Contacts of the helix formed by residues 323 - 347 (chain B) in PDB entry 4TVJ
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ILE* 4.5 7.5 - - - +
322B ARG* 1.3 81.1 + - - +
324B GLN* 1.3 63.7 + - - +
325B LYS* 2.6 54.0 + - + +
326B GLU* 3.1 20.0 + - + +
327B LEU* 2.9 29.1 + - - +
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Residues in contact with GLN 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ILE* 5.7 1.2 - - - +
323B THR* 1.3 79.3 + - - +
325B LYS* 1.3 64.8 + - - +
327B LEU* 3.3 10.5 + - - +
328B SER* 2.8 32.1 + - - -
453B THR* 2.8 35.6 + - - +
454B GLY* 3.8 17.0 + - - -
456B MET* 5.1 10.5 - - - +
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Residues in contact with LYS 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B THR* 2.6 42.2 + - + +
324B GLN* 1.3 89.9 + - - +
326B GLU* 1.3 72.2 + - - +
328B SER* 3.3 6.6 + - - -
329B GLU* 2.9 44.9 + - - +
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Residues in contact with GLU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B LEU 3.6 10.5 - - - +
321B ILE* 3.8 14.7 - - + +
322B ARG* 3.0 34.8 + - - +
323B THR* 3.1 29.0 + - + +
325B LYS* 1.3 88.4 + - - +
327B LEU* 1.3 66.0 + - - +
329B GLU* 3.4 16.6 + - - +
330B LYS* 3.3 26.5 + - - +
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Residues in contact with LEU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B LEU* 3.8 32.7 - - + +
285B ILE* 3.9 22.2 - - + -
286B GLU* 4.0 19.3 - - + +
289B ILE* 4.3 9.9 - - + -
321B ILE* 3.7 9.7 - - + +
323B THR 2.9 11.0 + - - +
324B GLN* 3.5 11.0 - - - +
326B GLU* 1.3 76.7 - - - +
328B SER* 1.3 57.3 + - - +
330B LYS* 3.1 6.8 + - - +
331B ILE* 2.9 32.8 + - + +
451B PRO* 4.2 13.0 - - + -
453B THR* 3.2 27.6 - - - +
454B GLY 5.0 2.9 - - - +
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Residues in contact with SER 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B GLN* 2.8 34.5 + - - -
325B LYS* 3.4 11.2 - - - -
327B LEU* 1.3 74.2 - - - +
329B GLU* 1.3 51.4 + - - +
331B ILE* 3.1 14.8 + - - +
332B GLN* 2.8 46.9 + - - +
454B GLY* 4.3 10.1 + - - -
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Residues in contact with GLU 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B MET* 4.5 4.3 - - + +
325B LYS* 2.9 32.2 + - - +
326B GLU* 3.7 20.9 - - - +
327B LEU 3.3 0.2 - - - -
328B SER* 1.3 74.7 - - - +
330B LYS* 1.3 67.4 + - - +
332B GLN* 3.4 19.6 + - - +
333B LEU* 3.0 26.0 + - - +
431B ARG* 6.0 0.9 - - - +
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Residues in contact with LYS 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B MET 4.3 6.9 + - - -
259B LYS* 5.3 2.0 - - - +
282B LEU* 3.5 24.2 - - + -
305B PHE* 3.5 25.2 - - + -
306B TYR* 5.1 1.7 + - + -
311B HIS* 2.9 30.4 + - - +
313B PHE* 5.1 4.2 - - - -
321B ILE* 3.9 26.2 - - + -
326B GLU 3.3 15.0 + - - +
327B LEU 3.1 7.9 + - - +
329B GLU* 1.3 86.6 - - - +
331B ILE* 1.3 59.3 + - - +
333B LEU* 3.3 13.9 + - + +
334B LEU* 2.9 31.9 + - - +
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Residues in contact with ILE 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B TYR* 4.6 5.8 - - + -
282B LEU* 4.0 15.3 - - + -
327B LEU* 2.9 21.5 + - + +
328B SER* 3.1 7.2 + - - +
330B LYS* 1.3 73.3 - - - +
332B GLN* 1.3 66.1 + - + +
334B LEU* 3.1 6.0 + - - +
335B GLU* 2.9 36.7 + - + +
450B ALA* 4.7 2.7 - - + -
451B PRO* 3.7 33.9 - - + +
454B GLY* 3.4 33.4 - - - +
455B TYR* 3.1 31.9 - - + +
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Residues in contact with GLN 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B MET* 4.2 9.2 - - + +
328B SER* 2.8 29.9 + - - +
329B GLU* 3.5 20.9 - - - +
330B LYS 3.3 0.2 - - - -
331B ILE* 1.3 72.8 - - + +
333B LEU* 1.3 56.6 + - - +
335B GLU* 3.4 11.6 + - - +
336B ALA* 3.0 29.6 + - - +
431B ARG* 3.4 27.4 + - - +
434B ASN* 5.5 1.2 + - - -
473B TYR* 4.2 21.0 - - - -
475B PHE* 3.9 20.7 - - - -
601B 09L 5.3 4.6 - - - +
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Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B MET* 3.9 24.7 - - - -
258B MET* 3.8 32.0 - - + +
260B TYR* 4.1 14.8 - - + -
305B PHE* 5.1 0.9 - - + -
309B ILE* 4.7 5.6 - - + -
311B HIS* 3.4 37.7 - - + +
329B GLU 3.0 13.8 + - - +
330B LYS* 3.5 20.6 - - + +
331B ILE 3.2 0.2 - - - -
332B GLN* 1.3 75.4 - - - +
334B LEU* 1.3 59.5 + - + +
336B ALA* 3.3 1.9 + - - -
337B LEU* 2.9 46.7 + - + +
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Residues in contact with LEU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ILE* 3.8 19.7 - - + +
278B GLY 3.5 6.5 - - - -
279B TYR* 3.3 60.2 + - + +
282B LEU* 3.8 12.8 - - + -
305B PHE* 4.2 6.5 - - + -
309B ILE* 3.5 36.3 - - + -
330B LYS 2.9 17.0 + - - +
331B ILE 3.1 3.6 + - - +
333B LEU* 1.3 78.5 - - + +
335B GLU* 1.3 56.7 + - - +
337B LEU* 3.3 16.0 + - + +
338B GLY* 2.9 25.1 + - - -
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Residues in contact with GLU 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B TYR* 3.3 18.4 + - - +
331B ILE* 2.9 32.9 + - + +
332B GLN* 3.9 11.6 - - - +
334B LEU* 1.3 70.3 - - - +
336B ALA* 1.3 63.4 + - - +
338B GLY* 3.2 3.9 + - - +
339B ASP* 3.0 27.0 + - - +
434B ASN* 4.8 5.8 - - - +
446B ALA* 3.8 12.0 - - - +
447B HIS 5.1 0.5 + - - -
455B TYR* 2.8 25.6 + - - -
601B 09L 3.5 48.4 - - + -
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Residues in contact with ALA 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B MET* 3.7 26.2 - - + -
258B MET* 4.6 5.6 - - - -
332B GLN 3.0 18.4 + - - +
333B LEU 3.8 3.1 - - - +
334B LEU 3.3 0.2 - - - -
335B GLU* 1.3 74.7 - - - +
337B LEU* 1.3 65.4 + - - +
339B ASP* 3.1 3.6 + - - +
340B ILE* 2.9 28.9 + - - +
431B ARG* 4.7 3.6 - - - -
433B SER* 3.9 4.3 - - - +
434B ASN* 3.4 26.5 - - - +
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Residues in contact with LEU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B MET* 3.9 14.1 - - + -
260B TYR* 3.9 27.1 - - + -
267B LEU* 3.8 24.0 - - + -
270B LEU* 3.5 31.5 - - + +
275B ILE* 3.7 8.0 - - + +
309B ILE* 4.2 4.3 - - + -
333B LEU* 2.9 35.8 + - + +
334B LEU* 3.6 26.5 - - + +
336B ALA* 1.3 76.1 - - - +
338B GLY* 1.3 56.0 + - - +
340B ILE* 3.3 5.6 + - + +
341B GLU* 2.9 30.5 + - - +
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Residues in contact with GLY 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B VAL* 6.5 0.4 - - - -
275B ILE* 3.6 16.5 - - - +
334B LEU 2.9 13.4 + - - -
335B GLU* 3.2 5.6 + - - -
336B ALA 3.2 0.2 - - - -
337B LEU* 1.3 76.3 - - - +
339B ASP* 1.3 63.7 + - - +
341B GLU* 3.3 6.9 + - - +
342B ILE* 3.2 27.1 + - - +
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Residues in contact with ASP 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B GLU 3.0 12.9 + - - +
336B ALA 3.1 6.0 + - - +
338B GLY* 1.3 74.8 - - - +
340B ILE* 1.3 60.9 + - - +
342B ILE* 3.4 10.6 + - - +
343B ALA* 2.9 27.9 + - - +
433B SER 4.2 2.2 - - - +
434B ASN* 3.4 49.3 + - - +
437B GLY* 4.0 8.1 + - - -
438B ILE* 4.3 3.8 - - - +
444B ARG* 3.2 38.5 + - - -
601B 09L 4.9 7.3 - - - -
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Residues in contact with ILE 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B VAL* 6.3 0.2 - - + -
251B MET* 3.9 32.1 - - + -
255B MET* 3.3 47.8 - - + -
267B LEU* 4.1 20.9 - - + +
336B ALA 2.9 18.1 + - - +
337B LEU* 3.7 6.3 - - + +
339B ASP* 1.3 74.5 - - - +
341B GLU* 1.3 68.6 + - - +
343B ALA* 3.7 5.6 - - - +
344B ILE* 2.9 47.0 + - + +
433B SER* 4.0 13.9 - - - +
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Residues in contact with GLU 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU 5.3 4.3 - - - -
270B LEU* 3.7 27.6 - - + +
271B THR* 4.7 1.1 - - - -
272B VAL* 3.8 32.7 + - + +
275B ILE* 4.5 7.9 - - + -
337B LEU 2.9 13.4 + - - +
338B GLY* 3.3 9.5 + - - +
340B ILE* 1.3 79.4 - - - +
342B ILE* 1.3 77.0 + - - +
344B ILE* 3.7 6.1 + - - +
345B LYS* 2.5 57.6 + - - +
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Residues in contact with ILE 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B GLY 3.2 15.1 + - - +
339B ASP* 3.4 13.9 - - - +
341B GLU* 1.3 85.7 - - - +
343B ALA* 1.3 68.4 + - - +
345B LYS* 3.3 8.1 + - - +
346B LEU* 2.9 23.7 + - + +
436B VAL* 4.7 2.2 - - + -
437B GLY* 4.2 8.3 - - - +
440B SER* 3.7 14.6 - - - +
441B HIS* 3.5 43.7 - - + +
444B ARG* 3.8 24.9 - - - +
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Residues in contact with ALA 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B VAL* 5.7 0.7 - - + -
251B MET* 3.3 35.9 - - + -
339B ASP 2.9 19.3 + - - +
340B ILE 3.1 4.4 + - - +
342B ILE* 1.3 74.1 - - - +
344B ILE* 1.3 63.0 + - - +
346B LEU* 3.1 1.3 + - - -
347B VAL* 2.9 32.4 + - + +
433B SER 5.2 0.4 - - - +
436B VAL* 3.8 26.0 - - + -
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Residues in contact with ILE 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B VAL* 4.5 26.7 - - + -
251B MET* 5.2 1.1 - - - -
267B LEU* 3.6 45.5 - - + +
268B GLY* 3.7 15.0 - - - +
340B ILE* 2.9 30.1 + - + +
341B GLU* 4.2 4.5 - - - +
343B ALA* 1.3 76.7 - - + +
345B LYS* 1.3 63.0 + - + +
347B VAL* 3.7 10.2 + - + +
348B LYS* 3.5 18.7 + - - +
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Residues in contact with LYS 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B GLY 6.0 0.4 + - - -
270B LEU 5.0 4.2 + - - -
271B THR* 6.1 0.6 - - - +
341B GLU* 2.5 43.8 + - - +
342B ILE* 3.3 9.5 + - - +
343B ALA 3.2 0.4 - - - -
344B ILE* 1.3 79.2 - - + +
346B LEU* 1.3 64.8 + - - +
348B LYS* 3.4 18.8 + - - +
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Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B CYS* 4.8 2.2 - - - -
342B ILE* 2.9 19.5 + - + +
343B ALA* 3.6 7.0 - - - +
345B LYS* 1.3 78.1 - - - +
347B VAL* 1.3 69.0 + - + +
348B LYS 3.3 3.2 + - - +
361B HIS* 3.8 31.0 + - + +
364B ASN* 3.2 59.8 + - + +
365B LEU* 4.0 5.8 - - + -
436B VAL* 3.9 16.2 - - + -
440B SER* 3.8 24.2 - - - +
441B HIS* 6.0 0.4 - - + -
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Residues in contact with VAL 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B CYS* 3.7 42.2 - - + +
248B VAL* 4.2 21.1 - - + -
343B ALA* 2.9 25.8 + - + +
344B ILE* 3.8 8.1 - - + +
345B LYS 3.3 0.2 - - - -
346B LEU* 1.3 79.3 - - + +
348B LYS* 1.3 67.6 + - - +
349B THR* 3.5 6.1 + - - +
361B HIS* 3.4 30.2 - - + +
436B VAL* 5.6 0.4 - - + -
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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