Contacts of the helix formed by residues 323 - 347 (chain A) in PDB entry 3KCZ
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 THR 323 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A ILE* 5.1 2.6 - - - +
321A ILE* 4.8 0.3 - - - +
322A ARG* 1.3 85.4 + - + +
324A GLN* 1.3 65.0 - - - +
325A LYS* 3.5 10.9 + - - +
326A GLU* 3.0 36.2 + - - +
327A LEU* 3.0 24.3 + - - +
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Residues in contact with GLN 324 (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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323A THR* 1.3 73.2 - - - +
325A LYS* 1.3 64.4 + - - +
327A LEU* 3.4 9.2 + - - +
328A SER* 2.8 33.5 + - - -
453A THR* 2.8 35.2 + - - +
454A GLY* 3.6 19.2 + - - -
455A TYR* 4.2 0.8 - - - +
456A MET* 5.1 4.6 - - - +
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Residues in contact with LYS 325 (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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323A THR* 3.1 10.8 + - - +
324A GLN* 1.3 86.6 + - - +
326A GLU* 1.3 58.5 + - + +
328A SER* 3.3 5.5 + - - -
329A GLU* 2.9 55.5 + - + +
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Residues in contact with GLU 326 (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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320A LEU 3.5 13.8 - - - +
321A ILE* 3.8 16.1 - - + +
322A ARG* 2.6 35.9 + - - +
323A THR* 3.0 26.8 + - - +
325A LYS* 1.3 77.9 - - + +
327A LEU* 1.3 62.0 + - - +
329A GLU* 3.4 18.6 + - - +
330A LYS* 3.3 28.1 + - - +
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Residues in contact with LEU 327 (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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282A LEU* 3.8 34.3 - - + +
285A ILE* 4.0 11.4 - - + -
286A GLU* 4.1 18.8 - - + -
289A ILE* 4.6 9.9 - - + -
321A ILE* 3.7 19.9 - - + +
323A THR 3.0 15.5 + - - +
324A GLN* 3.6 7.4 - - - +
326A GLU* 1.3 75.1 - - - +
328A SER* 1.3 64.0 + - - +
330A LYS* 3.1 6.2 + - - +
331A ILE* 3.0 28.4 + - + +
451A PRO* 4.2 13.9 - - + -
453A THR* 3.1 29.4 - - - +
454A GLY* 5.7 0.9 - - - -
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Residues in contact with SER 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A GLN* 2.8 36.5 + - - -
325A LYS* 3.4 9.0 - - - -
327A LEU* 1.3 74.8 - - - +
329A GLU* 1.3 56.8 + - - +
331A ILE* 3.2 13.8 + - - +
332A GLN* 2.9 48.1 + - - +
454A GLY* 4.2 10.2 + - - -
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Residues in contact with GLU 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A MET* 4.6 4.3 - - - +
325A LYS* 2.9 46.8 + - + +
326A GLU* 3.5 23.5 - - - +
327A LEU 3.2 0.2 - - - -
328A SER* 1.3 75.2 - - - +
330A LYS* 1.3 69.4 + - - +
332A GLN* 3.4 13.7 + - - +
333A LEU* 3.1 25.1 + - - +
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Residues in contact with LYS 330 (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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258A MET 4.4 6.9 + - - -
259A LYS* 5.4 1.4 - - - +
282A LEU* 3.7 23.3 - - + -
305A PHE* 3.5 26.3 - - + -
306A TYR* 4.9 3.7 + - + -
311A HIS* 2.8 31.1 + - + +
313A PHE* 5.2 3.0 - - - -
321A ILE* 3.9 26.5 - - + -
326A GLU 3.3 14.3 + - - +
327A LEU 3.1 7.5 + - - +
329A GLU* 1.3 85.2 + - - +
331A ILE* 1.3 65.7 + - - +
333A LEU* 3.3 12.6 + - + +
334A LEU* 3.0 26.7 + - - +
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Residues in contact with ILE 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A TYR* 4.5 7.0 - - + -
282A LEU* 4.0 15.9 - - + -
327A LEU* 3.0 24.1 + - + +
328A SER* 3.4 8.1 - - - +
330A LYS* 1.3 75.6 - - - +
332A GLN* 1.3 60.6 + - + +
334A LEU* 3.1 6.2 + - - +
335A GLU* 2.8 43.7 + - + +
451A PRO* 4.0 29.8 - - + +
454A GLY* 3.6 31.9 - - - +
455A TYR* 3.1 30.1 - - + +
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Residues in contact with GLN 332 (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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258A MET* 4.1 10.1 - - + +
328A SER* 2.9 36.3 + - - +
329A GLU* 3.6 14.7 - - - +
330A LYS 3.3 0.2 - - - -
331A ILE* 1.3 75.2 - - + +
333A LEU* 1.3 65.8 + - - +
335A GLU* 3.8 16.1 - - - +
336A ALA* 3.1 24.1 + - - +
431A ARG* 3.9 11.3 + - - +
434A ASN* 5.8 0.3 + - - -
473A TYR* 4.8 15.9 - - - -
475A PHE* 3.8 29.9 - - - -
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Residues in contact with LEU 333 (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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255A MET* 4.0 22.7 - - - -
258A MET* 3.7 31.5 - - + +
260A TYR* 4.2 18.4 - - + -
305A PHE* 5.2 0.9 - - + -
309A ILE* 4.4 8.5 - - + -
311A HIS* 3.4 37.2 - - + +
329A GLU 3.1 14.0 + - - +
330A LYS* 3.4 20.2 - - + +
332A GLN* 1.3 76.5 - - - +
334A LEU* 1.3 56.9 + - + +
336A ALA* 3.3 2.9 + - - +
337A LEU* 3.0 37.3 + - + +
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Residues in contact with LEU 334 (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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275A ILE* 3.9 15.9 - - + +
278A GLY 3.5 5.6 - - - -
279A TYR* 3.3 65.7 + - + +
282A LEU* 3.8 11.2 - - + -
305A PHE* 4.4 3.8 - - + -
309A ILE* 3.7 38.8 - - + -
330A LYS 3.0 15.8 + - - +
331A ILE 3.1 6.5 + - - +
333A LEU* 1.3 74.3 - - + +
335A GLU* 1.3 61.3 + - - +
337A LEU* 3.7 13.9 - - + +
338A GLY* 2.9 25.5 + - - -
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Residues in contact with GLU 335 (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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279A TYR* 3.3 15.3 + - - +
331A ILE* 2.8 32.5 + - + +
332A GLN* 3.8 16.8 - - - +
334A LEU* 1.3 72.7 - - - +
336A ALA* 1.3 60.7 + - - +
338A GLY* 3.3 3.0 + - - -
339A ASP* 3.1 26.4 + - - +
434A ASN* 4.7 6.3 - - - +
446A ALA* 4.4 8.8 - - - +
447A HIS 5.3 1.0 + - - +
455A TYR* 3.1 31.3 + - - -
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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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255A MET* 3.8 25.8 - - + -
258A MET* 4.6 4.7 - - - -
332A GLN 3.1 17.6 + - - +
333A LEU 3.6 4.5 - - - +
334A LEU 3.3 0.2 - - - -
335A GLU* 1.3 73.7 - - - +
337A LEU* 1.3 59.4 + - - +
339A ASP* 3.1 3.1 + - - +
340A ILE* 2.8 34.4 + - - +
431A ARG* 4.8 4.5 - - - -
433A SER* 3.9 4.5 - - - +
434A ASN* 3.3 25.7 - - - +
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Residues in contact with LEU 337 (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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255A MET* 4.0 14.8 - - + -
260A TYR* 3.8 33.0 - - + -
267A LEU* 3.9 28.7 - - + -
270A LEU* 3.2 28.8 - - + +
275A ILE* 3.7 8.5 - - + -
309A ILE* 4.0 10.3 - - + -
333A LEU* 3.0 26.5 + - + +
334A LEU* 3.7 26.9 - - + +
336A ALA* 1.3 74.3 - - - +
338A GLY* 1.3 56.8 + - - +
340A ILE* 3.3 3.8 + - + -
341A GLU* 2.8 26.2 + - - +
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Residues in contact with GLY 338 (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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275A ILE* 3.6 18.5 - - - +
334A LEU 2.9 14.3 + - - -
335A GLU* 3.7 3.8 - - - -
336A ALA 3.2 0.2 - - - -
337A LEU* 1.3 78.4 - - - +
339A ASP* 1.3 62.1 + - - +
341A GLU* 3.5 4.2 + - - +
342A ILE* 3.2 28.1 + - - +
444A ARG* 5.5 0.7 - - - -
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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
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335A GLU* 3.1 10.5 + - - +
336A ALA 3.1 7.6 + - - +
338A GLY* 1.3 73.0 - - - +
340A ILE* 1.3 60.2 + - - +
342A ILE* 3.4 7.8 - - - +
343A ALA* 2.9 27.5 + - - +
433A SER 4.3 3.6 - - - +
434A ASN* 3.2 50.8 + - - +
437A GLY* 3.7 9.3 + - - -
438A ILE* 4.3 1.9 - - - +
444A ARG* 2.7 45.3 + - - -
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Residues in contact with ILE 340 (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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251A MET* 3.8 38.1 - - + -
255A MET* 3.3 46.9 - - + -
267A LEU* 4.2 19.5 - - + -
270A LEU* 4.6 2.5 - - + -
336A ALA 2.8 20.4 + - - +
337A LEU* 3.6 7.0 - - - +
339A ASP* 1.3 71.4 - - - +
341A GLU* 1.3 66.2 + - - +
343A ALA* 3.2 5.6 + - - +
344A ILE* 2.9 43.0 + - + +
433A SER* 4.0 11.2 - - - +
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Residues in contact with GLU 341 (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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267A LEU 5.6 0.7 - - - -
270A LEU* 3.8 34.1 - - + +
271A THR* 4.5 1.1 - - - -
272A VAL* 3.4 35.9 + - + +
275A ILE* 4.2 6.1 - - + -
337A LEU 2.8 20.0 + - - +
338A GLY* 3.6 5.5 - - - +
340A ILE* 1.3 72.8 - - - +
342A ILE* 1.3 83.2 + - - +
344A ILE* 3.6 6.3 + - - +
345A LYS* 2.7 53.6 + - - +
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Residues in contact with ILE 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 GLY 3.2 15.5 + - - +
339A ASP* 3.4 11.0 - - - +
340A ILE 3.2 0.2 - - - -
341A GLU* 1.3 89.8 - - - +
343A ALA* 1.3 58.2 + - - +
345A LYS* 3.3 6.6 + - - +
346A LEU* 3.0 28.3 + - + +
436A VAL* 4.6 2.9 - - + +
437A GLY* 3.9 10.5 - - - +
440A SER* 3.5 24.0 - - - +
441A HIS* 3.7 33.0 - - + +
444A ARG* 3.7 25.4 - - - +
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Residues in contact with ALA 343 (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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246A CYS* 6.0 1.1 - - - -
248A VAL* 5.9 1.6 - - + -
251A MET* 3.5 33.9 - - + -
339A ASP 2.9 19.3 + - - +
340A ILE 3.2 4.2 + - - +
342A ILE* 1.3 74.4 - - - +
344A ILE* 1.3 57.4 + - - +
346A LEU* 3.2 1.7 + - - +
347A VAL* 2.9 33.9 + - - +
436A VAL* 3.8 25.8 - - + -
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Residues in contact with ILE 344 (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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248A VAL* 4.5 25.4 - - + -
251A MET* 5.2 0.7 - - - -
267A LEU* 3.4 45.5 - - + +
268A GLY* 3.7 17.3 - - - +
340A ILE* 2.9 31.1 + - + +
341A GLU* 4.1 4.9 - - - +
342A ILE 3.4 0.2 - - - -
343A ALA* 1.3 73.2 - - + +
345A LYS* 1.3 61.7 + - - +
347A VAL* 3.3 21.4 - - + +
348A LYS* 3.5 18.4 - - + +
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Residues in contact with LYS 345 (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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272A VAL* 4.7 6.3 - - - +
341A GLU* 2.7 40.0 + - - +
342A ILE* 3.3 9.7 + - - +
343A ALA 3.3 0.4 - - - -
344A ILE* 1.3 75.0 - - - +
346A LEU* 1.3 67.5 + - - +
348A LYS* 3.3 37.5 + - + +
364A ASN* 5.3 0.2 + - - -
350B GLU* 6.5 0.4 - - - -
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Residues in contact with LEU 346 (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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246A CYS* 4.8 6.5 - - - -
342A ILE* 3.0 19.4 + - + +
343A ALA 3.2 4.2 + - - +
345A LYS* 1.3 78.6 - - - +
347A VAL* 1.3 63.9 + - - +
348A LYS 3.2 2.8 + - - +
361A HIS* 3.8 30.9 + - + +
364A ASN* 3.0 58.3 + - + +
365A LEU* 3.7 14.4 - - + -
436A VAL* 3.7 28.3 - - + -
440A SER* 3.8 11.9 - - - +
441A HIS* 6.3 0.2 - - + -
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Residues in contact with VAL 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A CYS* 4.3 22.2 - - + +
248A VAL* 4.3 16.2 - - + -
343A ALA 2.9 14.2 + - - +
344A ILE* 3.3 22.9 - - + +
346A LEU* 1.3 78.0 - - + +
348A LYS* 1.3 65.6 + - + +
349A THR* 3.3 5.2 + - - +
361A HIS* 3.2 44.4 - - + +
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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