Contacts of the helix formed by residues 349 - 371 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ASP* 1.3 80.1 - - - +
350A GLU* 1.3 60.5 + - - +
351A TRP* 3.9 5.2 + - - +
352A ASP* 3.1 31.1 + - - +
353A TRP* 3.0 26.3 + - - +
586A GLY* 4.6 17.5 - - - +
588A SER 5.1 1.4 + - - -
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Residues in contact with GLU 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ASP 5.5 1.1 - - - +
349A THR* 1.3 74.2 - - - +
351A TRP* 1.3 66.3 + - + +
353A TRP* 3.4 8.1 + - - +
354A ILE* 3.1 32.6 + - + +
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Residues in contact with TRP 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A LEU* 4.2 14.6 - - + -
233A ARG* 4.5 9.9 - - - -
349A THR* 3.3 4.6 + - - +
350A GLU* 1.3 77.5 - - + +
352A ASP* 1.3 65.0 + - - +
354A ILE* 3.3 22.3 + - + +
355A MET* 3.0 23.2 + - - +
588A SER* 3.4 26.6 - - - +
589A ASN* 3.8 11.1 - - + +
590A HIS* 3.6 50.1 - + + +
593A ILE* 3.6 30.4 - - + +
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Residues in contact with ASP 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A TRP* 3.3 36.4 - - + -
348A ASP* 4.2 3.4 - - + +
349A THR* 3.1 32.2 + - - +
351A TRP* 1.3 77.8 - - - +
353A TRP* 1.3 56.8 + - - +
355A MET* 3.1 4.3 + - - +
356A ALA* 2.9 28.9 + - - +
584A GLU 5.1 0.9 - - - +
585A LYS* 3.5 4.9 - - - +
586A GLY* 2.7 26.5 + - - -
587A LYS 3.9 0.2 + - - -
588A SER* 2.7 43.6 + - - -
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Residues in contact with TRP 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ASP* 3.1 26.6 + - - -
327A PRO* 3.7 30.7 - - + -
329A ALA 4.0 12.1 - - - -
330A ILE* 3.8 28.9 - - + -
343A TRP* 3.7 22.0 - - + -
344A THR 3.9 8.3 - - - +
345A PRO* 3.6 51.7 - - + +
348A ASP* 4.8 2.4 - - + +
349A THR 3.0 17.2 + - - +
350A GLU* 3.7 7.9 - - - +
351A TRP 3.3 0.2 - - - -
352A ASP* 1.3 75.1 - - - +
354A ILE* 1.3 63.5 + - + +
356A ALA* 3.3 7.2 + - + +
357A LYS* 3.0 47.9 + - + +
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Residues in contact with ILE 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A LEU* 5.4 0.4 - - + -
232A TRP* 4.4 18.8 - - + -
233A ARG* 4.5 26.5 - - + +
350A GLU* 3.1 22.7 + - + +
351A TRP* 3.6 28.7 - - + +
353A TRP* 1.3 74.5 - - + +
355A MET* 1.3 67.4 + - - +
357A LYS* 3.3 22.8 + - - +
358A LEU* 3.1 32.3 + - + +
593A ILE* 3.9 17.5 - - + -
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Residues in contact with MET 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A TRP* 6.3 0.4 - - + -
351A TRP 3.0 14.0 + - - +
352A ASP 3.4 8.5 - - - +
354A ILE* 1.3 77.2 - - - +
356A ALA* 1.3 63.4 + - - +
358A LEU* 3.1 22.8 + - - +
359A TRP* 3.2 50.0 + - + +
577A MET* 5.4 1.6 - - - -
582A PRO* 4.1 22.0 - - + -
588A SER* 3.7 18.4 - - - +
592A VAL* 4.0 19.1 - - + -
593A ILE* 3.4 39.2 - - + +
596A SER* 4.4 13.9 - - - +
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Residues in contact with ALA 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ILE* 3.8 23.3 - - + +
332A LEU* 4.2 9.6 - - - +
343A TRP* 3.8 38.6 - - + -
352A ASP 2.9 13.0 + - - +
353A TRP* 3.6 11.0 - - + +
355A MET* 1.3 78.1 - - - +
357A LYS* 1.3 61.8 + - - +
359A TRP* 3.3 5.2 + - - +
360A LEU* 3.2 16.6 + - - +
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Residues in contact with LYS 357 (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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232A TRP* 5.0 2.8 + - - -
233A ARG* 3.2 25.9 + - - +
234A ASP 4.8 0.2 - - - -
235A ASP* 2.8 24.3 + - - +
238A PHE* 3.5 39.8 - - + +
330A ILE* 3.9 11.0 - - + -
353A TRP* 3.0 57.5 + - + +
354A ILE* 3.6 20.6 - - - +
355A MET 3.2 0.2 - - - -
356A ALA* 1.3 74.6 - - - +
358A LEU* 1.3 64.3 + - + +
360A LEU* 3.2 3.6 + - - +
361A ARG* 3.1 26.9 + - - +
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Residues in contact with LEU 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A TRP* 3.9 17.5 - - + -
354A ILE* 3.1 32.2 + - + +
355A MET* 3.1 14.1 + - - +
357A LYS* 1.3 76.7 - - + +
359A TRP* 1.3 57.5 + - + +
361A ARG* 3.4 4.1 + - + +
362A CYS* 3.0 27.5 + - - +
571A PRO* 3.2 32.5 - - + +
574A PRO* 3.7 17.0 - - + +
577A MET* 3.9 14.8 - - + -
593A ILE* 3.7 29.6 - - + -
597A LEU* 4.3 11.7 - - + -
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Residues in contact with TRP 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A TYR* 3.9 15.9 - - + -
310A ILE* 3.9 17.5 - - + +
311A THR* 3.7 26.0 + - + +
313A PRO* 4.3 4.1 - - - +
332A LEU* 3.7 26.5 - - + -
355A MET* 3.2 51.0 + - + +
356A ALA 3.8 2.0 - - - +
357A LYS 3.2 0.4 - - - -
358A LEU* 1.3 75.9 - - - +
360A LEU* 1.3 63.7 + - - +
362A CYS* 3.7 5.0 - - + +
363A ALA* 3.3 20.8 + - - +
577A MET* 3.2 39.9 - - + +
579A GLN 3.1 28.5 - - - -
580A PRO 3.7 1.3 + - - -
581A PRO* 3.5 34.0 - - + +
582A PRO* 4.5 4.7 - - + -
596A SER* 4.6 4.4 + - - -
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Residues in contact with LEU 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A PHE* 4.1 11.9 - - + -
242A PHE* 4.0 22.7 - - + -
290A THR* 4.0 5.8 - - - +
292A TYR* 3.9 18.1 - - + -
313A PRO* 3.8 28.7 - - + -
314A LEU 4.3 1.1 - - - +
315A GLY* 4.0 23.8 - - - +
317A PHE* 4.2 7.2 - - + -
327A PRO* 5.8 0.4 - - + -
330A ILE* 3.9 24.9 - - + -
332A LEU* 5.1 0.4 - - - +
356A ALA 3.2 11.5 + - - +
357A LYS 3.2 9.5 + - - +
359A TRP* 1.3 75.0 - - - +
361A ARG* 1.3 63.7 + - - +
363A ALA* 3.4 5.7 + - - +
364A ASP* 3.2 19.4 + - - +
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Residues in contact with ARG 361 (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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238A PHE* 3.2 37.0 - - + -
241A GLN* 3.8 36.3 + - - +
242A PHE* 3.6 32.2 - - - -
246A SER 5.9 1.0 - - - +
357A LYS 3.1 7.4 + - - +
358A LEU* 3.8 2.0 - - + +
360A LEU* 1.3 73.6 - - - +
362A CYS* 1.3 60.6 + - - +
364A ASP* 3.0 25.7 + - - +
365A THR* 2.9 32.2 + - - -
566A THR* 4.0 13.9 - - - +
571A PRO 5.6 0.7 - - - +
572A ASN* 3.1 22.8 + - - +
573A SER* 3.3 24.1 + - - -
574A PRO* 3.8 19.3 - - + -
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Residues in contact with CYS 362 (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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310A ILE* 3.4 21.5 - - + -
358A LEU 3.0 18.1 + - - +
359A TRP* 3.7 9.6 - - - +
360A LEU 3.3 0.2 - - - -
361A ARG* 1.3 76.7 - - - +
363A ALA* 1.3 62.9 + - - +
365A THR* 3.2 7.6 + - - -
366A GLN* 3.0 27.4 + - - -
574A PRO* 3.3 27.0 + - + +
576A LEU* 3.9 33.0 - - - -
577A MET* 4.1 11.7 - - + -
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Residues in contact with ALA 363 (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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292A TYR* 4.2 7.6 - - + -
295A LEU* 3.6 27.6 - - + +
310A ILE* 3.8 9.5 - - + +
311A THR* 4.7 0.4 - - - +
313A PRO* 3.5 34.3 - - + -
359A TRP 3.3 5.9 + - - +
360A LEU 3.5 4.7 - - - +
361A ARG 3.2 0.2 - - - -
362A CYS* 1.3 78.2 - - - +
364A ASP* 1.3 63.9 + - - +
366A GLN* 3.2 7.6 + - - +
367A TYR* 3.2 19.6 + - - +
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Residues in contact with ASP 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A PHE* 4.1 9.0 - - + -
247A ASN* 3.0 34.9 + - - +
250A VAL* 4.1 3.1 - - - +
292A TYR* 2.6 35.9 + - - +
360A LEU 3.2 8.3 + - - +
361A ARG* 3.0 36.9 + - - +
363A ALA* 1.3 79.0 - - - +
365A THR* 1.3 58.5 + - - +
367A TYR* 3.2 2.3 + - - +
368A HIS* 2.8 28.1 + - - +
567A TYR* 5.4 0.5 + - - -
573A SER* 5.0 1.2 + - - -
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Residues in contact with THR 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A ARG 2.9 8.5 + - - -
362A CYS 3.2 4.5 + - - -
364A ASP* 1.3 75.3 - - - +
366A GLN* 1.3 66.7 + - - +
368A HIS 3.2 0.2 + - - -
369A GLN* 3.0 29.0 + - + +
431A LEU* 4.1 10.8 - - + -
567A TYR* 3.5 30.6 - - + +
573A SER* 2.9 24.9 + - - -
574A PRO 2.9 26.7 + - - +
575A THR* 3.9 18.4 - - + -
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Residues in contact with GLN 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A LEU* 4.0 16.8 - - + -
310A ILE* 3.9 17.9 - - + -
362A CYS* 3.0 25.4 + - - +
363A ALA* 3.4 7.6 - - - +
365A THR* 1.3 77.9 - - - +
367A TYR* 1.3 63.0 + - - +
370A MET* 3.3 28.2 + - - +
431A LEU* 3.7 14.0 - - - +
432A SER* 3.5 13.6 + - - -
433A ILE* 3.3 44.9 + - + +
441A LEU* 3.7 3.5 - - - +
575A THR 2.8 29.1 + - - -
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Residues in contact with TYR 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ASN* 3.6 11.2 - - - +
249A GLU* 4.2 15.4 + - + +
250A VAL* 3.9 24.0 - - + +
291A ASP 5.9 2.0 - - - -
292A TYR* 4.2 17.7 - + + -
294A ILE* 4.0 24.2 - - + -
295A LEU* 5.3 3.1 - - + +
363A ALA 3.2 9.2 + - - +
364A ASP 3.4 9.2 - - - +
365A THR 3.2 0.4 - - - -
366A GLN* 1.3 80.5 - - - +
368A HIS* 1.3 57.0 + - - +
371A ILE* 2.9 55.9 + - + +
372A THR* 3.1 26.2 + - - -
376A ARG* 5.5 0.2 - - - -
441A LEU* 4.5 8.0 - - - +
445A HIS* 4.1 17.0 - - - -
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Residues in contact with HIS 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A SER* 2.9 32.3 + - - -
247A ASN* 3.7 14.8 - - + +
364A ASP* 2.8 20.5 + - - +
365A THR* 3.2 1.1 + - - +
367A TYR* 1.3 73.3 - - - +
369A GLN* 1.3 64.5 + - - +
372A THR* 3.3 18.2 + - + -
373A HIS* 2.8 35.3 + - + +
559A VAL* 2.8 29.5 + - + +
563A GLN* 3.5 28.9 - - + -
567A TYR* 2.8 29.6 + + - +
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Residues in contact with GLN 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A THR* 3.0 23.5 + - + +
366A GLN 4.2 0.2 - - - +
368A HIS* 1.3 80.8 + - - +
370A MET* 1.3 62.2 + - - +
373A HIS* 3.6 10.7 + - - +
374A LEU* 3.2 36.0 + - + +
427A ALA* 6.2 0.4 - - + -
430A VAL* 6.1 1.3 - - + -
431A LEU* 4.1 31.4 - - + -
563A GLN* 2.9 28.0 + - - +
567A TYR* 3.5 24.2 - - - -
606A MET* 3.8 17.0 - - + +
613A LEU* 4.5 8.4 - - - +
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Residues in contact with MET 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A GLN 3.3 15.9 + - - +
369A GLN* 1.3 81.7 - - - +
371A ILE* 1.3 60.6 + - - +
374A LEU* 3.7 23.5 - - + +
375A LEU* 3.0 28.1 + - - +
421A ILE* 4.9 3.8 - - + -
427A ALA* 4.2 7.2 - - + -
431A LEU* 3.6 29.8 - - + -
433A ILE* 4.0 11.7 - - + -
438A GLN* 3.3 44.2 - - + +
441A LEU* 4.0 10.1 - - + -
442A MET* 3.4 29.2 - - + +
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Residues in contact with ILE 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ILE* 3.7 30.3 - - + -
367A TYR* 2.9 45.7 + - + +
370A MET* 1.3 79.1 - - - +
372A THR* 1.3 60.0 + - - +
373A HIS 3.3 1.3 - - - -
375A LEU* 3.8 3.3 + - + -
376A ARG* 2.9 48.4 + - - +
441A LEU* 3.8 29.8 - - + +
442A MET* 4.8 1.8 - - - -
445A HIS* 3.7 36.8 - - + +
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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