Contacts of the helix formed by residues 349 - 371 (chain B) in PDB entry 3VF1
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 349 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ASP* 1.3 79.4 - - - +
350B GLU* 1.3 59.8 + - - +
351B TRP* 3.9 5.4 + - - +
352B ASP* 3.1 31.1 + - - +
353B TRP* 3.0 26.9 + - - +
585B LYS* 6.5 0.2 - - + -
586B GLY* 4.6 18.5 - - - +
588B SER 5.1 1.6 + - - -
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Residues in contact with GLU 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ASP 5.5 0.2 - - - +
349B THR* 1.3 74.5 - - - +
351B TRP* 1.3 66.2 + - + +
353B TRP* 3.4 7.6 + - - +
354B ILE* 3.1 32.3 + - + +
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Residues in contact with TRP 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B LEU* 4.2 14.8 - - + -
233B ARG* 4.5 9.6 - - - -
349B THR* 3.4 4.1 + - - +
350B GLU* 1.3 78.0 - - + +
352B ASP* 1.3 66.4 + - - +
354B ILE* 3.3 23.9 + - + +
355B MET* 3.0 22.7 + - - +
588B SER* 3.4 27.0 - - - +
589B ASN* 3.8 11.4 - - + +
590B HIS* 3.6 52.1 - + + +
593B ILE* 3.6 30.4 - - + +
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Residues in contact with ASP 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B TRP* 3.3 35.2 - - + -
348B ASP* 4.2 3.8 - - + +
349B THR* 3.1 31.6 + - - +
351B TRP* 1.3 77.7 - - - +
353B TRP* 1.3 56.5 + - - +
355B MET* 3.1 4.2 + - - +
356B ALA* 2.9 28.6 + - - +
584B GLU 5.1 0.5 - - - +
585B LYS* 3.5 4.9 - - - +
586B GLY* 2.7 27.1 + - - -
587B LYS* 3.9 0.7 + - - +
588B SER* 2.7 43.4 + - - -
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Residues in contact with TRP 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ASP* 3.1 26.4 + - - -
327B PRO* 3.7 30.5 - - + -
329B ALA 4.0 11.4 - - - -
330B ILE* 3.8 30.3 - - + -
343B TRP* 3.7 20.9 - - + -
344B THR 3.9 8.1 - - - +
345B PRO* 3.6 53.1 - - + +
348B ASP* 4.8 2.6 - - + +
349B THR 3.0 17.2 + - - +
350B GLU* 3.7 8.1 - - - +
352B ASP* 1.3 75.7 - - - +
354B ILE* 1.3 63.5 + - + +
356B ALA* 3.3 7.0 + - + +
357B LYS* 3.0 48.7 + - + +
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Residues in contact with ILE 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B LEU* 5.5 0.4 - - + -
232B TRP* 4.4 18.6 - - + -
233B ARG* 4.4 26.0 - - + +
350B GLU* 3.1 22.1 + - + +
351B TRP* 3.6 28.9 - - + +
352B ASP 3.2 0.2 - - - -
353B TRP* 1.3 75.3 - - + +
355B MET* 1.3 67.6 + - - +
357B LYS* 3.3 21.9 + - - +
358B LEU* 3.1 33.3 + - + +
593B ILE* 3.9 17.3 - - + -
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Residues in contact with MET 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B TRP* 6.4 0.2 - - + -
351B TRP 3.0 13.6 + - - +
352B ASP 3.1 8.0 + - - +
354B ILE* 1.3 77.6 - - - +
356B ALA* 1.3 64.2 + - - +
358B LEU* 3.1 22.9 + - - +
359B TRP* 3.2 50.5 + - + -
577B MET* 5.4 1.1 - - - -
582B PRO* 4.1 22.7 - - + -
588B SER* 3.7 18.4 - - - +
592B VAL* 4.0 19.5 - - + -
593B ILE* 3.4 40.8 - - + +
596B SER* 4.4 14.1 - - - +
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Residues in contact with ALA 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ILE* 3.8 24.4 - - + +
332B LEU* 4.2 9.6 - - - +
343B TRP* 3.8 38.8 - - + -
352B ASP 2.9 12.7 + - - +
353B TRP* 3.6 10.3 - - + +
354B ILE 3.3 0.2 - - - -
355B MET* 1.3 77.2 - - - +
357B LYS* 1.3 62.3 + - - +
359B TRP* 3.4 5.8 + - - +
360B LEU* 3.2 16.1 + - - +
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Residues in contact with LYS 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B TRP* 5.0 2.3 + - - -
233B ARG* 3.2 25.3 + - - +
234B ASP 4.8 0.2 - - - -
235B ASP* 2.8 24.8 + - - +
238B PHE* 3.5 39.3 - - + +
330B ILE* 3.9 11.0 - - + -
353B TRP* 3.0 58.4 + - + +
354B ILE* 3.6 20.4 - - - +
356B ALA* 1.3 74.3 - - - +
358B LEU* 1.3 64.7 + - + +
360B LEU* 3.2 3.6 + - - +
361B ARG* 3.1 26.9 + - - +
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Residues in contact with LEU 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B TRP* 3.9 17.9 - - + -
354B ILE* 3.1 31.8 + - + +
355B MET* 3.1 14.3 + - - +
357B LYS* 1.3 76.7 - - + +
359B TRP* 1.3 58.3 + - + +
361B ARG* 3.4 4.0 + - + +
362B CYS* 3.0 27.4 + - - +
571B PRO* 3.2 31.6 - - + +
574B PRO* 3.7 17.4 - - + +
577B MET* 3.9 15.3 - - + -
593B ILE* 3.7 29.6 - - + -
597B LEU* 4.3 11.9 - - + -
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Residues in contact with TRP 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B TYR* 3.9 17.0 - - + -
310B ILE* 3.9 15.8 - - + +
311B THR* 3.7 26.9 + - + +
313B PRO* 4.3 5.1 - - - +
332B LEU* 3.7 25.8 - - + -
355B MET* 3.2 50.1 + - + +
356B ALA 3.8 2.0 - - - +
357B LYS 3.2 0.4 - - - -
358B LEU* 1.3 76.8 - - - +
360B LEU* 1.3 63.8 + - - +
362B CYS* 3.7 4.8 - - + +
363B ALA* 3.3 20.8 + - - +
577B MET* 3.2 41.7 - - + +
579B GLN 3.1 28.0 - - - -
580B PRO 3.7 1.6 - - - -
581B PRO* 3.5 32.0 - - + +
582B PRO* 4.5 5.2 - - + -
596B SER* 4.6 3.4 - - - -
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Residues in contact with LEU 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B PHE* 4.1 11.2 - - + -
242B PHE* 4.0 23.3 - - + -
290B THR* 4.0 5.4 - - - +
292B TYR* 3.9 18.8 - - + -
313B PRO* 3.8 28.5 - - + -
314B LEU 4.3 1.3 - - - +
315B GLY* 4.0 24.5 - - - +
317B PHE* 4.2 7.9 - - + -
327B PRO* 5.8 0.4 - - + -
330B ILE* 3.9 23.3 - - + -
332B LEU* 5.1 0.4 - - - +
356B ALA 3.2 12.2 + - - +
357B LYS 3.2 9.7 + - - +
359B TRP* 1.3 75.9 - - - +
361B ARG* 1.3 63.5 + - - +
363B ALA* 3.4 6.1 + - - +
364B ASP* 3.2 19.1 + - - +
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Residues in contact with ARG 361 (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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238B PHE* 3.2 37.0 - - + -
241B GLN* 3.8 35.5 + - - +
242B PHE* 3.6 33.5 - - - -
246B SER 5.9 1.2 - - - +
357B LYS 3.1 7.6 + - - +
358B LEU* 3.8 2.0 - - + +
360B LEU* 1.3 73.6 - - - +
362B CYS* 1.3 61.5 + - - +
364B ASP* 3.0 26.7 + - - +
365B THR* 2.9 31.4 + - - -
566B THR* 4.0 14.3 - - - +
571B PRO 5.6 1.1 - - - +
572B ASN* 3.1 22.2 + - - +
573B SER* 3.3 23.6 + - - -
574B PRO* 3.7 20.0 - - + -
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Residues in contact with CYS 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ILE* 3.4 22.4 - - + -
358B LEU 3.0 17.7 + - - +
359B TRP* 3.7 10.3 - - + +
360B LEU 3.3 0.4 - - - -
361B ARG* 1.3 76.9 - - - +
363B ALA* 1.3 62.1 + - - +
365B THR* 3.2 7.4 + - - -
366B GLN* 3.0 26.6 + - - -
574B PRO* 3.3 25.5 - - + +
576B LEU* 3.9 32.8 - - - -
577B MET* 4.1 10.8 - - + -
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Residues in contact with ALA 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B TYR* 4.2 7.8 - - + -
295B LEU* 3.6 27.7 - - + +
310B ILE* 3.8 10.2 - - + +
311B THR* 4.7 0.4 - - - +
313B PRO* 3.5 34.8 - - + -
359B TRP 3.3 5.7 + - - +
360B LEU 3.6 4.7 - - - +
362B CYS* 1.3 78.6 - - - +
364B ASP* 1.3 62.8 + - - +
366B GLN* 3.2 7.0 + - - +
367B TYR* 3.2 19.4 + - - +
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Residues in contact with ASP 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B PHE* 4.1 9.9 - - + -
247B ASN* 3.0 34.9 + - - +
250B VAL* 4.1 2.8 - - - +
292B TYR* 2.6 36.1 + - - +
360B LEU 3.2 8.5 + - - +
361B ARG* 3.0 36.4 + - - +
363B ALA* 1.3 78.8 - - - +
365B THR* 1.3 58.1 + - - +
367B TYR* 3.2 2.1 + - - +
368B HIS* 2.8 28.1 + - - +
567B TYR* 5.4 0.9 + - - -
573B SER* 5.0 1.0 + - - -
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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
----------------------------------------------------------
361B ARG 2.9 8.7 + - - -
362B CYS 3.2 4.7 + - - -
364B ASP* 1.3 75.3 + - - +
366B GLN* 1.3 66.2 + - - +
368B HIS* 3.2 0.4 + - - -
369B GLN* 3.0 28.0 + - + +
431B LEU* 4.1 11.2 - - + -
567B TYR* 3.5 30.9 - - + +
573B SER* 2.9 26.0 + - - -
574B PRO 2.9 26.8 + - - +
575B THR* 3.9 17.9 - - + -
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Residues in contact with GLN 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 4.0 16.2 - - + -
310B ILE* 3.9 17.9 - - + -
362B CYS* 3.0 24.8 + - - +
363B ALA* 3.2 7.8 + - - +
365B THR* 1.3 79.1 - - - +
367B TYR* 1.3 63.3 + - - +
369B GLN* 4.2 0.3 - - - -
370B MET* 3.3 28.4 + - - +
431B LEU* 3.7 13.9 - - - +
432B SER* 3.5 13.7 + - - -
433B ILE* 3.3 44.0 + - + +
441B LEU* 3.7 3.5 - - - +
575B THR 2.8 29.9 + - - -
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Residues in contact with TYR 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ASN* 3.6 11.9 - - - +
249B GLU* 4.2 15.7 + - + +
250B VAL* 3.9 22.5 - - + +
291B ASP 5.9 2.2 - - - -
292B TYR* 4.2 17.0 - + + -
294B ILE* 4.0 24.2 - - + -
295B LEU* 5.3 2.9 - - + +
363B ALA 3.2 8.9 + - - +
364B ASP 3.4 8.7 - - - +
365B THR 3.2 0.2 - - - -
366B GLN* 1.3 79.1 - - - +
368B HIS* 1.3 56.0 + - - +
371B ILE* 2.9 56.9 + - + +
372B THR* 3.1 26.2 + - - -
376B ARG* 5.5 0.2 - - - -
441B LEU* 4.5 7.8 - - - +
445B HIS* 4.1 17.7 + - - -
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Residues in contact with HIS 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B SER* 2.9 32.4 + - - -
247B ASN* 3.7 15.5 - - + +
364B ASP* 2.8 20.4 + - - +
365B THR* 3.2 0.9 + - - +
367B TYR* 1.3 73.4 - - - +
369B GLN* 1.3 64.2 + - - +
372B THR* 3.3 18.6 + - + -
373B HIS* 2.8 35.5 + - + +
559B VAL* 2.8 29.5 + - + +
563B GLN* 3.5 28.9 - - + -
567B TYR* 2.8 29.5 + + - +
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Residues in contact with GLN 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B THR* 3.0 24.6 + - + +
366B GLN 4.2 0.2 - - - +
368B HIS* 1.3 81.3 + - - +
370B MET* 1.3 62.1 + - - +
373B HIS* 3.6 11.1 + - - +
374B LEU* 3.2 35.2 + - + +
427B ALA* 6.2 0.4 - - + -
430B VAL* 6.1 0.7 - - + -
431B LEU* 4.1 32.1 - - + -
563B GLN* 2.9 27.9 + - - +
567B TYR* 3.5 24.2 - - - -
606B MET* 3.8 17.0 - - + +
613B LEU* 4.5 8.5 - - - +
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Residues in contact with MET 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B GLN 3.3 15.6 + - - +
369B GLN* 1.3 81.6 - - - +
371B ILE* 1.3 60.9 + - - +
374B LEU* 3.7 23.3 - - + -
375B LEU* 3.0 27.6 + - - +
421B ILE* 4.9 3.8 - - + -
427B ALA* 4.2 7.6 - - + -
431B LEU* 3.6 29.4 - - + -
433B ILE* 4.0 12.1 - - + -
438B GLN* 3.3 41.3 - - + +
441B LEU* 4.0 10.5 - - + -
442B MET* 3.4 28.9 - - + +
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Residues in contact with ILE 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ILE* 3.7 29.4 - - + -
367B TYR* 2.9 44.9 + - + +
370B MET* 1.3 79.9 - - - +
372B THR* 1.3 61.8 + - - +
373B HIS 3.5 0.2 + - - -
375B LEU* 3.6 3.3 - - - +
376B ARG* 2.9 48.5 + - - +
441B LEU* 3.8 31.6 - - + +
442B MET* 4.8 2.0 - - - -
445B HIS* 3.8 36.3 - - + +
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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