Contacts of the helix formed by residues 356 - 379 (chain B) in PDB entry 4LOU
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 ILE 356 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B PHE* 3.9 28.7 - - + -
273B VAL* 5.3 2.5 - - + -
344B THR* 3.9 24.5 - - + -
345B LEU* 6.2 0.7 - - + -
348B PHE* 4.0 37.8 - - + -
355B GLY* 1.3 74.0 - - - +
357B PHE* 1.3 67.9 + - - +
359B PRO* 3.5 7.5 - - + +
360B MET* 3.1 35.2 + - + +
402B ILE* 5.4 0.4 - - + -
444B LEU* 4.8 10.8 - - + -
445B TYR* 3.4 31.6 + - + +
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Residues in contact with PHE 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ILE* 5.7 2.7 - - + -
148B GLN* 4.1 15.5 - - + -
149B GLY 6.1 0.4 - - - +
186B LEU* 4.0 26.0 - - + -
190B PHE* 3.7 24.0 - + + -
199B PHE* 4.1 25.1 - + - -
355B GLY* 3.7 0.8 - - - -
356B ILE* 1.3 75.9 - - - +
358B ALA* 1.3 56.7 + - - +
360B MET* 2.7 31.4 + - + +
361B LEU* 2.9 17.5 + - + +
398B LEU* 3.4 39.2 - - + +
402B ILE* 4.3 9.4 - - + -
404B ALA* 6.3 0.4 - - + -
407B THR* 4.8 8.7 - - + -
411B LEU* 4.6 7.0 - - + -
445B TYR* 4.0 28.5 - + - -
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Residues in contact with ALA 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B GLY* 4.2 8.3 - - - -
148B GLN* 3.3 26.3 - - - +
190B PHE* 4.6 0.2 - - - -
315B GLY* 3.7 15.8 - - - +
317B PHE* 3.7 26.4 - - + -
355B GLY 5.3 0.2 - - - -
357B PHE* 1.3 79.3 - - - +
359B PRO* 1.3 70.1 - - + +
360B MET 3.1 0.9 + - - -
361B LEU* 3.2 15.8 + - - +
362B ALA* 3.3 11.3 + - - +
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Residues in contact with PRO 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B VAL* 3.7 9.2 - - + +
145B LEU* 3.6 31.4 - - - +
146B GLY 4.1 0.2 - - - +
315B GLY 3.7 11.0 - - - +
340B ARG* 3.9 12.4 + - - +
344B THR* 3.8 27.7 + - + +
355B GLY 3.8 9.4 - - - +
356B ILE* 3.5 17.5 - - + +
358B ALA* 1.3 95.1 - - + +
360B MET* 1.3 57.0 + - - +
362B ALA* 4.0 2.9 + - - +
363B LEU* 3.2 28.8 + - - +
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Residues in contact with MET 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B PHE* 4.4 7.0 - - + -
344B THR* 5.7 0.2 - - + -
356B ILE* 3.1 51.3 + - + +
357B PHE* 2.7 12.8 + - + +
359B PRO* 1.3 73.1 - - - +
361B LEU* 1.3 56.9 + - - +
363B LEU* 2.8 27.3 + - + +
364B GLY* 2.9 11.4 + - - -
394B MET 4.3 1.1 - - - +
397B LEU* 3.5 36.7 - - + +
398B LEU* 3.4 32.5 - - + +
401B SER* 4.3 13.0 - - - -
402B ILE* 3.5 23.3 - - + -
444B LEU* 5.8 1.8 - - - -
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Residues in contact with LEU 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B PHE* 3.9 15.7 - - + -
317B PHE* 3.6 27.8 - - + -
320B ILE* 4.4 9.9 - - + -
357B PHE 2.9 13.9 + - - +
358B ALA* 3.5 8.1 - - - +
360B MET* 1.3 73.5 - - - +
362B ALA* 1.3 56.5 + - - +
364B GLY* 2.9 5.9 + - - -
365B THR* 2.9 31.1 + - - -
394B MET* 3.6 32.1 - - + +
398B LEU* 4.1 16.4 - - + +
411B LEU* 4.1 17.9 - - + -
412B VAL* 4.2 9.0 - - + -
415B MET* 3.8 20.2 - - + -
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Residues in contact with ALA 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B GLY* 3.4 39.9 - - - +
319B LEU* 3.7 10.5 - - + -
320B ILE* 4.2 7.0 - - + +
340B ARG* 4.4 9.8 - - - +
358B ALA 3.3 7.8 + - - +
359B PRO 4.3 3.8 - - - +
360B MET 3.3 0.8 - - - -
361B LEU* 1.3 79.0 - - - +
363B LEU* 1.3 61.9 + - - +
365B THR* 3.9 7.1 - - - -
366B VAL* 3.1 30.1 + - - +
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Residues in contact with LEU 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B PHE* 5.1 1.3 - - - -
265B PHE* 5.9 0.7 - - + -
269B PHE* 4.3 23.1 - - + -
337B PHE* 3.5 42.7 - - + +
340B ARG* 4.2 18.6 - - + +
341B VAL* 3.6 16.6 - - + +
344B THR* 4.4 10.1 - - + +
359B PRO 3.2 22.1 + - - +
360B MET* 2.8 11.0 + - + +
362B ALA* 1.3 78.3 - - - +
364B GLY* 1.3 58.7 + - - +
366B VAL* 3.3 4.0 + - - +
367B LEU* 2.9 28.9 + - - +
397B LEU* 3.9 25.1 - - + -
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Residues in contact with GLY 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B PHE* 3.4 16.8 - - - -
360B MET 2.9 11.5 + - - -
361B LEU 2.9 3.3 + - - -
363B LEU* 1.3 74.7 - - - +
365B THR* 1.3 58.7 + - - +
368B GLY* 2.9 26.0 + - - -
393B GLY* 3.2 33.4 - - - -
394B MET 4.0 1.6 - - - -
397B LEU* 5.0 0.6 - - - +
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Residues in contact with THR 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU* 5.4 0.2 - - - -
320B ILE* 3.5 37.0 - - + +
323B ALA* 4.0 10.1 - - + -
324B THR* 3.7 23.1 - - - +
361B LEU 2.9 14.9 + - - -
362B ALA* 4.1 3.6 - - - -
364B GLY* 1.3 75.6 - - - +
366B VAL* 1.3 58.4 + - - +
369B THR* 2.8 34.7 + - - -
390B ALA* 3.7 19.6 - - + +
394B MET* 3.4 20.0 - - - +
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Residues in contact with VAL 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU* 3.8 21.8 - - + -
323B ALA* 4.5 9.4 - - + -
328B PHE* 5.9 0.2 - - + -
333B LEU* 3.5 43.9 - - + +
336B ILE* 4.2 14.1 - - + -
337B PHE* 4.0 19.5 - - + +
340B ARG* 6.0 0.4 - - - -
362B ALA 3.1 20.2 + - - +
363B LEU* 3.7 3.8 - - - +
364B GLY 3.2 0.4 - - - -
365B THR* 1.3 76.3 - - - +
367B LEU* 1.3 65.6 + - - +
369B THR* 4.0 4.5 - - - -
370B ALA* 3.2 22.2 + - + +
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Residues in contact with LEU 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B LEU* 5.0 3.1 - - + -
261B ILE* 4.2 22.9 - - + -
262B PHE* 3.5 47.3 - - + -
265B PHE* 5.2 8.3 - - + -
337B PHE* 4.3 32.1 - - + -
363B LEU 2.9 16.3 + - - +
364B GLY 3.4 0.2 + - - -
366B VAL* 1.3 76.8 - - - +
368B GLY* 1.3 62.4 + - - +
370B ALA* 3.2 10.5 + - + +
371B PHE* 3.1 20.4 + - - +
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Residues in contact with GLY 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B LEU* 4.3 15.3 - - - -
262B PHE* 4.6 0.6 - - - -
364B GLY 2.9 17.0 + - - -
365B THR 4.0 0.2 - - - -
367B LEU* 1.3 73.9 - - - +
369B THR* 1.3 51.7 - - - +
371B PHE* 2.8 9.7 + - - +
372B GLY* 2.6 33.3 + - - -
389B PHE* 3.8 18.7 - - - +
390B ALA 3.8 7.4 - - - -
393B GLY* 4.6 0.7 - - - -
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Residues in contact with THR 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ALA* 3.1 33.0 + - - +
324B THR 5.4 0.4 - - - +
326B GLY* 4.9 1.1 - - - -
328B PHE* 5.9 0.7 - - + -
333B LEU* 3.5 21.1 - - + -
365B THR 2.8 22.6 + - - -
366B VAL 4.0 3.4 - - - -
368B GLY* 1.3 73.5 - - - +
370B ALA* 1.3 62.2 + - - +
372B GLY* 3.8 0.5 - - - -
373B MET* 3.1 38.6 + - + +
386B ALA* 4.2 16.1 - - + +
390B ALA* 3.0 19.0 - - - +
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Residues in contact with ALA 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B MET* 4.1 24.7 - - + +
333B LEU* 4.0 15.0 - - + +
334B VAL* 6.1 1.8 - - + +
366B VAL* 3.2 14.8 + - + +
367B LEU* 3.4 14.8 - - + +
368B GLY 3.0 0.8 - - - -
369B THR* 1.3 74.6 - - - +
371B PHE* 1.3 65.9 + - - +
373B MET* 3.1 13.4 + - - +
374B VAL* 3.2 18.3 + - - +
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Residues in contact with PHE 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B LEU* 3.6 31.4 - - + -
257B ILE* 3.6 32.8 - - + -
258B LEU* 3.5 33.2 - - + -
261B ILE* 4.2 17.0 - - + -
367B LEU 3.1 7.9 + - - +
368B GLY 2.8 11.9 + - - +
370B ALA* 1.3 72.8 - - - +
372B GLY* 1.3 60.0 + - - +
374B VAL* 3.2 11.5 + - + +
375B ALA* 3.1 24.2 + - + +
389B PHE* 3.7 29.8 - + - -
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Residues in contact with GLY 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B GLY 2.6 17.6 + - - -
369B THR 3.8 0.4 - - - -
371B PHE* 1.3 73.8 - - - +
373B MET* 1.3 59.6 + - - +
375B ALA* 3.6 1.8 + - - +
376B VAL* 3.3 28.9 + - - +
386B ALA* 3.3 16.8 - - - +
389B PHE* 3.6 29.6 - - - -
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Residues in contact with MET 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B GLY* 4.0 20.6 - - - +
328B PHE 3.2 28.0 - - - +
329B SER* 5.2 0.4 - - - -
330B MET* 4.5 21.1 - - + +
333B LEU* 4.2 11.2 - - + -
369B THR* 3.1 33.0 + - + +
370B ALA* 3.1 10.3 + - - +
372B GLY* 1.3 76.9 - - - +
374B VAL* 1.3 65.0 + - + +
375B ALA 3.3 0.2 - - - -
376B VAL* 3.9 6.4 + - - +
377B GLU* 3.8 22.3 + - - +
386B ALA* 4.1 9.6 - - + -
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Residues in contact with VAL 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B MET* 4.5 17.0 - - + -
370B ALA 3.2 18.2 - - - +
371B PHE* 3.2 10.9 + - + +
373B MET* 1.3 77.6 - - + +
375B ALA* 1.3 65.2 + - - +
377B GLU* 3.4 4.6 + - - +
378B LEU* 3.1 50.4 + - + +
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Residues in contact with ALA 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B LEU* 4.1 15.0 - - + -
371B PHE* 3.1 20.0 + - + +
372B GLY 3.8 5.4 - - - +
373B MET 3.3 0.2 - - - -
374B VAL* 1.3 73.7 - - - +
376B VAL* 1.3 65.5 + - - +
377B GLU 3.1 2.4 + - - -
378B LEU* 3.2 0.6 + - - -
379B PHE* 2.9 39.0 + - + +
384B LEU* 3.7 21.8 - - + -
389B PHE* 4.3 11.4 - - + -
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Residues in contact with VAL 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B GLY 3.3 17.6 + - - +
373B MET* 4.1 7.6 - - - +
374B VAL 3.5 0.4 - - - -
375B ALA* 1.3 77.0 - - - +
377B GLU* 1.3 63.4 - - + +
379B PHE 4.6 2.0 - - - -
380B PRO* 3.9 21.3 - - - +
384B LEU* 3.7 38.3 - - + +
386B ALA* 4.0 14.1 - - + +
57E THR* 5.0 15.7 - - + +
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Residues in contact with GLU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B MET 3.8 13.8 + - - +
374B VAL* 3.4 8.3 + - - +
375B ALA 3.1 0.6 - - - -
376B VAL* 1.3 83.7 - - + +
378B LEU* 1.3 68.6 + - + +
379B PHE 3.3 1.7 + - - -
380B PRO* 4.0 8.5 - - - +
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Residues in contact with LEU 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B VAL* 3.1 35.4 + - + +
375B ALA* 5.4 0.2 - - - -
377B GLU* 1.3 81.0 - - + +
379B PHE* 1.3 93.4 + - + +
380B PRO* 3.5 7.5 - - - +
381B GLN* 4.3 1.9 + - - +
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Residues in contact with PHE 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B TRP* 3.9 29.4 - + - -
254B LEU* 4.0 30.5 - - + -
375B ALA* 2.9 25.5 + - + +
376B VAL* 4.0 2.8 - - - +
378B LEU* 1.3 109.9 - - + +
380B PRO* 1.3 65.1 - - - +
381B GLN* 3.0 26.0 + - - +
382B TYR* 3.2 38.8 + + + +
383B HIS 4.2 1.6 + - - -
384B LEU* 4.3 5.2 + - + +
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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