Contacts of the helix formed by residues 315 - 347 (chain A) in PDB entry 1KZZ
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 GLY 315 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A ASN* 2.5 17.9 + - - +
314A THR* 1.3 76.1 - - - +
316A LEU* 1.3 61.3 + - - +
317A LEU 3.5 0.4 - - - -
318A GLU* 3.2 24.0 - - - +
319A SER* 3.5 8.5 + - - -
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Residues in contact with LEU 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ASN* 2.9 32.1 + - + +
315A GLY* 1.3 75.1 - - - +
317A LEU* 1.3 67.6 + - + +
318A GLU 2.9 1.3 - - - -
319A SER* 2.8 20.7 + - - +
320A GLN* 3.3 21.8 + - + +
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Residues in contact with LEU 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ASN 3.0 45.0 + - - +
314A THR* 5.4 2.2 - - - -
316A LEU* 1.3 79.4 - - + +
318A GLU* 1.3 65.0 + - + +
320A GLN* 3.2 11.5 + - - +
321A LEU* 2.9 29.0 + - + +
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Residues in contact with GLU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A THR* 2.8 33.7 + - - +
315A GLY* 3.2 15.9 - - - +
317A LEU* 1.3 79.1 - - + +
319A SER* 1.3 63.1 + - - +
321A LEU* 3.4 8.1 + - - +
322A SER* 3.2 20.3 + - - -
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Residues in contact with SER 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A GLY 3.5 7.2 + - - -
316A LEU* 2.8 17.9 + - - -
318A GLU* 1.3 78.7 - - - +
320A GLN* 1.3 63.2 + - - +
322A SER* 3.0 8.3 + - - -
323A ARG* 2.8 29.3 + - - +
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Residues in contact with GLN 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A LEU* 3.3 20.5 + - + +
317A LEU* 3.2 12.7 + - - +
319A SER* 1.3 82.0 - - - +
321A LEU* 1.3 63.6 + - - +
323A ARG* 3.1 47.5 + - - +
324A HIS* 3.1 27.0 + - + -
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Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A LEU* 2.9 19.8 + - + +
318A GLU* 3.8 7.6 - - - +
319A SER 3.3 0.2 - - - -
320A GLN* 1.3 76.9 - - - +
322A SER* 1.3 57.0 + - - +
324A HIS* 3.5 9.6 + - + +
325A ASP* 3.2 24.2 + - + +
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Residues in contact with SER 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A GLU 3.2 9.7 + - - -
319A SER* 3.0 10.8 + - - -
321A LEU* 1.3 76.7 - - - +
323A ARG* 1.3 55.4 + - - +
324A HIS 3.0 5.2 - - - -
325A ASP* 3.8 6.3 + - - +
326A GLN* 2.9 45.7 + - - +
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Residues in contact with ARG 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A SER 2.8 12.9 + - - +
320A GLN* 3.2 31.9 + - - +
322A SER* 1.3 77.5 - - - +
324A HIS* 1.3 99.9 + - - +
326A GLN* 4.0 10.1 + - - +
327A MET* 3.4 49.1 + - + +
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Residues in contact with HIS 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A GLN* 3.4 20.3 + - + -
321A LEU* 3.5 13.9 - - + +
322A SER 3.0 0.2 - - - -
323A ARG* 1.3 125.5 + - - +
325A ASP* 1.3 55.2 + - - +
327A MET* 3.2 5.2 + - - +
328A LEU* 2.5 46.7 + - + +
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Residues in contact with ASP 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LEU* 3.2 13.4 + - + +
322A SER* 3.8 8.6 + - - +
324A HIS* 1.3 73.9 - - - +
326A GLN* 1.3 63.1 + - - +
328A LEU* 2.8 14.0 + - - +
329A SER* 2.5 49.8 + - - -
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Residues in contact with GLN 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A SER* 2.9 32.8 + - - +
323A ARG* 4.0 8.7 - - - +
325A ASP* 1.3 87.4 + - - +
327A MET* 1.3 63.0 + - - +
329A SER* 2.8 20.3 + - - -
330A VAL* 3.1 9.9 + - - +
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Residues in contact with MET 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ARG* 3.4 44.8 + - + +
324A HIS* 3.2 5.9 + - - +
326A GLN* 1.3 78.9 - - - +
328A LEU* 1.3 65.0 + - - +
330A VAL* 3.0 27.7 + - + +
331A HIS* 3.2 33.3 + - + +
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Residues in contact with LEU 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A HIS* 2.5 32.2 + - + +
325A ASP* 3.1 14.6 - - - +
327A MET* 1.3 72.2 - - - +
329A SER* 1.3 66.1 + - - +
330A VAL 2.8 1.4 + - - -
331A HIS* 3.1 20.3 + - + +
332A ASP* 3.2 14.0 + - + +
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Residues in contact with SER 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ASP* 2.5 32.2 + - - -
326A GLN* 3.1 10.6 + - - -
328A LEU* 1.3 73.1 - - - +
330A VAL* 1.3 63.5 + - - +
332A ASP* 3.2 8.8 - - - +
333A ILE* 3.1 30.3 + - - +
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Residues in contact with VAL 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A GLN 3.7 11.9 - - - +
327A MET* 3.0 18.1 + - + +
328A LEU 2.8 0.8 + - - -
329A SER* 1.3 76.1 - - - +
331A HIS* 1.3 79.8 + - + +
333A ILE* 2.5 27.6 + - + +
334A ARG* 2.8 26.8 + - + +
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Residues in contact with HIS 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A MET* 3.2 36.3 + - + +
328A LEU* 3.1 15.1 + - + +
330A VAL* 1.3 82.9 - - + +
332A ASP* 1.3 54.3 + - - +
334A ARG* 2.5 38.1 + - - +
335A LEU* 2.5 26.6 + - + +
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Residues in contact with ASP 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A LEU* 3.2 10.4 + - + +
329A SER* 3.2 15.0 - - - +
331A HIS* 1.3 76.4 - - - +
333A ILE* 1.3 58.9 + - + +
335A LEU* 3.8 9.7 - - - +
336A ALA* 2.9 28.6 + - - +
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Residues in contact with ILE 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A SER* 3.1 21.1 - - - +
330A VAL* 2.5 26.9 + - + +
332A ASP* 1.3 70.9 - - + +
334A ARG* 1.3 61.6 + - + +
336A ALA* 2.8 24.6 - - + +
337A ASP* 3.1 17.0 + - - +
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Residues in contact with ARG 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A VAL* 2.8 27.8 + - + +
331A HIS* 2.5 21.8 + - - +
333A ILE* 1.3 69.2 - - + +
335A LEU* 1.3 66.4 + - - +
336A ALA 2.5 5.7 + - - -
337A ASP* 2.6 23.8 + - - +
338A MET* 2.9 23.4 + - + +
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Residues in contact with LEU 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A HIS* 2.5 25.1 + - + +
332A ASP* 3.8 9.4 - - - +
334A ARG* 1.3 72.5 - - - +
336A ALA* 1.3 60.3 + - - +
338A MET* 3.6 18.1 + - + +
339A ASP* 3.0 30.2 + - - +
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Residues in contact with ALA 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A ASP 2.9 16.1 + - - +
333A ILE* 2.8 21.5 - - + +
334A ARG 2.5 3.8 + - - -
335A LEU* 1.3 70.5 - - - +
337A ASP* 1.3 65.1 + - - +
339A ASP* 2.8 25.9 + - - +
340A LEU* 3.4 4.2 + - - +
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Residues in contact with ASP 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ILE* 3.4 19.4 - - - +
334A ARG* 2.6 17.1 + - - +
336A ALA* 1.3 75.4 - - - +
338A MET* 1.3 55.7 + - + +
340A LEU* 2.6 36.8 + - + +
341A ARG* 2.8 15.2 + - + -
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Residues in contact with MET 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ARG* 3.3 26.5 - - + +
335A LEU* 3.7 19.5 - - + +
337A ASP* 1.3 77.1 - - + +
339A ASP* 1.3 63.9 + - - +
340A LEU 2.9 1.4 + - - -
341A ARG* 3.5 34.4 - - - +
342A PHE* 3.2 39.3 + - + -
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Residues in contact with ASP 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A LEU* 3.0 18.7 + - - +
336A ALA* 2.8 17.2 + - - +
338A MET* 1.3 76.1 - - - +
340A LEU* 1.3 57.7 + - - +
342A PHE* 4.1 13.4 - - - +
343A GLN* 4.3 5.7 + - - +
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Residues in contact with LEU 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ALA 4.3 2.7 - - - +
337A ASP* 2.6 23.2 + - + +
339A ASP* 1.3 72.5 - - - +
341A ARG* 1.3 70.4 + - - +
342A PHE 2.9 2.2 - - - -
343A GLN* 2.7 62.5 + - + +
344A VAL* 3.4 13.9 + - + +
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Residues in contact with ARG 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ASP* 2.8 15.5 + - - +
338A MET* 3.5 37.0 - - - +
340A LEU* 1.3 74.7 - - - +
342A PHE* 1.3 66.2 + - + +
344A VAL* 3.2 14.9 + - - +
345A LEU* 3.0 25.2 - - + +
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Residues in contact with PHE 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A MET* 3.2 34.1 + - + +
339A ASP* 4.1 10.5 - - - +
340A LEU 2.7 3.4 + - - -
341A ARG* 1.3 75.5 - - + +
343A GLN* 1.3 68.0 + - - +
344A VAL 2.7 2.4 + - - -
345A LEU* 2.9 23.6 + - + +
346A GLU* 2.9 33.2 + - + +
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Residues in contact with GLN 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ASP 4.3 4.8 + - - +
340A LEU* 2.7 46.4 + - - +
342A PHE* 1.3 75.0 - - - +
344A VAL* 1.3 53.2 + - - +
346A GLU* 3.3 17.0 + - - +
347A THR* 2.4 43.1 + - + +
359A ARG* 5.4 7.0 + - - +
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Residues in contact with VAL 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A LEU* 4.2 17.3 - - + +
341A ARG* 3.3 17.7 - - + +
342A PHE 2.7 4.6 + - - -
343A GLN* 1.3 73.7 - - + +
345A LEU* 1.3 74.7 + - + +
347A THR* 2.8 16.6 + - - -
348A ALA* 2.8 14.0 + - + +
379A GLN* 4.6 9.1 - - + +
380A PRO* 4.3 33.9 - - + +
382A TYR* 5.3 5.4 - - - +
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Residues in contact with LEU 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ARG* 3.0 38.4 - - + +
342A PHE* 2.9 12.4 + - + +
344A VAL* 1.3 81.7 - - + +
346A GLU* 1.3 56.4 + - - +
347A THR 2.3 16.1 + - - -
348A ALA* 2.4 30.5 + - - +
350A TYR* 5.2 9.8 - - - +
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Residues in contact with GLU 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A PHE* 2.9 33.0 + - + +
343A GLN* 3.3 20.3 + - - +
345A LEU* 1.3 77.8 - - - +
347A THR* 1.3 63.9 + - + +
348A ALA 5.1 1.0 - - - +
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Residues in contact with THR 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A GLN* 2.4 31.2 + - + +
344A VAL* 2.8 9.0 + - - -
345A LEU 2.3 10.7 + - - -
346A GLU* 1.3 81.4 - - + +
348A ALA* 1.3 59.3 + - - -
349A SER* 4.1 1.4 + - - -
359A ARG* 6.0 4.5 - - - +
379A GLN* 2.6 44.7 + - - +
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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