Contacts of the helix formed by residues 724 - 739 (chain S) in PDB entry 1BKD
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 LYS 724 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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722S ARG 3.1 6.1 + - - +
723S GLY* 1.3 70.9 - - - +
725S ALA* 1.3 59.6 + - - +
727S LYS* 4.1 22.8 + - - +
728S LYS* 4.2 6.2 + - - +
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Residues in contact with ALA 725 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723S GLY 3.1 0.4 - - - -
724S LYS* 1.3 76.7 - - - +
726S MET* 1.3 66.1 + - + +
727S LYS 3.3 0.4 - - - -
728S LYS* 3.3 16.9 + - - +
729S TRP* 3.5 10.0 + - - +
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Residues in contact with MET 726 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648S PHE* 4.5 2.7 - - + -
683S GLN* 4.7 17.7 - - - +
686S GLN* 3.1 33.4 - - - +
687S LEU* 5.7 3.1 - - + -
690S LEU* 4.2 22.7 - - - -
721S VAL* 3.7 15.7 - - + -
722S ARG* 4.9 1.8 - - + +
723S GLY* 3.0 30.1 + - - +
725S ALA* 1.3 78.0 - - + +
727S LYS* 1.3 60.1 + - - +
729S TRP* 3.1 16.6 + - + +
730S VAL* 2.8 34.0 + - + +
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Residues in contact with LYS 727 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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721S VAL* 3.7 23.8 - - + +
722S ARG* 3.4 19.9 + - - +
723S GLY 2.8 16.7 + - - +
724S LYS* 4.1 16.5 - - - +
725S ALA 3.3 0.4 - - - -
726S MET* 1.3 75.7 - - - +
728S LYS* 1.3 61.8 + - - +
730S VAL* 3.2 9.6 + - - +
731S GLU* 3.1 31.3 + - + +
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Residues in contact with LYS 728 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724S LYS 4.2 5.7 + - - +
725S ALA* 3.3 12.8 + - - +
726S MET 3.2 0.6 - - - -
727S LYS* 1.3 79.1 - - - +
729S TRP* 1.3 60.7 + - - +
731S GLU* 3.5 40.4 + - - +
732S SER* 4.6 3.5 + - - -
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Residues in contact with TRP 729 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687S LEU* 3.4 42.6 - - + -
690S LEU* 3.7 31.2 - - + -
691S ASN* 3.5 22.2 - - - -
694S ARG* 3.3 30.2 + - - +
725S ALA 3.5 8.8 + - - +
726S MET* 3.1 19.0 + - + +
728S LYS* 1.3 74.9 - - - +
730S VAL* 1.3 73.5 + - + +
731S GLU 3.1 5.6 + - - -
732S SER* 3.3 25.4 + - - -
733S ILE* 4.4 2.1 + - + -
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Residues in contact with VAL 730 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690S LEU* 4.0 36.6 - - + -
718S ILE* 3.5 39.7 - - + +
721S VAL* 4.1 12.3 - - + -
726S MET 2.8 18.3 + - - +
727S LYS* 3.2 8.0 + - - +
729S TRP* 1.3 80.0 - - + +
731S GLU* 1.3 63.7 + - + +
732S SER 3.1 2.5 - - - -
733S ILE* 3.1 22.5 + - + +
734S THR* 3.3 10.6 + - - +
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Residues in contact with GLU 731 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727S LYS* 3.1 20.1 + - - +
728S LYS* 3.5 48.5 + - - +
729S TRP 3.1 0.8 - - - -
730S VAL* 1.3 78.1 - - + +
732S SER* 1.3 57.3 + - - +
733S ILE 3.2 0.2 - - - -
734S THR* 3.4 10.6 + - - -
735S LYS* 3.0 27.4 + - - +
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Residues in contact with SER 732 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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694S ARG* 4.7 13.7 - - - -
728S LYS 4.7 3.1 + - - -
729S TRP* 3.3 17.9 + - - -
730S VAL 3.1 0.6 - - - -
731S GLU* 1.3 79.6 - - - +
733S ILE* 1.3 59.6 + - - +
735S LYS* 3.5 8.9 + - - +
736S ILE* 3.3 27.5 + - - +
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Residues in contact with ILE 733 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690S LEU* 3.3 42.2 - - + +
693S CYS* 4.6 2.0 - - + -
694S ARG* 4.0 39.3 - - + +
697S VAL* 5.0 2.9 - - + +
714S MET* 4.8 9.6 - - + -
718S ILE* 3.8 33.4 - - + -
729S TRP* 5.5 1.3 - - + -
730S VAL* 3.1 20.3 + - + +
732S SER* 1.3 76.7 - - - +
734S THR* 1.3 65.1 + - - +
736S ILE* 3.2 19.9 + - + +
737S ILE* 3.2 17.4 + - + +
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Residues in contact with THR 734 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715S GLU* 6.0 1.6 - - - +
718S ILE* 3.6 19.6 - - - +
730S VAL* 3.3 11.1 + - - +
731S GLU* 3.4 13.2 + - - -
733S ILE* 1.3 79.6 - - - +
735S LYS* 1.3 62.0 + - - +
737S ILE* 3.2 12.5 + - + +
738S GLN* 3.1 41.7 + - + +
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Residues in contact with LYS 735 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731S GLU 3.0 16.6 + - - +
732S SER* 3.6 9.9 - - - +
733S ILE 3.2 0.4 - - - -
734S THR* 1.3 77.8 - - - +
736S ILE* 1.3 61.0 + - - +
738S GLN* 3.4 17.9 + - + +
739S ARG* 3.0 59.7 + - - +
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Residues in contact with ILE 736 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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694S ARG* 3.6 35.2 - - + +
697S VAL* 4.2 13.2 - - + +
698S GLU* 3.4 50.3 - - - +
732S SER* 3.3 16.6 - - - +
733S ILE* 3.2 10.2 + - + +
735S LYS* 1.3 76.7 - - - +
737S ILE* 1.3 63.5 + - - +
739S ARG* 3.2 23.8 + - - +
740S LYS* 3.1 26.1 + - - +
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Residues in contact with ILE 737 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697S VAL* 3.4 25.4 - - + -
701S PHE* 4.5 4.4 - - + -
711S LEU* 4.1 18.2 - - + -
714S MET* 3.8 28.3 - - + -
715S GLU* 4.0 32.3 - - + +
718S ILE* 5.0 4.9 - - + -
733S ILE* 3.2 16.5 + - + +
734S THR* 3.2 12.1 + - + +
736S ILE* 1.3 76.3 - - - +
738S GLN* 1.3 63.9 + - + +
740S LYS* 3.1 13.5 + - - +
741S LYS* 3.2 32.7 - - + +
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Residues in contact with GLN 738 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715S GLU* 6.0 1.6 - - - +
734S THR* 3.1 34.7 + - + +
735S LYS* 3.8 20.1 - - + +
737S ILE* 1.3 77.2 - - + +
739S ARG* 1.3 61.8 + - - +
741S LYS* 3.4 26.5 + - - +
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Residues in contact with ARG 739 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698S GLU* 3.8 16.2 + - - -
735S LYS* 3.0 50.8 + - - +
736S ILE* 3.3 40.0 - - - +
737S ILE 3.1 0.2 - - - -
738S GLN* 1.3 74.3 - - - +
740S LYS* 1.3 64.9 + - + +
741S LYS 3.0 17.1 + - - +
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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