Contacts of the helix formed by residues 370 - 396 (chain A) in PDB entry 3V6A
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 LEU 370 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A PHE* 5.9 1.3 - - - -
361A LEU* 3.3 44.9 - - + +
362A THR* 5.2 3.1 - - - +
364A LYS 6.1 2.7 - - - -
367A ALA* 3.4 20.6 + - - +
368A GLU 3.2 0.4 - - - -
369A LYS* 1.3 76.1 - - - +
371A LYS* 1.3 60.3 + - - +
373A PHE* 3.1 39.0 + - + +
374A LYS* 3.2 8.6 + - + +
429A PHE 6.0 1.8 - - - +
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Residues in contact with LYS 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A GLU* 3.8 20.0 + - + +
369A LYS 3.4 0.4 - - - -
370A LEU* 1.3 73.1 - - - +
372A ASP* 1.3 56.6 + - - +
373A PHE 3.0 4.9 - - - -
374A LYS* 3.7 21.3 - - + +
375A ILE* 3.0 28.9 + - + +
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Residues in contact with ASP 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A LEU* 6.0 0.9 - - - -
320A LEU* 3.5 12.6 - - - +
368A GLU 3.8 5.1 + - - +
369A LYS* 3.2 51.7 + - + +
371A LYS* 1.3 76.0 - - - +
373A PHE* 1.3 57.2 + - - +
375A ILE* 3.3 17.1 - - - +
376A ARG* 3.0 42.2 + - - +
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Residues in contact with PHE 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A PHE* 3.9 19.7 - + + -
314A LEU* 4.1 11.2 - - + -
315A LEU* 3.5 31.4 - - + -
318A MET* 3.8 17.0 - - + -
350A PHE* 5.3 2.9 - + - -
361A LEU* 4.4 27.1 - - + -
369A LYS 2.9 7.9 + - - +
370A LEU* 3.1 23.6 - - + +
371A LYS 3.0 0.2 - - - -
372A ASP* 1.3 75.7 - - - +
374A LYS* 1.3 59.1 + - - +
375A ILE 3.1 0.7 - - - -
376A ARG* 2.7 29.4 + - + +
377A LEU* 3.0 35.5 + - + +
428A LEU* 4.3 27.1 - - + -
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Residues in contact with LYS 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A LEU* 3.2 9.8 + - + +
371A LYS* 3.7 26.2 - - + +
373A PHE* 1.3 79.5 - - - +
375A ILE* 1.3 56.3 + - - +
377A LEU* 3.2 11.6 + - + +
378A GLN* 2.8 51.5 + - + +
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Residues in contact with ILE 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LEU* 3.5 14.6 - - + -
321A PRO* 3.4 32.9 - - + +
371A LYS* 3.0 12.6 + - + +
372A ASP* 3.3 38.4 - - - +
374A LYS* 1.3 75.9 - - - +
376A ARG* 1.3 64.7 + - - +
378A GLN* 3.7 9.2 + - + +
379A TYR* 3.1 25.6 + - - +
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Residues in contact with ARG 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A LEU* 3.0 54.0 + - + +
318A MET* 3.1 40.9 + - + +
319A PRO* 3.4 25.1 - - - +
320A LEU* 3.5 27.8 - - + +
369A LYS* 4.6 6.7 - - - +
372A ASP* 3.0 37.2 + - - +
373A PHE* 2.7 15.4 + - + +
375A ILE* 1.3 82.7 - - + +
377A LEU* 1.3 55.7 + - - -
379A TYR* 3.8 3.2 + - - +
380A PHE* 3.2 26.2 + - - +
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Residues in contact with LEU 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A MET* 3.4 36.1 - - + -
347A LEU* 5.3 3.1 - - + -
373A PHE* 3.0 37.8 + - + +
374A LYS* 3.6 11.7 - - + +
376A ARG* 1.3 74.2 - - - +
378A GLN* 1.3 59.1 + - - +
379A TYR 3.1 1.6 - - - -
380A PHE* 2.9 5.2 + - - +
381A ALA* 2.7 37.8 + - - +
425A ILE* 4.1 35.1 - - + +
428A LEU* 3.7 28.0 - - + +
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Residues in contact with GLN 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A LYS* 2.8 43.1 + - + +
375A ILE* 3.9 11.2 - - + +
377A LEU* 1.3 71.9 - - - +
379A TYR* 1.3 63.2 + - - +
381A ALA* 3.7 6.5 + - - +
382A ARG* 3.2 53.4 + - - +
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Residues in contact with TYR 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A PRO* 4.1 29.8 - - + -
320A LEU 4.1 10.7 + - - -
321A PRO* 3.8 44.0 + - + -
338A LEU* 4.9 10.2 - - + +
375A ILE 3.1 16.3 + - - +
376A ARG* 3.9 4.3 - - - +
377A LEU 3.1 0.8 - - - -
378A GLN* 1.3 78.4 - - - +
380A PHE* 1.3 65.5 + - - +
382A ARG* 3.4 24.5 - - + +
383A GLY* 3.4 13.3 + - - -
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Residues in contact with PHE 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A TYR 3.5 20.6 - - - -
318A MET* 4.1 20.6 - - + -
319A PRO* 4.4 1.8 - - + -
338A LEU* 3.6 43.8 - - + +
339A GLN 4.8 0.2 - - - -
340A PHE* 3.8 26.7 - + - -
343A VAL* 3.6 35.2 - - + -
376A ARG 3.2 15.3 + - - +
377A LEU* 2.9 7.7 + - - +
379A TYR* 1.3 72.5 - + - +
381A ALA* 1.3 55.1 + - - +
382A ARG 3.0 1.6 - - - -
383A GLY* 2.7 24.8 + - - +
384A LEU* 2.7 20.8 + - + +
421A ILE* 4.1 19.7 - - + -
425A ILE* 4.5 7.2 - - + -
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Residues in contact with ALA 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LEU 2.7 20.0 + - - +
378A GLN* 3.8 7.2 - - - +
380A PHE* 1.3 72.4 - - - +
382A ARG* 1.3 61.2 + - - +
384A LEU* 3.2 27.1 - - - +
385A GLN* 3.4 17.5 + - - +
422A ASN* 5.2 8.7 - - - +
425A ILE* 4.5 18.2 - - + +
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Residues in contact with ARG 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A PRO* 6.3 1.0 - - - +
378A GLN* 3.2 47.6 + - - +
379A TYR* 3.4 27.8 - - + +
380A PHE 3.0 0.2 - - - -
381A ALA* 1.3 81.8 - - - +
383A GLY* 1.3 60.3 + - - +
385A GLN* 3.4 23.8 + - - +
386A VAL* 3.5 19.4 + - + +
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Residues in contact with GLY 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A LEU* 4.1 13.7 - - - -
340A PHE* 4.0 9.4 - - - -
379A TYR 3.4 4.9 + - - -
380A PHE 2.7 12.9 + - - -
382A ARG* 1.3 74.0 - - - +
384A LEU* 1.3 62.2 + - - +
386A VAL* 3.6 9.8 + - - +
387A TYR* 3.1 23.7 + - - +
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Residues in contact with LEU 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A PHE* 3.5 29.6 - - + -
380A PHE* 2.7 18.3 + - + +
381A ALA* 3.2 19.7 - - - +
383A GLY* 1.3 74.4 - - - +
385A GLN* 1.3 57.0 + - + +
387A TYR* 3.0 4.9 + - - +
388A ILE* 2.8 42.0 + - + +
418A THR* 3.7 27.4 - - - +
421A ILE* 4.0 13.0 - - + -
422A ASN* 3.7 47.8 - - + +
425A ILE* 4.7 2.9 - - + -
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Residues in contact with GLN 385 (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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381A ALA* 3.4 16.8 + - - +
382A ARG* 3.4 15.5 + - - +
384A LEU* 1.3 74.8 - - + +
386A VAL* 1.3 57.3 - - + +
388A ILE* 3.1 9.8 + - - +
389A ARG* 2.7 37.7 + - - +
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Residues in contact with VAL 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A ARG* 3.5 19.1 - - + +
383A GLY* 3.8 10.3 - - - +
384A LEU 3.3 0.2 - - - -
385A GLN* 1.3 76.7 - - + +
387A TYR* 1.3 64.6 + - - +
389A ARG* 3.2 28.8 + - - +
390A GLN* 3.0 47.3 + - - +
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Residues in contact with TYR 387 (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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340A PHE* 3.5 36.8 - + + -
383A GLY 3.1 14.2 + - - +
384A LEU* 3.0 5.6 + - - +
386A VAL* 1.3 80.5 - - - +
388A ILE* 1.3 61.4 + - - +
390A GLN* 3.2 22.2 + - + +
391A LEU* 3.0 58.7 + - + +
411A LYS* 5.8 0.8 + - - -
414A ALA* 4.2 12.9 - - + +
418A THR* 3.5 25.4 - - + -
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Residues in contact with ILE 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A LEU* 2.8 34.1 + - + +
385A GLN* 3.5 7.0 - - - +
387A TYR* 1.3 71.7 - - - +
389A ARG* 1.3 57.1 + - - +
391A LEU* 3.2 8.8 + - - +
392A ARG* 2.9 40.0 + - + +
415A LEU* 4.0 13.2 - - + -
418A THR* 3.3 36.6 - - - +
419A ASN* 3.9 26.9 - - - +
422A ASN* 5.2 4.5 - - + -
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Residues in contact with ARG 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A GLN 2.7 20.0 + - - +
386A VAL* 3.5 37.0 - - - +
388A ILE* 1.3 72.3 - - - +
390A GLN* 1.3 73.0 + - - +
392A ARG* 3.8 4.8 - - - +
393A LEU* 2.9 52.7 + - + +
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Residues in contact with GLN 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A VAL* 3.0 33.9 + - - +
387A TYR* 3.4 28.7 - - + +
389A ARG* 1.3 91.2 - - - +
391A LEU* 1.3 62.6 + - + +
393A LEU* 3.8 8.4 - - + +
394A ALA* 3.2 23.9 + - - +
411A LYS* 5.8 0.3 + - - -
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Residues in contact with LEU 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A TYR* 3.0 57.4 + - + +
388A ILE 3.6 4.9 - - - +
390A GLN* 1.3 75.0 - - + +
392A ARG* 1.3 66.7 + - - +
394A ALA* 3.1 6.5 + - - +
395A LEU* 3.1 29.4 + - + +
411A LYS* 4.0 40.8 - - + +
414A ALA* 3.8 33.7 - - + +
415A LEU* 4.1 21.3 - - + +
418A THR* 4.4 2.9 - - - +
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Residues in contact with ARG 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ILE* 2.9 29.1 + - + +
389A ARG* 3.9 4.7 - - - +
391A LEU* 1.3 76.4 - - - +
393A LEU* 1.3 63.2 - - + +
395A LEU* 3.4 6.4 + - - +
396A GLN* 3.3 23.9 + - - +
415A LEU* 4.0 29.4 - - + -
419A ASN* 6.2 0.2 - - - +
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Residues in contact with LEU 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ARG* 2.9 46.2 + - + +
390A GLN* 3.8 7.6 - - - +
392A ARG* 1.3 79.0 - - + +
394A ALA* 1.3 62.8 + - - +
395A LEU 3.1 1.0 + - - -
396A GLN* 3.3 34.8 + - - +
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Residues in contact with ALA 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A GLN 3.2 14.3 + - - +
391A LEU* 3.1 6.1 + - - +
393A LEU* 1.3 78.9 - - - +
395A LEU* 1.3 59.8 + - - +
396A GLN 3.8 0.6 + - - +
398A LYS* 3.0 29.1 + - - -
408A ASN* 5.1 0.5 - - - +
411A LYS* 4.2 27.8 - - + +
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Residues in contact with LEU 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A LEU* 3.1 16.4 + - + +
392A ARG* 4.0 5.4 - - - +
393A LEU 3.1 0.6 - - - -
394A ALA* 1.3 81.5 - - - +
396A GLN* 1.3 59.4 + - - +
398A LYS* 3.2 26.8 + - - +
403A LEU* 4.4 14.6 - - + +
408A ASN* 4.2 24.5 - - + +
411A LYS* 3.7 33.0 - - + -
412A VAL* 4.2 22.0 - - + +
415A LEU* 3.6 31.2 - - + -
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Residues in contact with GLN 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A ARG 3.3 11.9 + - - +
393A LEU* 3.3 32.7 + - - +
394A ALA 4.9 0.5 - - - +
395A LEU* 1.3 74.8 - - - +
397A GLY* 1.3 59.2 + - - +
398A LYS* 3.1 13.5 + - - +
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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