Contacts of the helix formed by residues 414 - 442 (chain E) in PDB entry 2BG9
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 SER 414 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415E CYS* 1.3 68.9 + - - +
416E VAL* 2.6 33.0 - - - +
417E GLU* 3.4 9.8 + - - +
418E ALA* 3.2 22.0 + - - +
421E PHE* 5.6 0.2 - - - -
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Residues in contact with CYS 415 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374D SER 3.8 14.4 - - - +
376D ILE* 4.7 3.1 - - - -
377D GLU* 3.1 33.9 - - + -
380D LYS* 3.1 27.9 - - - +
414E SER* 1.3 83.4 + - - +
416E VAL* 1.3 71.4 + - - +
418E ALA* 3.4 6.2 + - - +
419E CYS* 3.1 30.7 + - - -
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Residues in contact with VAL 416 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ILE* 3.8 30.5 - - + -
380D LYS* 3.5 21.1 - - - +
414E SER 2.6 29.2 - - - +
415E CYS* 1.3 84.0 - - - +
417E GLU* 1.3 80.8 + - + +
419E CYS* 3.3 2.9 + - - +
420E ASN* 2.5 52.8 + - - +
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Residues in contact with GLU 417 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ILE* 5.7 5.3 - - + +
379A VAL* 5.8 5.9 - - + +
414E SER* 3.4 10.1 + - - +
415E CYS 3.3 0.4 - - - -
416E VAL* 1.3 90.3 - - + +
418E ALA* 1.3 54.2 + - - +
420E ASN* 3.7 11.7 - - + +
421E PHE* 2.5 78.0 + - + -
424E LYS* 6.4 0.9 - - + -
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Residues in contact with ALA 418 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414E SER 3.2 16.3 + - - +
415E CYS* 3.8 7.6 - - - +
417E GLU* 1.3 76.4 - - - +
419E CYS* 1.3 62.0 + - - +
421E PHE* 3.2 32.3 - - + +
422E ILE* 3.4 15.5 + - - +
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Residues in contact with CYS 419 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377D GLU* 4.7 3.1 - - - -
380D LYS* 3.4 39.0 - - + +
381D TYR* 3.9 28.0 - - - -
384D GLU* 4.8 0.6 - - + +
415E CYS* 3.1 18.6 + - - +
416E VAL 3.9 2.5 - - - +
417E GLU 3.1 0.4 - - - -
418E ALA* 1.3 79.5 - - - +
420E ASN* 1.3 64.5 + - - +
421E PHE 3.1 1.6 - - - -
422E ILE* 3.2 17.1 - - + +
423E ALA* 3.1 24.6 + - - +
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Residues in contact with ASN 420 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ILE* 5.3 4.4 - - - +
379A VAL* 3.5 37.0 - - + +
380A LYS* 6.1 0.4 - - - +
416E VAL* 2.5 51.3 + - - +
417E GLU* 3.1 14.1 + - + +
419E CYS* 1.3 74.0 - - - +
421E PHE* 1.3 63.9 + - - +
423E ALA* 4.1 4.4 - - - +
424E LYS* 3.0 43.7 + - + +
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Residues in contact with PHE 421 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414E SER 5.6 0.4 - - - -
417E GLU* 2.5 66.6 + - + +
418E ALA* 3.2 20.6 - - + +
420E ASN* 1.3 75.8 - - + +
422E ILE* 1.3 67.1 + - + +
424E LYS* 3.3 11.9 + - + +
425E SER* 3.2 15.8 + - - -
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Residues in contact with ILE 422 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381D TYR* 5.1 6.5 - - + -
384D GLU* 3.4 40.5 - - + +
418E ALA 3.4 10.1 - - - +
419E CYS* 3.2 36.3 - - + +
421E PHE* 1.3 78.4 - - + +
423E ALA* 1.3 56.5 + - - +
425E SER* 2.8 29.4 + - - -
426E THR* 3.2 7.4 + - - -
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Residues in contact with ALA 423 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384D GLU* 4.2 10.3 - - - +
419E CYS 3.1 18.9 + - - +
420E ASN* 4.1 4.5 - - - +
422E ILE* 1.3 71.8 - - - +
424E LYS* 1.3 60.3 + - + +
425E SER 2.7 10.6 + - - -
426E THR* 3.0 19.0 + - - +
427E LYS* 3.3 10.7 + - - +
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Residues in contact with LYS 424 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A VAL* 4.2 26.2 - - + -
382A ILE* 3.2 36.8 - - - +
417E GLU* 6.4 1.3 - - + -
420E ASN* 3.0 36.5 + - + +
421E PHE* 3.5 13.5 - - + +
423E ALA* 1.3 75.4 - - + +
425E SER* 1.3 56.2 + - - +
427E LYS* 3.5 23.5 - - + +
428E GLU* 3.3 24.6 + - - +
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Residues in contact with SER 425 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421E PHE 3.2 8.1 + - - -
422E ILE* 2.8 22.4 + - - -
423E ALA 2.7 1.0 - - - -
424E LYS* 1.3 75.5 - - - +
426E THR* 1.3 53.7 + - - -
427E LYS 2.9 2.4 + - - -
428E GLU* 2.9 6.4 + - - +
429E GLN* 2.2 50.6 + - - +
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Residues in contact with THR 426 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384D GLU* 4.8 5.5 + - - -
387D LYS* 4.0 30.3 + - + +
391D GLU* 4.5 12.5 + - - +
422E ILE 3.2 6.3 + - - -
423E ALA* 3.0 12.2 + - - -
425E SER* 1.3 78.3 + - - +
427E LYS* 1.3 56.0 + - - +
429E GLN* 3.7 19.1 + - + +
430E ASN* 2.7 42.2 + - + +
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Residues in contact with LYS 427 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A ILE 4.3 1.0 + - - -
383A ALA* 3.5 24.7 + - - +
386A MET* 3.4 39.7 - - + +
423E ALA 3.3 7.2 + - - +
424E LYS* 3.5 25.6 - - + +
425E SER 2.9 0.8 + - - -
426E THR* 1.3 79.9 - - - +
428E GLU* 1.3 58.7 + - - +
430E ASN* 3.9 2.3 - - - +
431E ASP* 2.8 29.6 + - + +
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Residues in contact with GLU 428 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424E LYS 3.3 10.6 + - - +
425E SER* 2.9 7.7 + - - +
427E LYS* 1.3 80.8 - - - +
429E GLN* 1.3 57.2 + - - +
431E ASP* 3.3 13.7 - - - +
432E SER* 2.8 37.3 + - - +
435E GLU* 5.7 0.9 - - - +
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Residues in contact with GLN 429 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391D GLU* 3.9 20.0 + - - +
425E SER* 2.2 44.8 + - - +
426E THR* 3.7 16.8 + - + +
428E GLU* 1.3 65.5 - - - +
430E ASN* 1.3 67.5 + - + +
432E SER* 3.2 17.8 + - - -
433E GLY* 3.2 8.0 + - - -
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Residues in contact with ASN 430 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426E THR* 2.7 31.2 + - + +
427E LYS* 4.1 2.5 - - - +
429E GLN* 1.3 73.8 - - + +
431E ASP* 1.3 51.8 + - - +
433E GLY* 2.7 7.8 + - - +
434E SER* 2.7 38.5 + - - -
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Residues in contact with ASP 431 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427E LYS* 2.8 21.5 + - + +
428E GLU* 3.3 16.8 - - - +
430E ASN* 1.3 76.0 - - - +
432E SER* 1.3 50.0 + - - +
434E SER* 3.0 10.3 + - - +
435E GLU* 2.6 62.4 + - - +
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Residues in contact with SER 432 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428E GLU* 2.8 20.1 + - - +
429E GLN* 3.2 12.6 + - - -
431E ASP* 1.3 75.5 - - - +
433E GLY* 1.3 57.0 + - - +
435E GLU* 2.7 38.2 + - - +
436E ASN* 2.9 14.5 + - - +
439E TRP* 4.2 3.6 - - - -
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Residues in contact with GLY 433 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429E GLN 3.2 4.9 + - - -
430E ASN* 2.7 17.6 + - - -
432E SER* 1.3 70.0 - - - +
434E SER* 1.3 53.9 + - - -
435E GLU 2.9 4.3 - - - -
436E ASN* 2.7 41.4 + - - +
437E GLU* 3.4 7.5 + - - +
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Residues in contact with SER 434 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430E ASN* 2.7 20.9 + - - -
431E ASP* 3.7 13.1 + - - -
433E GLY* 1.3 72.1 - - - -
435E GLU* 1.3 61.8 + - - +
437E GLU* 3.0 30.7 - - - +
438E ASN* 3.2 4.7 + - - +
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Residues in contact with GLU 435 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428E GLU* 5.7 1.4 - - - +
431E ASP* 2.6 51.0 + - - +
432E SER* 2.7 31.4 + - - +
434E SER* 1.3 70.2 - - - +
436E ASN* 1.3 67.1 + - - +
438E ASN* 2.7 27.4 + - - +
439E TRP* 2.7 45.2 + - + -
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Residues in contact with ASN 436 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312E ASN* 3.8 20.3 - - - +
432E SER 2.9 22.4 + - - +
433E GLY* 2.7 22.3 + - - +
435E GLU* 1.3 73.5 - - - +
437E GLU* 1.3 72.2 + - - +
439E TRP* 2.7 34.7 + - - +
440E VAL* 3.0 14.4 + - - +
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Residues in contact with GLU 437 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312E ASN* 4.8 20.1 + - - +
313E THR* 5.8 2.1 - - - +
433E GLY 3.4 8.8 - - - +
434E SER* 3.0 31.4 - - - +
436E ASN* 1.3 83.5 - - - +
438E ASN* 1.3 52.6 + - - +
440E VAL* 3.0 6.8 + - - +
441E LEU* 2.6 56.9 + - + +
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Residues in contact with ASN 438 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434E SER 3.2 3.3 + - - +
435E GLU* 2.7 23.5 + - - +
437E GLU* 1.3 75.7 - - - +
439E TRP* 1.3 88.4 + - - +
440E VAL 2.6 12.3 + - - -
441E LEU* 2.9 15.1 + - - -
442E ILE* 3.0 41.2 + - - +
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Residues in contact with TRP 439 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432E SER* 4.2 3.4 - - - -
435E GLU* 2.7 49.8 - - + -
436E ASN* 2.7 49.8 + - - +
438E ASN* 1.3 96.7 - - - +
440E VAL* 1.3 64.1 + - + +
442E ILE* 4.3 10.1 + - - +
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Residues in contact with VAL 440 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310E THR* 2.9 23.9 - - - +
311E PRO* 3.0 50.0 - - + -
312E ASN* 3.5 26.2 - - + +
313E THR* 3.5 20.2 - - + +
436E ASN* 3.0 16.2 + - + +
437E GLU* 3.0 10.1 + - - +
438E ASN 2.6 6.1 + - - -
439E TRP* 1.3 83.5 - - + +
441E LEU* 1.4 58.6 + - - +
442E ILE 3.4 4.4 + - - -
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Residues in contact with LEU 441 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309E ARG* 6.3 0.7 - - - +
310E THR* 5.0 0.7 - - - -
313E THR* 3.6 34.1 - - + +
437E GLU* 2.6 48.9 + - + +
438E ASN* 4.1 7.0 - - - +
440E VAL* 1.4 70.8 - - - +
442E ILE* 1.3 64.6 + - + +
443E GLY* 2.9 10.0 + - - -
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Residues in contact with ILE 442 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438E ASN* 3.0 50.6 + - - +
439E TRP* 4.3 7.9 - - - +
440E VAL 3.4 5.9 + - - +
441E LEU* 1.3 75.9 - - + +
443E GLY* 1.3 49.8 + - - +
444E LYS* 2.6 41.6 + - + +
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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