Contacts of the helix formed by residues 717 - 731 (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 717 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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678B SER* 5.8 0.2 - - - -
682B MET* 3.6 28.5 - - + -
706B PHE* 3.8 24.0 - - + -
709B ILE* 4.1 10.3 - - + -
710B ALA* 3.7 29.4 - - + -
713B ILE* 3.6 5.8 - - + +
714B GLY 3.0 14.1 + - - +
716B ASP* 1.3 74.8 - - - +
718B ILE* 1.3 67.4 + - - +
719B PRO* 3.3 2.2 - - - -
720B TYR* 2.9 20.0 + - + +
721B LEU* 3.2 32.8 + - + -
724B ILE* 3.9 29.8 - - + -
761B ILE* 4.2 17.5 - - + -
765B LEU* 5.6 6.3 - - + -
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Residues in contact with ILE 718 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715B ALA* 3.1 32.5 + - + +
717B PHE* 1.3 75.4 - - - +
719B PRO* 1.3 70.0 - - + +
721B LEU* 2.9 27.1 + - + +
722B ASN 4.4 1.2 + - - -
765B LEU* 3.9 18.6 - - + -
768B LYS* 4.6 8.5 - - + -
771B ALA* 3.7 33.0 - - + -
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Residues in contact with PRO 719 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679B ASP* 6.0 0.9 - - - +
715B ALA 4.1 1.8 - - - +
716B ASP* 3.3 16.8 - - - +
717B PHE 3.3 5.2 - - - -
718B ILE* 1.3 95.2 - - + +
720B TYR* 1.3 73.3 + - + +
721B LEU 3.9 0.2 + - - -
722B ASN* 5.1 1.6 + - - +
723B ASP* 4.0 11.6 - - - +
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Residues in contact with TYR 720 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678B SER* 5.0 1.6 - - - -
679B ASP* 3.2 38.9 + - - +
682B MET* 3.7 52.5 - - + -
683B ASN* 2.6 36.8 + - - -
686B ALA* 5.1 7.2 - - + -
716B ASP 4.3 9.4 - - - -
717B PHE* 2.9 18.1 + - + +
719B PRO* 1.3 91.6 - - + +
721B LEU* 1.3 64.0 + - - +
722B ASN 3.4 1.8 - - - -
723B ASP* 3.3 11.2 + - + +
724B ILE* 3.0 26.5 + - + +
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Residues in contact with LEU 721 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717B PHE* 3.2 22.1 + - + +
718B ILE* 2.9 27.1 + - + +
720B TYR* 1.3 76.1 - - - +
722B ASN* 1.3 58.8 + - - +
724B ILE* 3.3 1.9 + - - +
725B MET* 2.8 46.2 + - + +
761B ILE* 3.9 29.6 - - + -
765B LEU* 4.2 13.0 - - + -
771B ALA* 3.3 35.7 - - + +
772B LEU* 4.7 2.2 - - + +
775B TYR* 3.5 20.2 - - + +
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Residues in contact with ASN 722 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718B ILE 4.4 1.4 + - - -
719B PRO 5.1 1.5 + - - +
720B TYR 3.4 0.6 - - - -
721B LEU* 1.3 79.4 - - - +
723B ASP* 1.3 70.4 + - - +
725B MET* 3.3 2.8 + - - +
726B ALA* 3.0 24.3 + - - +
775B TYR* 2.9 37.8 + - - +
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Residues in contact with ASP 723 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686B ALA* 5.3 8.7 - - + -
719B PRO 4.0 15.1 - - - +
720B TYR* 3.3 11.4 + - + +
721B LEU 3.2 0.6 - - - -
722B ASN* 1.3 84.2 - - - +
724B ILE* 1.3 69.2 + - + +
726B ALA* 3.4 8.5 + - - +
727B LEU* 3.3 25.2 + - + +
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Residues in contact with ILE 724 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682B MET* 3.7 12.3 - - + -
686B ALA* 4.3 12.8 - - + -
706B PHE* 3.5 57.2 - - + -
717B PHE* 3.9 21.8 - - + -
720B TYR* 3.0 21.7 + - + +
721B LEU 3.8 2.5 - - - +
723B ASP* 1.3 78.8 - - + +
725B MET* 1.3 64.9 + - - +
727B LEU* 3.3 11.3 + - + +
728B CYS* 3.1 29.8 + - - -
757B ALA* 5.2 0.4 - - + -
761B ILE* 4.1 19.3 - - + -
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Residues in contact with MET 725 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721B LEU* 2.8 38.9 + - + +
722B ASN 3.3 4.9 + - - +
724B ILE* 1.3 72.6 - - - +
726B ALA* 1.3 64.2 + - - +
728B CYS* 3.2 7.2 - - - +
729B VAL* 3.0 26.2 - - + +
758B TYR* 3.5 30.7 - - + +
761B ILE* 4.4 9.6 - - - -
772B LEU* 5.9 0.4 - - - -
775B TYR* 3.6 52.0 - - + +
778B THR* 3.3 34.3 - - + -
779B ILE* 4.4 4.3 - - + -
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Residues in contact with ALA 726 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722B ASN* 3.0 17.0 + - - +
723B ASP* 3.5 11.9 - - - +
724B ILE 3.2 0.2 - - - -
725B MET* 1.3 75.3 - - - +
727B LEU* 1.3 63.8 + - + +
729B VAL* 3.3 5.4 + - - +
730B ALA* 3.2 25.2 + - - +
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Residues in contact with LEU 727 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686B ALA* 4.2 12.8 - - + +
689B ILE* 3.6 52.5 - - + +
690B SER* 3.8 13.5 - - - +
699B LYS* 5.6 0.9 - - - -
703B LEU* 4.6 11.7 - - + +
706B PHE* 3.9 22.4 - - + -
723B ASP* 3.3 15.2 + - + +
724B ILE* 3.3 14.9 + - + +
726B ALA* 1.3 79.1 - - + +
728B CYS* 1.3 57.7 + - - +
730B ALA* 3.9 5.3 - - - +
731B ALA* 3.2 25.8 + - - +
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Residues in contact with CYS 728 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703B LEU* 3.7 14.1 - - + -
724B ILE* 3.1 31.1 + - - -
725B MET* 3.2 7.7 - - - +
727B LEU* 1.3 74.1 - - - +
729B VAL* 1.3 57.4 + - - +
731B ALA* 4.0 6.1 - - - -
732B GLN* 4.2 4.3 - - - -
754B VAL* 3.6 26.9 - - + -
757B ALA* 4.1 21.3 - - - -
758B TYR* 2.5 48.9 + - - -
761B ILE* 5.6 0.2 - - - -
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Residues in contact with VAL 729 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725B MET* 3.0 23.8 - - + +
726B ALA* 3.3 5.3 + - - +
727B LEU 3.4 0.2 + - - -
728B CYS* 1.3 77.3 - - - +
730B ALA* 1.3 67.7 + - - +
731B ALA 3.2 0.8 - - - +
732B GLN* 3.3 14.6 + - + +
733B ASN* 3.1 43.4 + - - +
758B TYR* 4.1 0.4 - - - +
778B THR* 3.3 32.3 - - + +
781B GLN* 5.9 4.9 - - - +
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Residues in contact with ALA 730 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699B LYS* 5.8 0.7 - - - -
726B ALA 3.2 14.1 + - - +
727B LEU* 3.9 5.8 - - - +
729B VAL* 1.3 82.3 - - - +
731B ALA* 1.3 59.9 + - - +
733B ASN* 3.5 6.3 + - - +
734B THR* 2.9 26.0 + - - -
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Residues in contact with ALA 731 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699B LYS* 4.2 14.6 - - - +
703B LEU* 4.0 9.9 - - + -
727B LEU 3.2 17.3 + - - +
728B CYS* 4.0 1.1 - - - -
729B VAL 3.2 0.4 - - - -
730B ALA* 1.3 80.0 - - - +
732B GLN* 1.3 60.8 + - - +
734B THR* 3.1 24.0 + - - +
747B GLN* 5.3 0.3 + - - +
750B VAL* 3.9 30.5 - - + +
751B LEU* 4.5 2.3 - - - +
754B VAL* 3.9 14.6 - - + -
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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