Contacts of the helix formed by residues 403 - 430 (chain B) 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 GLU 403 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B ALA* 1.3 87.2 + - - +
405B VAL* 3.3 9.1 - - + +
406B GLU* 3.3 26.3 + - - +
407B ALA* 3.0 23.6 + - - +
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Residues in contact with ALA 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A GLU* 3.1 43.1 - - + +
380A LYS* 3.7 7.1 - - - +
381A TYR* 5.7 2.5 - - - +
403B GLU* 1.3 88.9 + - + +
405B VAL* 1.3 62.8 + - + +
407B ALA* 2.6 36.1 + - + +
408B ILE 3.2 3.5 + - - -
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Residues in contact with VAL 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ILE* 4.4 15.7 - - + -
380A LYS* 3.5 21.2 - - - +
403B GLU* 4.6 8.1 - - + +
404B ALA* 1.3 76.4 - - + +
406B GLU* 1.3 59.0 + - + +
408B ILE* 2.6 34.8 - - - +
409B LYS* 2.9 28.0 - - - +
423C ILE* 3.8 13.9 - - + -
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Residues in contact with GLU 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B GLU 3.3 22.2 + - - +
404B ALA 3.1 0.4 - - - -
405B VAL* 1.3 78.7 - - + +
407B ALA* 1.3 53.3 + - - +
409B LYS* 2.9 27.6 - - + +
410B TYR* 2.6 35.8 + - - +
413B GLU* 4.3 3.5 - - - +
422C GLY* 3.2 37.5 - - - +
423C ILE* 4.4 3.4 - - + +
425C SER* 4.7 3.6 - - - -
426C THR* 3.6 4.7 + - - +
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Residues in contact with ALA 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A LYS* 5.6 0.7 - - + -
381A TYR* 5.7 6.3 - - + +
403B GLU* 3.0 8.4 + - - +
404B ALA* 2.6 32.2 + - + +
406B GLU* 1.3 69.1 - - - +
408B ILE* 1.3 50.7 + - - +
410B TYR* 2.8 12.2 + - + +
411B ILE* 2.5 50.3 + - + +
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Residues in contact with ILE 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A LYS* 3.1 65.4 - - + +
383A ALA* 4.9 7.4 - - + -
384A GLU* 3.5 16.7 - - + +
387A LYS* 5.8 3.1 + - + +
404B ALA 3.2 2.0 + - - -
405B VAL 2.6 28.0 + - - +
407B ALA* 1.3 77.0 - - - +
409B LYS* 1.3 70.6 + - + +
411B ILE* 3.0 14.1 + - + +
412B ALA* 2.6 37.4 + - + +
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Residues in contact with LYS 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B VAL* 2.9 41.5 + - - +
406B GLU* 2.9 26.9 - - + +
408B ILE* 1.3 87.8 - - + +
410B TYR* 1.3 47.1 + - - +
412B ALA* 2.6 12.9 + - - +
413B GLU* 2.4 42.3 + - - +
423C ILE* 3.1 30.4 - - - +
426C THR* 2.6 48.8 - - + +
427C ASN* 5.0 7.6 - - - +
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Residues in contact with TYR 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B GLU 2.6 15.8 + - - +
407B ALA* 3.0 16.8 - - + +
409B LYS* 1.3 73.7 - - - +
411B ILE* 1.3 61.5 + - + +
413B GLU* 3.1 27.4 + - + +
414B GLN* 2.9 52.1 + - + +
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Residues in contact with ILE 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A TYR* 5.0 16.6 - - + +
384A GLU* 3.0 45.3 - - + +
387A LYS* 4.7 1.7 + - - -
407B ALA* 2.5 43.6 + - + +
408B ILE* 3.3 14.1 - - + +
410B TYR* 1.3 79.0 - - + +
412B ALA* 1.3 56.0 + - - +
414B GLN* 4.0 4.7 - - - +
415B LEU* 3.2 24.6 + - - +
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Residues in contact with ALA 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A LYS* 4.7 10.5 - - - +
408B ILE* 2.6 17.7 + - + +
409B LYS* 2.6 21.3 + - - +
411B ILE* 1.3 72.2 - - - +
413B GLU* 1.3 62.7 + - + +
415B LEU* 3.2 14.6 + - - +
416B GLU* 3.5 15.4 + - - +
426C THR* 5.7 1.6 - - + -
429C ILE* 6.0 3.6 - - + -
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Residues in contact with GLU 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B GLU* 4.3 3.6 - - - +
409B LYS* 2.4 23.4 + - - +
410B TYR* 3.1 42.4 + - + +
412B ALA* 1.3 74.7 - - + +
414B GLN* 1.3 57.1 + - + +
416B GLU* 4.6 1.4 - - - +
417B SER* 2.5 33.6 + - - -
426C THR* 4.4 15.7 + - + +
429C ILE* 4.5 30.6 - - + +
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Residues in contact with GLN 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B TYR* 2.9 42.8 + - + +
411B ILE* 4.3 5.6 - - - +
413B GLU* 1.3 80.5 - - + +
415B LEU* 1.3 66.1 + - - +
417B SER* 3.5 9.1 + - - -
418B ALA* 2.7 39.5 + - + +
421B PHE* 5.6 2.5 - - - -
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Residues in contact with LEU 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A GLU* 5.6 0.4 - - - +
387A LYS* 4.1 32.8 - - + +
411B ILE 3.2 17.4 + - - +
412B ALA* 3.2 6.9 + - - +
414B GLN* 1.3 83.0 - - - +
416B GLU* 1.3 75.3 + - + +
418B ALA* 3.6 2.6 - - - +
419B SER* 3.3 20.9 + - - +
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Residues in contact with GLU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B ALA 3.5 11.0 + - - +
413B GLU* 4.6 1.3 - - - +
415B LEU* 1.3 92.0 - - + +
417B SER* 1.3 69.2 + - - +
419B SER* 3.2 4.3 + - - -
420B GLU* 3.0 34.9 + - + +
429C ILE* 4.9 0.9 - - - +
430C VAL* 5.4 2.8 - - - +
433C ILE* 2.6 59.1 - - - +
436C LYS* 5.7 0.5 + - - -
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Residues in contact with SER 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B GLU 2.5 26.0 + - - -
414B GLN* 3.3 15.1 + - - -
416B GLU* 1.3 80.6 - - - +
418B ALA* 1.3 69.4 + - - +
420B GLU* 3.1 15.2 + - - +
421B PHE* 2.8 40.3 + - - -
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Residues in contact with ALA 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B GLN* 2.7 38.0 + - + +
415B LEU* 3.6 3.6 - - - +
417B SER* 1.3 73.6 + - - +
419B SER* 1.3 60.0 + - - +
421B PHE* 3.0 26.8 - - - +
422B ASP* 3.5 8.5 + - - +
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Residues in contact with SER 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B LEU* 3.3 13.0 + - - +
416B GLU* 3.2 10.3 + - - -
418B ALA* 1.3 76.3 - - - +
420B GLU* 1.3 64.4 + - - +
421B PHE 3.1 1.8 - - - -
422B ASP* 2.9 12.6 + - - +
423B ASP* 2.7 36.5 + - - +
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Residues in contact with GLU 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B GLU* 3.0 32.3 + - + +
417B SER* 3.1 6.1 + - - +
419B SER* 1.3 78.0 + - - +
421B PHE* 1.3 51.8 + - + +
423B ASP* 3.0 10.9 + - + +
424B LEU* 2.3 59.7 + - + +
433C ILE* 5.9 0.3 - - - +
436C LYS* 5.8 2.4 + - - -
437C ASN* 4.6 20.4 + - - +
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Residues in contact with PHE 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B GLN* 5.6 3.6 - - - -
417B SER* 2.8 48.5 - - - -
418B ALA* 3.0 19.3 - - - +
420B GLU* 1.3 76.2 - - + +
422B ASP* 1.3 53.9 + - - +
424B LEU* 3.0 24.2 - - + +
425B LYS* 2.4 35.9 + - - +
428B TRP* 4.1 3.4 + - + +
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Residues in contact with ASP 422 (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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418B ALA 3.5 4.1 + - - +
419B SER* 2.9 26.3 + - - +
421B PHE* 1.3 80.7 - - - +
423B ASP* 1.3 58.4 + - - +
425B LYS* 3.0 31.5 + - - +
426B LYS* 3.3 18.1 + - - +
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Residues in contact with ASP 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B SER* 2.7 27.5 + - - +
420B GLU* 3.1 10.1 - - + +
422B ASP* 1.3 73.4 - - - +
424B LEU* 1.3 62.5 + - - +
425B LYS 3.1 0.7 - - - -
426B LYS* 3.4 44.1 + - + +
427B ASP* 3.5 5.4 + - - +
430B TYR* 4.1 5.2 + - - +
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Residues in contact with LEU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B GLU* 2.3 48.1 + - + +
421B PHE* 2.8 41.0 + - + +
423B ASP* 1.3 69.4 - - - +
425B LYS* 1.3 59.6 + - - +
426B LYS 3.2 0.7 - - - -
427B ASP* 3.0 17.8 + - + +
428B TRP* 2.8 59.1 - - + -
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Residues in contact with LYS 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ASN* 5.8 0.4 - - - -
421B PHE 2.4 19.1 + - - +
422B ASP* 3.0 23.3 - - - +
424B LEU* 1.3 70.1 - - - +
426B LYS* 1.3 63.2 + - - +
428B TRP* 2.7 25.4 + - + +
429B GLN* 2.9 34.0 + - - +
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Residues in contact with LYS 426 (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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310B ASN* 3.6 41.9 + - + +
422B ASP* 3.3 15.4 + - - +
423B ASP* 3.4 34.8 + - - +
425B LYS* 1.3 79.5 - - - +
427B ASP* 1.3 56.2 + - - +
429B GLN* 3.1 7.0 + - - +
430B TYR* 2.8 66.4 + - + +
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Residues in contact with ASP 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B ASP 3.5 3.9 + - - +
424B LEU* 3.0 24.2 + - + +
426B LYS* 1.3 75.4 - - - +
428B TRP* 1.3 94.4 + - + +
429B GLN 3.0 0.9 + - - -
430B TYR* 3.1 22.5 + - + +
431B VAL* 3.1 25.3 + - - +
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Residues in contact with TRP 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B PHE* 4.1 3.6 + - + +
424B LEU* 2.8 50.4 + - + +
425B LYS* 2.7 35.1 - - + +
427B ASP* 1.3 102.2 - - - +
429B GLN* 1.3 63.3 + - - +
431B VAL* 2.7 24.7 - - - +
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Residues in contact with GLN 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ARG* 3.4 16.1 + - - -
308B SER* 4.6 4.8 + - - -
309B PRO* 4.6 19.8 - - + +
310B ASN* 4.2 19.5 + - + +
425B LYS* 2.9 24.9 + - - +
426B LYS* 3.3 13.2 - - - +
427B ASP 3.0 0.2 - - - -
428B TRP* 1.3 86.2 + - - +
430B TYR* 1.3 61.1 + - + +
431B VAL* 3.7 2.8 + - - +
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Residues in contact with TYR 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ARG* 4.1 8.1 - - - +
308B SER* 4.2 3.8 - - - +
310B ASN 5.5 0.2 - - - -
311B THR* 2.7 51.1 - - + +
423B ASP* 4.1 6.4 + - - +
426B LYS* 2.8 63.7 + - + +
427B ASP* 3.4 18.5 - - + +
429B GLN* 1.3 75.1 - - + +
431B VAL* 1.3 59.9 + - - +
432B ALA 3.7 1.5 + - - -
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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) + - + + + + + -
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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