Contacts of the helix formed by residues 451 - 464 (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 HIS 451 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B HIS* 3.4 58.1 + + + -
413B LEU* 4.0 24.9 - - + +
414B PRO* 4.6 11.1 - - + +
417B LEU* 4.6 5.9 - - + +
445B SER 4.0 13.9 + - - -
446B ILE* 3.6 19.5 - - + -
447B ASP* 3.1 18.5 + - - +
450B GLN* 1.3 88.8 - - + +
452B LEU* 1.3 67.9 - - - +
453B PRO* 3.2 4.0 - - - +
454B GLY* 3.0 15.6 + - - +
455B VAL* 3.1 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 452 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B ILE* 3.5 18.3 - - + +
447B ASP 3.3 3.8 + - - +
448B PRO* 3.7 17.3 - - + +
451B HIS* 1.3 75.9 - - - +
453B PRO* 1.4 62.9 - - + +
455B VAL* 3.4 4.1 + - + +
456B VAL* 3.1 29.9 + - + +
480B LEU* 4.4 15.5 - - + -
484B LEU* 3.8 25.4 - - + -
491B PRO* 3.6 39.0 - - + +
492B ILE* 4.3 9.6 - - + +
495B PHE* 3.6 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 453 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B PRO 3.7 11.4 - - - +
449B GLN 4.2 11.0 - - - +
450B GLN 4.2 1.8 - - - -
451B HIS 3.2 14.1 - - - +
452B LEU* 1.4 91.6 - - + +
454B GLY* 1.3 59.1 + - - +
456B VAL* 3.5 3.0 + - + +
457B GLN* 3.0 29.6 + - - +
495B PHE* 4.0 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 454 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B LEU* 3.5 25.6 - - - +
450B GLN 5.7 0.6 + - - -
451B HIS* 3.0 8.1 + - - -
453B PRO* 1.3 80.3 - - - +
455B VAL* 1.3 56.0 + - - +
457B GLN* 3.6 6.7 + - - +
458B ALA* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 455 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B LEU* 4.3 14.6 - - + -
417B LEU* 3.6 18.2 - - + -
435B ILE* 3.8 24.2 - - + -
446B ILE* 4.2 20.0 - - + -
451B HIS 3.1 12.8 + - - +
452B LEU* 3.6 9.9 - - + +
454B GLY* 1.3 73.8 - - - +
456B VAL* 1.3 66.5 + - - +
458B ALA* 2.9 6.2 + - - +
459B CYS* 2.9 23.8 + - - -
480B LEU* 3.6 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 456 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B LEU* 3.1 24.9 + - + +
453B PRO 3.8 4.7 - - - +
455B VAL* 1.3 78.7 - - - +
457B GLN* 1.3 57.6 + - - +
459B CYS* 3.1 8.4 + - - +
460B LEU* 2.9 53.5 + - + +
480B LEU* 5.0 7.0 - - + -
492B ILE* 5.1 1.1 - - + -
495B PHE* 4.0 41.3 - - + -
498B ALA* 4.7 4.7 - - + -
499B LEU* 4.0 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 457 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B PRO 3.0 18.5 + - - +
454B GLY* 3.8 8.1 - - - +
456B VAL* 1.3 78.8 - - - +
458B ALA* 1.3 61.1 + - - +
460B LEU* 3.4 16.7 + - - +
461B ILE* 3.0 51.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 458 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B LEU* 3.6 23.3 - - + +
420B MET* 3.7 35.0 - - + +
435B ILE* 4.7 6.7 - - + -
454B GLY 3.1 13.1 + - - +
455B VAL 2.9 11.2 + - - +
457B GLN* 1.3 76.1 - - - +
459B CYS* 1.3 62.4 + - - +
461B ILE* 3.5 7.1 + - - +
462B GLY 3.1 17.0 + - - -
473B CYS* 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 459 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B ILE* 4.8 4.5 - - - -
455B VAL* 2.9 25.7 + - - +
456B VAL* 3.1 10.1 + - - +
458B ALA* 1.3 76.9 - - - +
460B LEU* 1.3 58.9 + - - +
462B GLY* 3.2 2.1 + - - -
463B LEU* 3.0 32.9 + - - +
473B CYS* 3.8 16.1 - - + -
476B THR* 3.8 28.7 - - - -
477B ILE* 4.0 30.7 - - + -
480B LEU* 4.9 2.7 - - - -
499B LEU* 4.9 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 460 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B VAL* 2.9 38.3 + - + +
457B GLN* 3.9 18.8 - - - +
459B CYS* 1.3 70.5 - - - +
461B ILE* 1.3 68.1 + - - +
463B LEU* 3.6 26.3 + - + +
464B GLN* 3.6 20.8 + - - +
498B ALA* 3.5 36.6 - - + +
499B LEU* 4.0 20.2 - - + -
502B GLY* 4.4 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 461 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B MET* 4.3 26.7 - - + +
421B ASN* 4.9 11.2 - - - +
457B GLN* 3.0 39.7 + - + +
458B ALA* 3.6 9.6 - - - +
460B LEU* 1.3 76.5 - - - +
462B GLY* 1.3 60.3 + - - +
464B GLN* 3.1 25.6 + - - +
465B ASP* 3.4 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 462 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B MET* 3.7 7.4 - - - -
458B ALA 3.1 7.3 + - - -
459B CYS 3.2 1.0 + - - -
461B ILE* 1.3 76.6 - - - +
463B LEU* 1.3 63.0 + - - +
465B ASP* 3.2 12.5 + - - -
469B VAL* 3.4 15.8 - - - +
470B ALA* 3.2 20.3 + - - +
473B CYS* 3.6 22.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 463 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B CYS 3.0 19.9 + - - +
460B LEU* 3.9 19.5 - - + +
461B ILE 3.3 0.2 - - - -
462B GLY* 1.3 75.2 - - - +
464B GLN* 1.3 58.9 + - + +
465B ASP 3.4 0.2 - - - -
470B ALA* 3.7 18.9 - - + +
473B CYS* 4.1 7.9 - - + -
474B SER* 3.6 24.9 - - - +
477B ILE* 4.0 18.6 - - + -
502B GLY* 3.7 33.7 - - - +
503B LEU* 3.9 12.1 - - + +
506B ALA* 4.2 18.7 + - + +
509B ARG* 3.5 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 464 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B LEU* 3.6 15.5 + - - +
461B ILE* 3.1 12.5 + - - +
463B LEU* 1.3 76.5 - - + +
465B ASP* 1.3 62.8 + - - +
509B ARG* 4.9 2.6 + - - +
----------------------------------------------------------
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