Contacts of the helix formed by residues 401 - 419 (chain B) in PDB entry 2BKU
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 ASP 401 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B ASN* 2.6 38.4 + - - +
399B GLY 3.8 0.2 + - - -
400B PRO* 1.3 75.5 - - - +
402B LYS* 1.3 63.4 + - - +
403B VAL* 3.0 22.7 + - - +
404B GLN* 3.1 21.4 + - - +
405B ARG* 3.1 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B ASP* 1.3 73.7 - - - +
403B VAL* 1.3 64.4 + - + +
405B ARG* 3.4 23.2 + - - +
406B THR* 2.9 46.4 + - - +
442B VAL* 4.6 5.4 - - + -
444B GLU* 3.5 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B ASP* 3.0 10.4 + - - +
402B LYS* 1.3 89.1 - - + +
404B GLN* 1.3 74.8 + - - +
406B THR* 3.7 4.6 - - - -
407B TYR* 3.0 26.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B ASN* 3.7 23.8 - - - +
367B LEU* 3.6 29.4 - - + +
400B PRO* 4.5 2.9 - - + -
401B ASP* 3.1 15.8 + - - +
403B VAL* 1.3 88.3 - - - +
405B ARG* 1.3 65.2 + - - +
407B TYR* 3.3 6.5 + - - +
408B TYR* 3.0 54.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B LEU* 5.9 2.7 - - + -
396B ILE 4.2 8.7 - - - +
397B MET* 3.3 47.3 + - + +
398B ASP* 4.8 3.0 + - - +
399B GLY 5.1 2.2 - - - -
400B PRO* 2.8 38.3 + - + -
401B ASP* 3.1 10.1 + - - +
402B LYS* 3.4 26.2 - - - +
404B GLN* 1.3 78.3 - - - +
406B THR* 1.3 57.7 + - - +
408B TYR* 4.0 2.4 - - - -
409B VAL* 2.9 37.3 + - - +
441B SER* 3.5 14.6 + - - -
442B VAL* 3.4 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B LYS* 2.9 31.3 + - - +
403B VAL* 3.7 5.4 - - - -
405B ARG* 1.3 75.6 - - - +
407B TYR* 1.3 66.1 + - - +
409B VAL* 3.9 0.3 - - - +
410B HIS* 2.9 27.8 + - + +
442B VAL* 4.8 1.9 - - - +
444B GLU* 4.0 15.4 + - - +
445B SER* 3.7 37.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B VAL* 3.0 20.5 + - + +
404B GLN* 3.3 7.8 + - - +
406B THR* 1.3 80.2 - - - +
408B TYR* 1.3 95.6 + + - +
410B HIS* 3.5 6.3 + - - +
411B GLN* 3.2 46.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B LEU* 4.3 14.7 - - + +
371B LEU* 3.4 49.9 - - + +
393B PHE* 3.8 8.0 - - + -
397B MET* 6.0 1.1 - - + -
404B GLN* 3.0 52.1 + - - +
405B ARG* 4.4 2.5 - - - +
407B TYR* 1.3 101.4 - + - +
409B VAL* 1.3 61.0 + - - +
411B GLN* 3.6 23.4 - - - +
412B ALA* 2.9 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B PHE* 3.9 16.2 - - + -
397B MET* 3.6 28.7 - - - -
405B ARG 2.9 24.4 + - - +
406B THR 3.9 2.5 - - - +
408B TYR* 1.3 72.1 - - - +
410B HIS* 1.3 68.3 + - - +
411B GLN 3.0 0.3 + - - -
412B ALA 3.1 0.2 + - - -
413B LEU* 2.9 37.7 + - + +
438B ILE* 3.7 26.0 - - + -
442B VAL* 4.0 6.5 - - + -
445B SER* 3.5 21.5 - - - +
446B ILE* 3.9 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 410 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B THR* 2.9 22.7 + - + +
407B TYR* 3.5 7.3 + - - +
409B VAL* 1.3 78.8 - - - +
411B GLN* 1.3 62.7 + - - +
414B PRO* 4.0 6.8 - - - +
445B SER 4.9 7.0 - - - +
447B ASP* 5.0 7.9 + - + -
450B GLN* 5.8 1.8 + - - -
451B HIS* 3.4 44.0 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 411 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B TYR* 3.2 45.8 + - - +
408B TYR* 3.6 25.5 - - - +
409B VAL 3.0 0.6 - - - -
410B HIS* 1.3 82.7 - - - +
412B ALA* 1.3 60.3 + - + +
413B LEU 3.9 0.3 + - - -
414B PRO* 4.0 7.4 - - - +
415B SER* 4.8 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B LEU* 6.0 1.3 - - + -
374B VAL* 5.5 7.2 - - + -
378B ILE* 6.4 0.2 - - + -
393B PHE* 4.0 22.0 - - + -
408B TYR 2.9 17.0 + - - +
411B GLN* 1.3 75.3 - - + +
413B LEU* 1.3 64.9 + - - +
414B PRO* 3.4 3.1 - - - -
415B SER* 3.2 14.1 + - - +
416B ILE* 3.1 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B VAL* 2.9 20.6 + - + +
412B ALA* 1.3 76.3 - - - +
414B PRO* 1.3 66.8 - - + +
416B ILE* 2.9 10.9 + - + +
417B LEU* 2.7 58.0 + - + +
435B ILE* 4.6 5.8 - - + -
438B ILE* 3.8 27.1 - - + -
446B ILE* 3.7 29.8 - - + -
451B HIS* 4.0 28.7 - - + +
455B VAL* 4.3 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 414 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B HIS 4.0 9.6 - - - +
411B GLN 4.0 11.0 - - - +
412B ALA 3.5 2.9 - - - -
413B LEU* 1.3 93.6 - - + +
415B SER* 1.3 61.7 + - - +
417B LEU* 3.7 9.8 + - + +
418B ASN* 3.1 24.4 + - - +
451B HIS* 4.6 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B ILE* 4.1 27.5 - - - +
379B THR* 5.7 4.0 - - - -
411B GLN 4.8 2.4 + - - -
412B ALA* 3.2 17.0 + - - -
414B PRO* 1.3 75.1 - - - +
416B ILE* 1.3 66.9 + - - +
418B ASN* 3.4 20.3 + - - +
419B LEU* 3.4 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B VAL* 6.2 0.7 - - + -
378B ILE* 4.4 9.2 - - + -
390B VAL* 4.2 22.7 - - + -
393B PHE* 3.6 41.1 - - + -
412B ALA* 3.1 23.8 + - + +
413B LEU* 2.9 13.9 + - + +
415B SER* 1.3 72.5 - - - +
417B LEU* 1.3 67.6 + - - +
418B ASN 3.1 1.1 - - - -
419B LEU* 2.9 18.3 + - - +
431B THR* 3.3 23.2 - - + +
434B CYS* 4.4 12.6 - - + -
435B ILE* 4.2 19.5 - - + -
438B ILE* 4.4 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B LEU* 2.7 45.3 + - + +
414B PRO* 4.0 7.2 - - + +
416B ILE* 1.3 74.2 - - - +
418B ASN* 1.3 61.4 + - - +
419B LEU 3.2 0.9 + - - -
420B MET* 3.3 21.3 + - - +
421B ASN* 5.2 1.0 + - - +
435B ILE* 3.4 28.5 - - + -
451B HIS* 4.6 7.0 - - + +
454B GLY* 3.5 39.9 - - - +
455B VAL* 3.6 16.8 - - + +
458B ALA* 3.6 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B THR* 5.5 9.1 - - - +
414B PRO 3.1 18.9 + - - +
415B SER* 3.4 11.7 + - - +
416B ILE 3.1 0.8 - - - -
417B LEU* 1.3 77.8 - - - +
419B LEU* 1.3 63.7 + - - +
420B MET 3.2 1.7 + - - -
421B ASN* 3.3 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B ILE* 3.8 36.3 - - + +
379B THR* 5.8 2.0 - - + -
386B ARG* 4.1 12.6 - - - +
390B VAL* 3.4 36.6 - - + -
415B SER 3.6 11.2 - - - +
416B ILE* 2.9 8.4 + - - +
418B ASN* 1.3 76.3 - - - +
420B MET* 1.3 60.5 + - - +
421B ASN 3.0 5.6 - - - -
422B ASP* 3.1 43.0 + - - +
427B VAL* 4.0 9.1 - - + +
428B LYS* 3.8 6.2 - - - +
431B THR* 3.3 19.1 + - - +
----------------------------------------------------------
Back to top of page
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