Contacts of the helix formed by residues 313 - 340 (chain E) in PDB entry 4KYI
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 ALA 313 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312E GLU* 1.3 76.8 - - - +
314E GLY* 1.3 60.4 + - - +
315E THR* 3.4 13.5 - - - +
316E ALA* 3.4 8.3 + - + +
317E PHE* 2.8 27.9 + - - +
375E ASN* 4.0 0.9 - - - -
376E THR* 3.3 10.1 - - - +
380E THR* 5.1 13.7 - - + -
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Residues in contact with GLY 314 (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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313E ALA* 1.3 74.0 - - - +
315E THR* 1.3 51.6 + - - +
317E PHE* 3.1 2.4 + - - +
318E GLU* 2.7 46.8 + - - +
375E ASN* 3.2 26.7 + - - -
376E THR* 4.1 2.2 + - - -
377E GLY* 4.7 8.6 + - - +
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Residues in contact with THR 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313E ALA* 4.3 9.0 - - - +
314E GLY* 1.3 74.5 - - - +
316E ALA* 1.3 64.9 + - - +
318E GLU* 3.4 15.1 + - - +
319E ASP* 3.1 33.6 + - - +
245G LYS* 6.1 1.2 - - - +
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Residues in contact with ALA 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312E GLU* 4.0 19.2 - - + +
313E ALA* 3.4 15.6 + - + +
314E GLY 3.3 0.4 - - - -
315E THR* 1.3 80.4 + - - +
317E PHE* 1.3 64.4 + - - +
319E ASP* 3.6 5.3 + - - +
320E ARG* 3.2 24.9 + - - +
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Residues in contact with PHE 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312E GLU* 3.4 22.4 + - + +
313E ALA 2.8 17.8 + - - +
314E GLY 3.4 3.8 - - - +
316E ALA* 1.3 78.1 - - - +
318E GLU* 1.3 63.8 + - + +
320E ARG* 3.5 9.1 + - - +
321E VAL* 3.2 48.0 + - + +
373E TYR* 3.5 33.7 - - + -
374E ILE 4.1 3.8 - - - -
375E ASN* 3.4 44.9 - - + +
401E GLN* 4.0 29.2 - - + -
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Residues in contact with GLU 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314E GLY* 2.7 27.2 + - - +
315E THR* 3.7 14.7 - - - +
316E ALA 3.3 0.2 - - - -
317E PHE* 1.3 77.4 - - + +
319E ASP* 1.3 59.4 + - - +
321E VAL* 3.3 4.3 + - - +
322E ASN* 2.9 46.4 + - - +
375E ASN* 5.3 6.2 + - - +
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Residues in contact with ASP 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315E THR* 3.1 23.4 + - - +
316E ALA* 4.1 5.2 - - - +
318E GLU* 1.3 81.0 - - - +
320E ARG* 1.3 61.4 + - - +
322E ASN* 4.2 6.4 - - - +
323E LYS* 3.2 41.9 + - - +
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Residues in contact with ARG 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312E GLU* 2.6 37.5 + - - +
316E ALA 3.2 15.2 + - - +
317E PHE* 3.5 20.2 + - - -
319E ASP* 1.3 76.9 - - - +
321E VAL* 1.3 84.6 + - - +
323E LYS* 4.4 5.3 - - - +
324E ALA* 3.3 21.8 + - - +
373E TYR* 3.4 55.6 - - - +
401E GLN* 5.9 2.0 - - - +
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Residues in contact with VAL 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317E PHE* 3.2 37.7 + - + +
318E GLU* 3.8 4.3 - - - +
320E ARG* 1.3 98.9 - - - +
322E ASN* 1.3 60.9 + - - +
324E ALA* 3.1 5.4 + - - +
325E LYS* 2.7 65.8 + - + +
401E GLN* 5.9 2.2 - - - +
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Residues in contact with ASN 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318E GLU* 2.9 35.5 + - - +
319E ASP* 4.2 6.8 - - - +
321E VAL* 1.3 81.9 - - - +
323E LYS* 1.3 60.0 + - + +
325E LYS* 3.0 9.9 + - - +
326E GLN* 2.9 29.9 + - - +
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Residues in contact with LYS 323 (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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319E ASP* 3.2 30.9 + - - +
320E ARG* 4.4 5.5 - - - +
322E ASN* 1.3 76.5 - - + +
324E ALA* 1.3 59.0 + - - +
326E GLN* 3.3 13.8 + - - +
327E SER* 3.1 28.4 + - - -
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Residues in contact with ALA 324 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320E ARG* 3.3 19.9 + - - +
321E VAL* 3.1 8.4 + - - +
323E LYS* 1.3 78.1 - - - +
325E LYS* 1.3 67.2 + - + +
326E GLN 3.2 0.4 + - - -
327E SER* 4.5 4.5 - - - -
328E ALA* 3.8 19.1 + - - +
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Residues in contact with LYS 325 (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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321E VAL* 2.7 46.2 + - + +
322E ASN* 3.0 10.7 + - - +
324E ALA* 1.3 81.3 - - + +
326E GLN* 1.3 57.9 + - - +
328E ALA* 4.2 6.8 - - - +
329E MET* 3.2 29.5 + - - +
404E GLN* 4.8 13.3 - - - +
558E VAL 5.3 9.4 - - - +
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Residues in contact with GLN 326 (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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322E ASN 2.9 14.9 + - - +
323E LYS* 3.7 14.2 - - - +
324E ALA 3.2 0.2 - - - -
325E LYS* 1.3 78.2 - - - +
327E SER* 1.3 60.4 + - - +
328E ALA 3.1 1.8 - - - -
329E MET* 3.0 16.2 + - + +
330E GLU* 2.9 55.3 + - + +
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Residues in contact with SER 327 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323E LYS 3.1 15.3 + - - -
324E ALA* 4.0 6.0 + - - -
326E GLN* 1.3 76.9 - - - +
328E ALA* 1.3 58.1 + - - +
330E GLU* 4.0 10.3 - - - +
331E ALA* 3.3 23.9 + - - +
360E ASN* 5.1 6.1 - - - +
361E ARG* 4.8 23.4 + - - +
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Residues in contact with ALA 328 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324E ALA 3.8 16.1 + - - +
325E LYS* 4.4 6.3 - - - +
326E GLN 3.1 0.6 - - - -
327E SER* 1.3 79.5 - - - +
329E MET* 1.3 62.6 + - + +
331E ALA* 3.8 8.3 + - - +
332E ILE* 3.3 24.6 + - - +
543E GLU* 4.1 28.1 - - - +
557E LYS* 5.7 6.2 - - + +
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Residues in contact with MET 329 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325E LYS* 3.2 21.3 - - - +
326E GLN* 3.0 20.3 + - + +
328E ALA* 1.3 79.0 - - + +
330E GLU* 1.3 62.0 + - + +
332E ILE* 3.3 12.3 + - - +
333E SER* 3.1 24.1 + - - -
557E LYS* 5.0 16.2 - - + -
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Residues in contact with GLU 330 (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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326E GLN* 2.9 44.2 + - + +
327E SER* 4.4 6.7 - - - +
329E MET* 1.3 74.5 - - + +
331E ALA* 1.3 57.9 + - - +
332E ILE 3.1 0.7 - - - -
333E SER* 3.8 8.3 - - - -
334E TRP* 2.7 61.8 + - + +
359E LEU* 4.6 9.2 - - - +
360E ASN* 5.9 1.6 - - + -
601E EDO 4.7 9.0 - - - +
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Residues in contact with ALA 331 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327E SER 3.3 19.2 + - - +
328E ALA* 3.9 10.1 - - - +
329E MET 3.3 0.2 - - - -
330E GLU* 1.3 77.5 - - - +
332E ILE* 1.3 61.1 + - + +
334E TRP* 4.2 1.8 - - - +
335E PHE* 3.8 16.3 + - - +
360E ASN* 4.5 23.5 + - + +
539E TRP 4.7 1.7 - - - +
540E ALA 5.1 0.2 - - - -
541E PRO* 4.0 21.6 - - + +
542E ILE* 5.5 4.0 - - + +
543E GLU* 5.8 6.7 - - + -
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Residues in contact with ILE 332 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328E ALA 3.3 20.6 - - - +
329E MET* 3.7 8.3 - - - +
330E GLU 3.1 0.4 - - - -
331E ALA* 1.3 76.6 - - + +
333E SER* 1.3 60.8 + - - +
334E TRP 3.4 0.4 - - - -
335E PHE* 3.3 9.7 + - + +
336E LYS* 3.1 28.9 + - + +
541E PRO* 4.7 18.4 - - + -
553E ALA 5.5 3.6 - - - +
555E ASP* 3.8 30.3 - - + +
556E PHE* 4.1 19.1 - - - +
557E LYS* 4.1 9.4 - - + +
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Residues in contact with SER 333 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329E MET 3.1 14.5 + - - -
330E GLU* 3.0 13.6 + - - -
332E ILE* 1.3 78.8 - - - +
334E TRP* 1.3 56.6 + - - +
336E LYS* 3.4 7.2 + - - +
337E ALA* 2.9 27.9 + - - +
601E EDO 3.2 26.8 + - - -
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Residues in contact with TRP 334 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330E GLU* 2.7 52.3 + - + +
331E ALA 4.6 1.6 - - - +
333E SER* 1.3 73.1 - - - +
335E PHE* 1.3 59.9 + - - +
337E ALA* 3.5 14.8 - - + +
338E ARG* 3.4 15.2 + - - +
355E THR* 4.3 22.2 - - + -
359E LEU* 3.6 41.3 + - + +
360E ASN* 4.4 14.6 - - + +
539E TRP* 3.8 43.4 - + + -
601E EDO 3.4 37.7 + - - -
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Residues in contact with PHE 335 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331E ALA 3.8 6.3 + - - +
332E ILE* 3.3 14.0 + - + +
333E SER 3.2 0.4 - - - -
334E TRP* 1.3 76.8 - - - +
336E LYS* 1.3 61.4 + - + +
337E ALA 3.0 4.7 - - - -
338E ARG* 2.9 19.6 + - + +
339E MET* 3.1 48.0 + - + +
536E ASN* 3.5 20.0 - - + -
539E TRP* 3.2 33.0 + - + +
540E ALA* 3.8 5.4 - - + -
541E PRO* 3.7 20.9 - - + -
553E ALA* 3.5 41.7 - - + -
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Residues in contact with LYS 336 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332E ILE* 3.1 18.1 + - + +
333E SER* 3.7 6.5 - - - +
335E PHE* 1.3 80.7 - - + +
337E ALA* 1.3 56.5 + - - +
339E MET* 4.0 6.5 - - + +
340E ASP* 3.1 57.5 + - - +
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Residues in contact with ALA 337 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333E SER 2.9 17.4 + - - +
334E TRP* 3.5 26.2 - - + +
335E PHE 3.0 0.4 - - - -
336E LYS* 1.3 78.9 - - - +
338E ARG* 1.3 55.3 + - - +
340E ASP* 3.8 4.5 - - - -
341E SER* 3.3 23.7 + - - -
601E EDO 5.0 9.0 - - - -
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Residues in contact with ARG 338 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334E TRP 3.4 10.0 + - - +
335E PHE* 2.9 12.7 + - + +
337E ALA* 1.3 77.8 - - - +
339E MET* 1.3 62.5 + - - +
340E ASP 3.2 1.3 - - - -
341E SER* 3.1 28.9 + - - -
342E LEU* 3.3 39.4 - - - +
516E ASN* 5.9 0.2 + - - -
519E GLU* 2.5 36.0 + - - -
532E THR* 3.6 10.1 + - - +
535E LEU* 3.2 33.1 + - - +
536E ASN* 2.9 33.0 + - - +
539E TRP* 4.1 32.6 - - + +
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Residues in contact with MET 339 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335E PHE* 3.1 46.8 + - + +
336E LYS* 4.6 4.5 - - + +
338E ARG* 1.3 77.0 - - - +
340E ASP* 1.3 66.5 + - - +
341E SER 3.2 1.9 + - - -
342E LEU* 3.8 22.3 + - + +
536E ASN* 3.8 34.1 - - + +
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Residues in contact with ASP 340 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336E LYS* 3.1 50.0 + - - +
337E ALA* 3.8 6.1 - - - +
338E ARG 3.2 0.2 - - - -
339E MET* 1.3 84.7 - - - +
341E SER* 1.3 55.3 + - - +
342E LEU 3.3 4.5 - - - -
343E VAL* 3.1 22.8 - - + +
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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
------------------------------------------------------------
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