Contacts of the helix formed by residues 775 - 789 (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 TYR 775 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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721D LEU* 3.3 31.3 - - + +
722D ASN* 3.3 38.1 + - - +
725D MET* 3.5 49.8 - - + -
771D ALA 3.7 16.2 - - - -
772D LEU* 2.9 17.9 + - + +
773D PHE 2.9 0.2 + - - -
774D PRO* 1.3 96.6 - - + +
776D VAL* 1.3 68.4 + - - +
777D GLY 3.3 2.7 - - - -
778D THR* 3.0 22.2 + - - -
779D ILE* 3.1 15.5 + - + +
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Residues in contact with VAL 776 (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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772D LEU* 3.6 9.8 + - + +
773D PHE* 3.3 17.6 + - - +
774D PRO 3.7 0.2 - - - -
775D TYR* 1.3 75.3 - - - +
777D GLY* 1.3 66.4 + - - +
779D ILE* 2.9 12.3 + - - +
780D PHE* 2.9 39.4 + - + +
809D ILE* 4.4 11.9 - - + -
813D PHE* 3.9 27.8 - - + -
818D ILE* 4.1 14.4 - - + -
821D PHE* 3.5 33.0 - - + -
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Residues in contact with GLY 777 (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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773D PHE 5.1 0.2 + - - -
774D PRO 5.5 0.6 - - - -
775D TYR 3.3 0.8 - - - -
776D VAL* 1.3 78.3 - - - +
778D THR* 1.3 52.3 + - - +
780D PHE* 3.5 1.8 + - - +
781D GLN* 2.8 35.5 + - - +
821D PHE* 3.5 29.8 - - - -
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Residues in contact with THR 778 (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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725D MET* 3.6 15.6 - - + +
729D VAL* 3.4 33.0 - - + +
732D GLN* 3.7 8.3 + - - +
758D TYR* 3.5 14.1 - - - +
774D PRO 5.1 1.0 + - - -
775D TYR* 3.0 20.7 + - - +
777D GLY* 1.3 74.6 - - - +
779D ILE* 1.3 60.7 + - - +
781D GLN* 3.4 13.6 + - - +
782D PHE* 3.1 17.2 + - - +
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Residues in contact with ILE 779 (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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725D MET* 4.4 5.8 - - + -
758D TYR* 3.9 41.1 - - + +
761D ILE* 5.5 1.6 - - + -
762D VAL* 4.1 8.5 - - + -
772D LEU* 4.0 27.8 - - + -
775D TYR 3.1 13.0 + - - +
776D VAL* 2.9 7.0 + - - +
778D THR* 1.3 73.8 - - - +
780D PHE* 1.3 60.3 + - - +
782D PHE* 2.9 5.9 + - - +
783D ILE* 2.8 36.2 + - + +
805D LEU* 4.2 17.0 - - + -
809D ILE* 3.8 30.1 - - + -
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Residues in contact with PHE 780 (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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776D VAL* 2.9 37.3 + - + +
777D GLY 3.8 3.8 - - - +
779D ILE* 1.3 77.7 - - - +
781D GLN* 1.3 54.9 + - - +
783D ILE* 4.0 14.8 - - + -
784D ALA* 3.0 21.7 + - - +
806D ILE* 4.4 11.7 - - + -
809D ILE* 4.1 15.9 - - + -
821D PHE* 4.0 32.8 - + + -
822D TYR* 3.5 42.8 - + - -
824D GLN* 5.4 0.2 - - - +
826D TRP* 3.1 39.1 - + + -
827D VAL* 4.1 23.6 - - + -
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Residues in contact with GLN 781 (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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729D VAL* 6.2 1.6 - - - +
732D GLN* 4.3 13.4 - - - +
733D ASN* 5.4 7.8 + - - +
777D GLY 2.8 20.9 + - - +
778D THR* 3.6 12.8 + - - +
779D ILE 3.2 0.4 - - - -
780D PHE* 1.3 73.6 - - - +
782D PHE* 1.3 61.7 + - - +
784D ALA* 3.3 22.0 + - + +
785D GLN* 3.4 12.6 + - + +
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Residues in contact with PHE 782 (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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732D GLN* 3.6 37.6 - - + +
751D LEU* 3.2 50.5 - - + -
754D VAL* 3.9 10.3 - - + -
755D LEU* 3.7 33.7 - - + -
758D TYR* 3.7 22.9 - + + -
778D THR 3.1 5.8 + - - +
779D ILE 2.9 9.8 + - - +
781D GLN* 1.3 72.6 - - - +
783D ILE* 1.3 71.6 + - + +
785D GLN* 3.2 22.2 + - + +
786D VAL* 3.2 28.2 + - + +
792D LEU* 5.1 4.7 - - + -
798D THR* 6.4 0.2 - - + -
805D LEU* 5.5 1.3 - - + -
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Residues in contact with ILE 783 (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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779D ILE* 2.8 32.7 + - + +
780D PHE* 3.6 27.1 - - + +
782D PHE* 1.3 77.9 - - + +
784D ALA* 1.3 58.5 + - - +
786D VAL* 2.9 11.9 + - - +
787D ALA* 2.9 26.0 + - - +
802D ALA* 4.6 9.9 - - + +
805D LEU* 4.2 22.7 - - + -
806D ILE* 3.9 39.9 - - + +
809D ILE* 5.2 0.4 - - + -
826D TRP* 3.8 16.6 - - + -
830D TYR* 4.7 11.2 - - + -
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Residues in contact with ALA 784 (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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780D PHE 3.0 12.9 + - - +
781D GLN* 3.3 17.3 - - + +
782D PHE 3.2 0.2 - - - -
783D ILE* 1.3 76.1 - - - +
785D GLN* 1.3 56.3 + - + +
787D ALA* 3.3 1.4 + - - +
788D GLU* 3.0 41.3 + - - +
826D TRP* 3.4 28.2 - - + -
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Residues in contact with GLN 785 (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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732D GLN* 3.0 60.0 + - - +
733D ASN* 3.7 7.9 + - - -
751D LEU* 3.7 14.7 - - - +
781D GLN* 3.4 10.8 + - + +
782D PHE* 3.2 14.3 + - + +
783D ILE 3.2 0.2 - - - -
784D ALA* 1.3 73.4 - - + +
786D VAL* 1.3 67.3 + - - +
788D GLU* 3.1 6.9 + - - +
789D ASP* 2.9 23.8 + - + +
792D LEU* 3.7 14.6 - - + +
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Residues in contact with VAL 786 (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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755D LEU* 5.3 0.9 - - + -
782D PHE* 3.4 36.1 - - + +
783D ILE* 2.9 12.6 + - - +
785D GLN* 1.3 79.1 - - - +
787D ALA* 1.3 63.3 + - - +
789D ASP 3.3 6.4 - - - +
792D LEU* 3.6 27.6 - - + -
793D TYR* 3.2 29.1 - - - +
798D THR* 4.1 13.5 - - + -
802D ALA* 3.9 18.4 - - + -
830D TYR* 3.6 24.0 - - + +
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Residues in contact with ALA 787 (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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783D ILE 2.9 12.2 + - - +
784D ALA 3.5 8.7 - - - +
786D VAL* 1.3 74.6 - - - +
788D GLU* 1.3 64.9 + - - +
793D TYR* 3.1 11.1 - - - -
826D TRP* 4.2 17.3 - - + +
830D TYR* 3.8 29.7 - - + -
833D ARG* 3.1 30.3 + - - +
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Residues in contact with GLU 788 (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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784D ALA* 3.0 24.7 + - - +
785D GLN* 3.1 7.4 + - - +
787D ALA* 1.3 89.3 - - - +
789D ASP* 1.3 61.1 + - + +
790D PRO* 3.3 12.1 - - - +
793D TYR* 3.6 3.8 - - - -
826D TRP* 5.7 4.3 - - - +
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Residues in contact with ASP 789 (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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747D GLN* 5.0 3.6 - - - +
748D ILE* 4.6 6.4 - - - +
751D LEU* 5.7 1.9 - - - +
785D GLN* 2.9 18.0 + - + +
786D VAL 3.3 2.3 - - - +
788D GLU* 1.3 72.8 - - + +
790D PRO* 1.3 69.9 - - - +
791D GLN* 2.8 46.2 + - - +
792D LEU* 3.0 23.7 + - + +
793D TYR* 3.1 14.8 + - - -
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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
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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