - - - -
339E GLN* 1.3 80.6 - - - +
341E VAL* 1.3 61.8 + - - +
343E THR* 3.0 11.3 + - - -
344E VAL* 2.9 25.9 + - - +
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Residues in contact with VAL 341 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282E CYS 4.3 0.2 - - - -
283E ASP* 3.4 30.7 - - - +
284E ASP 3.1 30.1 - - - +
285E VAL* 3.7 20.6 - - + -
288E LEU* 3.9 4.9 - - + -
337E CYS 3.0 17.7 - - - +
338E GLN* 3.1 10.2 + - - +
340E ALA* 1.3 76.3 - - - +
342E ASP* 1.3 57.8 + - - +
344E VAL* 3.0 11.8 + - - +
345E LEU* 2.9 39.0 + - + +
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Residues in contact with ASP 342 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338E GLN* 3.0 35.4 + - - +
339E GLN* 3.2 12.4 + - + +
341E VAL* 1.3 78.5 - - - +
343E THR* 1.3 57.1 + - - +
345E LEU* 3.5 10.9 + - - +
346E ALA* 2.8 29.9 + - - +
516E LYS* 5.9 0.2 - - - -
286F LEU* 3.8 24.8 - - + +
289F LEU* 4.2 14.1 - - + +
334F LYS* 3.9 31.7 + - + +
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Residues in contact with THR 343 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E THR* 3.6 24.4 - - + +
278E MET* 3.5 30.7 - - + +
339E GLN 2.9 14.7 + - - -
340E ALA 3.0 9.1 + - - -
342E ASP* 1.3 76.9 - - - +
344E VAL* 1.3 63.6 + - - +
346E ALA* 3.4 6.7 - - - +
347E LYS* 3.1 17.0 + - - +
289F LEU* 4.9 2.0 - - - +
293F LEU* 3.9 22.0 - - + -
333F GLN* 3.5 18.7 + - - +
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Residues in contact with VAL 344 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277E ALA* 3.7 28.7 - - + +
278E MET* 4.3 8.5 - - - +
281E LYS* 3.6 22.0 - - + +
282E CYS 3.2 24.5 - - - +
283E ASP* 3.9 4.9 - - - +
340E ALA 2.9 20.7 + - - +
341E VAL 3.0 6.5 + - - +
343E THR* 1.3 74.1 - - - +
345E LEU* 1.3 65.8 + - - +
347E LYS* 3.1 19.7 + - + +
348E LYS* 3.3 31.1 + - - +
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Residues in contact with LEU 345 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283E ASP* 3.9 29.6 - - + +
341E VAL* 2.9 30.0 + - + +
342E ASP* 4.0 10.3 - - - +
344E VAL* 1.3 76.4 - - - +
346E ALA* 1.3 53.4 + - - +
348E LYS* 3.4 15.1 + - + +
349E ARG* 2.8 36.5 + - - +
466E ASP* 4.9 1.9 - - - +
511E LYS* 4.3 25.8 - - + +
286F LEU* 4.4 24.5 - - + -
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Residues in contact with ALA 346 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342E ASP 2.8 20.2 + - - +
343E THR* 3.4 11.9 - - - +
344E VAL 3.1 0.2 - - - -
345E LEU* 1.3 75.9 - - - +
347E LYS* 1.3 64.6 + - - +
349E ARG* 3.1 9.2 + - - +
350E VAL* 3.0 29.2 + - - +
286F LEU* 3.8 13.9 - - - +
289F LEU* 4.3 7.2 - - + -
290F GLY* 3.8 23.7 - - - +
293F LEU* 4.7 2.2 - - + -
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Residues in contact with LYS 347 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278E MET* 3.9 26.1 - - + +
343E THR 3.1 11.7 + - - +
344E VAL* 3.1 12.4 + - + +
346E ALA* 1.3 77.4 - - - +
348E LYS* 1.3 57.1 + - + +
350E VAL* 3.0 11.0 + - + +
351E ASP* 2.7 56.4 + - - +
290F GLY* 5.7 0.7 - - - -
294F GLU* 4.7 15.9 + - + +
297F TYR* 5.8 3.6 + - - -
304F LYS* 5.7 5.1 - - - +
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Residues in contact with LYS 348 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281E LYS* 3.7 23.4 + - - +
283E ASP* 4.4 12.4 - - + +
344E VAL* 3.3 35.5 + - - +
345E LEU* 3.8 17.7 - - + +
347E LYS* 1.3 78.1 - - + +
349E ARG* 1.3 62.6 + - - +
351E ASP* 4.0 8.2 - - - +
352E SER* 3.1 27.4 + - - -
466E ASP* 4.1 16.1 - - + +
467E GLN* 5.5 9.2 - - - +
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Residues in contact with ARG 349 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345E LEU* 2.8 14.2 + - - +
346E ALA* 3.2 17.7 - - - +
348E LYS* 1.3 77.2 - - - +
350E VAL* 1.3 56.7 + - - +
352E SER* 3.0 13.9 + - - -
353E LEU* 4.0 5.7 - - - +
465E ILE* 3.1 17.0 - - - +
466E ASP* 3.0 28.6 + - - -
511E LYS* 3.5 17.2 - - - +
516E LYS* 2.9 35.3 + - - +
517E ARG* 3.1 27.4 + - - +
284F ASP* 4.6 0.7 - - - -
286F LEU* 3.1 37.8 - - - +
287F LEU* 3.5 40.7 - - + +
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Residues in contact with VAL 350 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346E ALA 3.0 15.4 + - - +
347E LYS* 3.0 9.6 + - + +
349E ARG* 1.3 77.4 - - + +
351E ASP* 1.3 62.2 + - - +
352E SER 3.1 1.6 - - - -
353E LEU* 2.9 22.3 + - - +
354E GLN* 3.1 42.9 + - + +
287F LEU* 4.6 7.6 - - + +
290F GLY* 3.7 30.3 - - - +
291F MET* 3.7 19.7 - - + +
294F GLU* 4.0 11.9 - - - +
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Residues in contact with ASP 351 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347E LYS* 2.7 54.8 + - - +
348E LYS* 3.9 7.8 + - - +
350E VAL* 1.3 77.8 - - - +
352E SER* 1.3 57.9 + - - +
353E LEU 3.0 5.2 + - - -
354E GLN* 4.5 3.1 - - - +
355E LEU* 3.3 56.7 + - + +
360E MET* 4.0 8.8 - - + +
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Residues in contact with SER 352 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348E LYS 3.1 11.8 + - - -
349E ARG 3.0 18.7 + - - -
351E ASP* 1.3 75.4 - - - +
353E LEU* 1.3 63.2 + - - +
355E LEU 4.9 2.7 - - - -
360E MET* 4.2 20.9 - - - +
466E ASP* 3.1 38.5 + - - -
467E GLN 5.5 1.3 - - - -
517E ARG* 4.1 5.0 + - - -
519E GLN* 4.6 3.1 + - - -
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Residues in contact with LEU 353 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349E ARG 4.0 5.2 - - - +
350E VAL* 2.9 7.0 + - + +
351E ASP 4.2 0.2 - - - -
352E SER* 1.3 88.2 - - - +
354E GLN* 1.3 68.1 + - + +
355E LEU 4.6 2.9 - - - +
517E ARG* 3.2 32.8 - - - +
519E GLN* 6.0 2.7 - - + -
287F LEU* 3.6 30.7 - - + -
291F MET* 5.9 3.1 - - - -
310F GLN* 4.7 10.5 + - - +
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Residues in contact with GLN 354 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350E VAL* 3.1 37.6 + - + +
351E ASP* 5.0 2.0 - - - +
353E LEU* 1.3 82.1 - - + +
355E LEU* 1.3 68.7 + - + +
356E THR* 3.5 5.7 + - - +
359E GLN* 4.7 1.2 - - - +
291F MET* 4.0 11.6 - - + +
294F GLU* 3.2 22.6 + - - -
304F LYS* 3.6 27.4 - - - +
309F GLU* 4.6 6.3 - - + +
310F GLN* 3.6 39.6 + - + +
313F HIS* 5.5 2.5 + - - +
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Residues in contact with LEU 355 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351E ASP* 3.3 47.0 + - + +
352E SER 4.9 0.9 - - - +
353E LEU 4.6 2.9 - - - +
354E GLN* 1.3 83.1 + - + +
356E THR* 1.3 69.0 + - - +
357E ARG 3.8 0.2 + - - -
359E GLN* 3.4 31.2 - - + +
360E MET* 3.8 15.3 - - + +
363E ASN* 3.6 26.0 - - - +
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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