Contacts of the helix formed by residues 697 - 714 (chain D) 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 GLU 697 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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657D ILE* 3.3 21.8 - - + +
695D ARG* 2.6 45.8 + - - +
696D ARG* 1.3 92.1 + - + +
698D LEU* 1.3 61.7 + - - +
699D LYS 3.4 0.2 - - - -
700D PRO* 3.5 10.3 - - - +
701D ALA* 3.3 22.2 + - - +
746D TYR* 4.9 1.8 - - - -
749D LYS* 5.6 8.7 - - - +
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Residues in contact with LEU 698 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651D VAL* 3.7 40.6 - - + +
656D SER* 3.7 30.5 - - - +
657D ILE* 4.1 9.6 - - + +
660D VAL* 3.8 29.4 - - + -
688D MET* 3.9 18.6 - - + +
689D ILE* 5.6 1.8 - - - -
694D ALA* 3.9 11.4 - - + -
695D ARG* 3.4 16.9 + - + +
696D ARG 3.1 1.0 + - - -
697D GLU* 1.3 76.4 - - - +
699D LYS* 1.3 60.2 + - - +
701D ALA* 3.8 3.3 - - + +
702D VAL* 3.0 38.3 + - + +
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Residues in contact with LYS 699 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689D ILE* 4.2 32.8 - - + +
694D ALA* 5.9 0.8 - - + +
695D ARG 4.1 3.9 + - - +
696D ARG 3.5 2.1 + - - +
698D LEU* 1.3 78.6 - - - +
700D PRO* 1.4 66.1 - - + +
702D VAL* 3.5 2.1 + - - +
703D LEU* 3.0 41.1 + - + +
731D ALA* 4.8 7.9 - - - +
734D THR* 4.3 23.1 + - - +
746D TYR* 3.5 20.7 - - + +
750D VAL* 3.9 26.7 - - + -
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Residues in contact with PRO 700 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838B GLN* 4.4 6.7 - - - +
696D ARG 3.2 13.7 - - - +
697D GLU* 3.5 13.9 - - - +
699D LYS* 1.4 96.7 - - + +
701D ALA* 1.3 62.6 + - - +
703D LEU* 4.1 3.4 - - + -
704D SER* 3.0 29.2 + - - -
746D TYR* 3.9 14.6 - - + +
749D LYS* 3.8 25.8 - - + +
750D VAL* 4.3 6.1 - - + -
753D ALA* 3.4 21.8 - - + +
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Residues in contact with ALA 701 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838B GLN* 4.6 18.8 - - + +
657D ILE* 4.4 18.4 - - + +
660D VAL* 3.4 27.1 - - + +
697D GLU 3.3 19.2 + - - +
698D LEU* 3.8 7.6 - - - +
699D LYS 3.4 0.2 - - - -
700D PRO* 1.3 77.3 - - - +
702D VAL* 1.3 57.2 + - - +
704D SER* 3.9 2.4 - - - -
705D VAL* 3.1 21.3 + - - +
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Residues in contact with VAL 702 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660D VAL* 4.1 7.0 - - + -
685D LEU* 4.0 25.1 - - + +
688D MET* 3.8 32.1 - - + -
689D ILE* 4.3 15.5 - - + +
698D LEU* 3.0 28.9 + - + +
699D LYS 3.9 3.6 - - - +
701D ALA* 1.3 75.0 - - - +
703D LEU* 1.3 65.1 + - - +
705D VAL* 3.3 8.9 - - - +
706D PHE* 3.2 49.3 + - + -
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Residues in contact with LEU 703 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689D ILE* 5.6 6.3 - - + -
699D LYS* 3.0 35.8 + - + +
700D PRO* 3.6 7.2 - - + +
702D VAL* 1.3 76.7 - - + +
704D SER* 1.3 61.9 + - - +
706D PHE* 3.4 24.4 - - + +
727D LEU* 4.5 5.4 - - + +
728D CYS* 3.8 36.3 - - + +
731D ALA* 4.2 9.9 - - + -
750D VAL* 4.0 33.4 - - + +
753D ALA* 3.7 14.6 - - + +
754D VAL* 4.6 3.4 - - + -
757D ALA* 3.4 23.1 - - + +
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Residues in contact with SER 704 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838B GLN* 3.1 27.6 + - - -
842B GLN* 4.7 1.2 - - - +
700D PRO 3.0 14.0 + - - -
701D ALA 3.9 4.0 - - - -
703D LEU* 1.3 77.6 - - - +
705D VAL* 1.3 53.2 + - - +
707D GLY* 2.8 27.4 + - - -
708D ASP* 3.3 10.8 + - - +
753D ALA* 3.5 9.9 + - - +
756D ASP* 2.9 37.8 + - - +
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Residues in contact with VAL 705 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660D VAL* 3.6 37.2 - - + +
663D ILE* 4.0 11.9 - - + -
664D ALA* 3.7 25.8 - - + +
685D LEU* 3.6 28.7 - - + -
701D ALA 3.1 13.4 + - - +
702D VAL* 3.3 19.0 + - - +
704D SER* 1.3 73.1 - - - +
706D PHE* 1.3 65.4 + - + +
708D ASP* 3.4 9.1 + - + +
709D ILE* 3.0 28.6 + - - +
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Residues in contact with PHE 706 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682D MET* 3.8 28.5 - - + -
685D LEU* 4.0 20.9 - - + -
686D ALA* 4.4 7.6 - - + -
689D ILE* 5.3 2.5 - - + -
702D VAL* 3.2 37.6 + - + -
703D LEU* 3.4 26.2 - - + +
704D SER 3.2 0.4 - - - -
705D VAL* 1.3 76.4 - - - +
707D GLY* 1.3 54.2 + - - +
709D ILE* 3.3 3.8 + - + +
710D ALA* 2.7 38.7 + - - +
717D PHE* 3.9 5.1 - - + -
724D ILE* 3.7 47.1 - - + -
727D LEU* 4.0 20.2 - - + -
728D CYS* 6.0 0.4 - - - -
757D ALA* 4.4 8.1 - - + -
761D ILE* 5.9 0.7 - - + -
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Residues in contact with GLY 707 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842B GLN* 3.7 7.9 - - - -
703D LEU 3.7 2.4 + - - -
704D SER 2.8 12.8 + - - -
706D PHE* 1.3 77.8 - - - +
708D ASP* 1.3 60.7 + - - -
710D ALA* 3.7 0.8 - - - +
711D SER* 3.0 26.9 + - - -
756D ASP 3.7 21.3 - - - -
757D ALA* 3.8 9.0 - - - +
760D GLY* 3.6 9.1 - - - -
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Residues in contact with ASP 708 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842B GLN* 3.5 10.9 + - - +
845B LYS* 3.0 31.2 + - - +
664D ALA* 3.5 15.4 - - - +
667D SER* 3.6 14.6 - - - +
668D ASN* 2.8 28.2 + - - +
704D SER* 3.3 8.1 + - - +
705D VAL* 3.5 20.0 - - + +
707D GLY* 1.3 73.2 - - - +
709D ILE* 1.3 61.1 + - - +
711D SER* 3.1 12.0 + - - -
712D ASN* 2.7 25.7 + - - +
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Residues in contact with ILE 709 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663D ILE* 3.9 18.6 - - + -
667D SER* 4.3 8.7 - - - +
674D PHE* 3.8 29.4 - - + -
678D SER* 5.0 4.3 - - - +
681D MET* 4.9 2.9 - - + -
682D MET* 3.9 29.8 - - + -
685D LEU* 3.8 28.3 - - + -
705D VAL* 3.0 22.1 + - + +
706D PHE* 3.8 3.8 - - - +
708D ASP* 1.3 74.5 - - - +
710D ALA* 1.3 68.6 + - - +
711D SER 3.2 0.3 + - - -
713D ILE* 3.1 37.9 + - + +
717D PHE* 4.4 7.6 - - + -
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Residues in contact with ALA 710 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706D PHE 2.7 21.4 + - - +
707D GLY 3.7 2.2 - - - +
709D ILE* 1.3 72.4 - - - +
711D SER* 1.3 56.6 + - - +
713D ILE* 4.1 0.2 - - - +
714D GLY* 3.1 28.8 + - - +
717D PHE* 3.3 36.7 - - + +
760D GLY 3.7 19.3 - - - +
761D ILE* 3.9 13.0 - - + -
764D GLY* 3.6 6.7 - - - -
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Residues in contact with SER 711 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842B GLN* 3.3 22.4 + - - -
846B ASP* 4.1 10.7 + - - -
668D ASN* 4.7 1.6 + - - -
707D GLY 3.0 13.9 + - - -
708D ASP* 3.1 10.4 + - - -
710D ALA* 1.3 77.0 - - - +
712D ASN* 1.3 70.5 + - - +
713D ILE 3.6 0.3 + - - -
714D GLY 4.4 1.4 + - - -
760D GLY* 3.3 16.1 + - - -
763D ALA* 4.4 6.8 - - - -
764D GLY* 3.9 13.1 + - - -
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Residues in contact with ASN 712 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835B ARG* 4.1 3.4 - - - +
667D SER* 3.0 26.9 + - - +
668D ASN* 2.9 30.2 + - - +
671D GLU* 3.1 50.6 + - - +
672D GLU* 3.0 29.8 - - - +
708D ASP 2.7 21.7 + - - +
709D ILE 4.2 2.0 - - - +
711D SER* 1.3 85.1 + - - +
713D ILE* 1.3 58.7 + - + +
714D GLY 3.7 0.4 - - - -
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Residues in contact with ILE 713 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671D GLU 4.0 6.5 - - - +
672D GLU* 5.2 0.2 - - - -
674D PHE* 3.6 29.8 - - + -
675D ARG* 3.0 64.7 + - + +
678D SER* 4.6 8.7 - - - +
709D ILE* 3.1 28.3 + - + +
710D ALA* 4.1 2.2 - - - +
712D ASN* 1.3 78.3 - - + +
714D GLY* 1.3 65.7 + - - +
715D ALA 3.2 0.9 + - - -
716D ASP* 3.3 27.8 + - + +
717D PHE* 3.8 13.5 - - + +
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Residues in contact with GLY 714 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675D ARG* 4.3 4.5 - - - -
710D ALA 3.1 11.4 + - - +
711D SER 4.4 1.6 + - - -
712D ASN 3.7 1.8 - - - -
713D ILE* 1.3 74.0 - - - +
715D ALA* 1.3 63.9 + - - -
717D PHE* 2.9 23.7 + - - +
764D GLY* 3.2 24.5 - - - -
765D LEU* 3.6 11.3 - - - +
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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
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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