Contacts of the helix formed by residues 674 - 689 (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 PHE 674 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B LEU* 5.3 1.6 - - + -
663B ILE* 3.9 9.6 - - + -
666B ILE* 3.3 33.2 - - + -
667B SER* 3.7 30.3 - - - -
670B LEU* 4.1 13.4 - - + +
671B GLU 3.4 16.4 + - - +
672B GLU 3.2 0.2 - - - -
673B ASP* 1.3 72.6 - - - +
675B ARG* 1.3 59.2 + - - +
676B ARG 3.0 2.7 - - - -
677B TYR* 2.8 45.6 + + + -
678B SER* 2.8 19.2 + - - -
681B MET* 3.9 25.4 - - + -
709B ILE* 3.9 23.8 - - + -
712B ASN* 5.2 0.4 - - + -
713B ILE* 3.3 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 675 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672B GLU* 3.1 42.0 + - - +
673B ASP 3.1 0.2 - - - -
674B PHE* 1.3 77.5 - - - +
676B ARG* 1.3 60.3 + - - +
677B TYR 3.4 0.5 + - - -
678B SER* 3.5 13.4 + - - -
679B ASP* 4.7 6.4 + - - +
712B ASN 4.8 1.2 + - - -
713B ILE* 3.0 48.8 + - + +
714B GLY* 4.4 6.7 - - - -
715B ALA* 4.6 9.5 - - - +
716B ASP* 3.0 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 676 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B GLU* 4.2 10.8 + - - -
673B ASP* 3.3 13.9 + - - +
674B PHE 3.0 0.8 + - - -
675B ARG* 1.3 79.6 - - - +
677B TYR* 1.3 89.3 + - + +
679B ASP 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 677 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B GLU* 2.9 36.2 + - - +
637B LEU* 3.7 48.2 - - + -
638B GLU* 4.7 18.2 + - + +
641B SER* 6.1 2.2 - - - -
670B LEU* 4.1 6.1 - - + -
673B ASP 3.7 19.7 - - - -
674B PHE* 2.8 25.8 + + + +
676B ARG* 1.3 102.4 + - + +
678B SER* 1.3 65.4 + - - +
679B ASP 3.3 3.8 + - - -
680B ALA* 3.6 7.9 + - - +
681B MET* 3.3 27.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 678 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674B PHE* 2.8 25.6 + - - -
675B ARG* 3.5 19.7 + - - -
677B TYR* 1.3 76.3 - - - +
679B ASP* 1.3 68.0 + - - +
681B MET* 3.4 4.5 + - - +
682B MET* 3.0 38.6 + - - +
709B ILE* 5.0 0.9 - - - -
713B ILE* 3.7 30.1 - - - +
716B ASP* 4.6 4.1 + - - +
717B PHE* 5.8 0.2 - - - -
720B TYR* 5.0 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 679 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675B ARG 4.7 4.9 + - - +
676B ARG 5.4 0.4 + - - -
677B TYR 3.3 0.8 - - - -
678B SER* 1.3 86.1 + - - +
680B ALA* 1.3 61.3 + - - +
682B MET 3.2 0.5 + - - -
683B ASN* 2.9 38.7 + - - +
716B ASP* 4.4 10.2 - - - +
719B PRO* 6.4 0.7 - - - -
720B TYR* 3.2 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 680 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B SER* 5.5 2.9 - - - +
645B LEU* 3.9 11.8 - - + +
677B TYR* 3.6 9.0 + - - +
678B SER 3.5 0.4 - - - -
679B ASP* 1.3 79.0 - - - +
681B MET* 1.3 72.8 + - + +
683B ASN* 3.7 9.7 + - - +
684B VAL* 3.6 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 681 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B LEU* 5.8 4.0 - - + -
641B SER* 4.3 12.6 - - - +
644B LEU* 3.4 34.1 - - + -
645B LEU* 3.5 36.1 - - + -
648B LEU* 4.5 3.3 - - - +
663B ILE* 3.8 16.6 - - + -
666B ILE* 5.9 0.7 - - - -
674B PHE* 3.9 24.9 - - + -
677B TYR* 3.3 22.0 - - + +
678B SER 3.5 6.3 - - - +
679B ASP 3.2 0.4 - - - -
680B ALA* 1.3 82.3 - - + +
682B MET* 1.3 52.1 + - - +
684B VAL* 3.1 7.0 + - - +
685B LEU* 2.8 49.3 + - + +
709B ILE* 5.0 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 682 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678B SER* 3.0 19.3 + - - +
679B ASP 3.2 0.2 + - - -
681B MET* 1.3 76.0 - - - +
683B ASN* 1.3 61.3 + - - +
685B LEU* 4.0 5.2 - - - -
686B ALA* 2.8 35.0 + - - +
706B PHE* 3.7 18.4 - - + -
709B ILE* 3.5 36.8 - - + -
717B PHE* 3.6 28.5 - - + -
720B TYR* 3.7 40.5 - - + -
724B ILE* 3.7 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 683 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B ASP* 2.9 25.6 + - - +
680B ALA* 3.9 9.6 - - - +
681B MET 3.3 0.2 - - - -
682B MET* 1.3 77.1 - - - +
684B VAL* 1.3 61.8 + - + +
686B ALA* 4.6 3.5 - - - +
687B GLN* 4.1 16.3 + - - +
720B TYR* 2.6 39.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 684 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645B LEU* 3.6 21.5 - - + -
648B LEU* 3.8 29.4 - - + -
649B ASN* 3.8 30.5 - - - +
680B ALA 3.6 14.6 - - - +
681B MET 3.1 6.6 + - - +
683B ASN* 1.3 78.3 - - + +
685B LEU* 1.3 64.3 + - - +
686B ALA 3.2 1.6 - - - -
687B GLN* 3.1 12.5 + - - +
688B MET* 3.0 27.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 685 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B LEU* 3.8 14.6 - - + -
660B VAL* 4.4 8.3 - - + -
663B ILE* 4.0 18.6 - - + -
681B MET 2.8 27.1 + - - +
682B MET* 3.3 8.0 + - - +
684B VAL* 1.3 73.2 - - - +
686B ALA* 1.3 60.2 + - - +
687B GLN 3.4 0.5 + - - -
688B MET* 3.5 34.7 + - - +
689B ILE* 4.1 2.6 - - - +
702B VAL* 3.8 19.5 - - + +
705B VAL* 3.9 24.0 - - + -
706B PHE* 3.8 16.1 - - + -
709B ILE* 3.5 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 686 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682B MET 2.8 18.6 + - - +
683B ASN* 4.6 4.9 - - - +
685B LEU* 1.3 76.8 - - - +
687B GLN* 1.3 59.5 + - - +
689B ILE* 4.2 10.1 - - - +
690B SER* 5.0 3.1 + - - -
706B PHE* 4.5 9.4 - - - -
720B TYR* 5.1 8.7 - - + -
723B ASP* 5.3 8.3 - - + -
724B ILE* 4.3 17.9 - - + -
727B LEU* 4.2 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 687 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649B ASN* 3.3 27.8 + - - +
651B VAL* 6.3 0.2 - - + -
683B ASN 4.1 10.1 + - - +
684B VAL* 3.1 20.7 + - - +
686B ALA* 1.3 79.2 - - - +
688B MET* 1.3 72.7 + - + +
689B ILE 3.3 0.9 - - - -
690B SER* 2.9 19.8 + - - -
691B ASN* 3.5 18.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 688 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B LEU* 3.4 58.1 - - + +
649B ASN* 5.4 1.6 - - - +
651B VAL* 4.1 12.9 - - + +
656B SER* 4.3 2.7 - - - -
660B VAL* 4.0 2.2 - - + -
684B VAL* 3.0 21.1 + - + +
685B LEU* 3.5 26.0 + - - +
687B GLN* 1.3 80.8 - - + +
689B ILE* 1.3 63.7 + - - +
691B ASN* 3.0 20.8 + - - +
694B ALA* 3.7 9.9 - - - +
698B LEU* 3.5 38.6 - - + -
702B VAL* 4.0 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 689 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685B LEU 4.1 12.6 - - - +
686B ALA 4.2 4.0 - - - +
688B MET* 1.3 77.6 - - - +
690B SER* 1.3 60.4 + - - +
691B ASN 3.3 6.6 + - - +
694B ALA* 4.4 8.7 - - - +
698B LEU* 5.6 1.6 - - - -
699B LYS* 3.8 44.3 - - + +
702B VAL* 4.4 19.3 - - + -
703B LEU* 5.6 4.3 - - + -
706B PHE* 4.7 0.9 - - + -
727B LEU* 3.6 54.5 - - + +
----------------------------------------------------------
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