Contacts of the helix formed by residues 708 - 720 (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 ALA 708 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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704S PHE 4.1 6.6 + - - -
705S GLU 5.1 1.2 + - - -
706S ARG 4.2 0.8 - - - -
707S ASP* 1.3 73.6 + - - +
709S TYR* 1.3 62.4 + - - +
711S LEU* 3.2 9.2 + - - +
712S GLN* 3.0 21.3 + - - +
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Residues in contact with TYR 709 (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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638S GLN* 3.8 19.7 - - - -
707S ASP* 3.2 10.5 + - - +
708S ALA* 1.3 75.1 - - - +
710S LEU* 1.3 66.0 + - - +
712S GLN* 3.2 34.7 + - - +
713S ARG* 2.9 54.9 + - + +
716S GLU* 5.3 2.4 + - - -
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Residues in contact with LEU 710 (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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637S PRO* 3.8 37.9 - - + +
638S GLN* 3.4 28.4 - - + +
641S LEU* 3.7 19.2 - - + +
696S TRP* 4.3 5.2 - - + -
703S ASP* 3.4 34.1 - - + +
704S PHE* 3.4 26.0 - - + -
707S ASP* 2.9 20.9 + - + +
709S TYR* 1.3 77.7 - - - +
711S LEU* 1.3 62.7 + - - +
713S ARG* 3.5 1.7 + - - -
714S MET* 3.2 20.6 + - - +
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Residues in contact with LEU 711 (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* 5.8 0.7 - - + -
701S PHE* 4.1 15.9 - - + -
704S PHE* 3.6 42.7 - - + +
707S ASP 3.3 1.4 + - - -
708S ALA* 3.2 12.2 + - - +
710S LEU* 1.3 77.1 - - - +
712S GLN* 1.3 54.5 + - - +
714S MET* 3.0 5.7 + - + +
715S GLU* 2.8 49.4 + - + +
737S ILE* 4.1 26.9 - - + -
741S LYS* 3.9 30.3 - - + +
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Residues in contact with GLN 712 (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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708S ALA 3.0 12.6 + - - +
709S TYR* 3.4 35.6 - - + +
711S LEU* 1.3 74.9 - - - +
713S ARG* 1.3 57.8 + - - +
715S GLU* 3.0 12.2 + - - +
716S GLU* 2.8 58.4 + - + +
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Residues in contact with ARG 713 (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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638S GLN* 2.9 51.7 + - - +
641S LEU* 3.5 23.8 - - + +
642S SER* 2.9 33.0 + - - +
645S ILE* 3.8 21.6 - - + +
709S TYR* 2.9 51.2 + - + +
710S LEU 3.8 0.4 - - - +
712S GLN* 1.3 75.3 - - - +
714S MET* 1.3 56.9 + - - +
716S GLU* 3.8 14.4 - - - +
717S PHE* 3.0 29.1 + - - +
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Residues in contact with MET 714 (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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641S LEU* 3.9 26.9 - - + -
693S CYS* 4.2 24.0 - - + -
696S TRP* 5.4 2.9 - - + -
697S VAL* 3.7 26.5 - - + -
704S PHE* 3.5 28.0 - - + -
710S LEU 3.2 8.0 + - - +
711S LEU* 3.0 14.2 + - + +
713S ARG* 1.3 75.6 - - - +
715S GLU* 1.3 59.2 + - - +
717S PHE* 3.4 6.3 + - - +
718S ILE* 2.9 63.5 + - + +
733S ILE* 4.8 1.6 - - + -
737S ILE* 3.8 13.2 - - + -
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Residues in contact with GLU 715 (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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711S LEU* 2.8 36.3 + - + +
712S GLN* 3.0 10.4 + - - +
714S MET* 1.3 73.3 - - - +
716S GLU* 1.3 64.4 + - + +
718S ILE* 3.9 7.2 - - - +
719S GLY* 3.1 19.6 + - - -
734S THR* 6.0 1.6 - - - +
737S ILE* 4.0 19.7 - - + +
738S GLN* 6.0 1.6 - - - +
741S LYS* 3.8 23.3 + - - -
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Residues in contact with GLU 716 (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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709S TYR* 5.3 2.1 + - - -
712S GLN* 2.8 44.1 + - + +
713S ARG* 3.8 18.3 - - - +
715S GLU* 1.3 76.3 - - + +
717S PHE* 1.3 62.4 + - - +
719S GLY* 3.3 4.0 + - - -
720S THR* 3.2 24.7 + - - -
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Residues in contact with PHE 717 (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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641S LEU* 4.9 3.4 - - + -
644S ILE* 4.5 3.8 - - + -
645S ILE* 3.7 40.8 - - + -
648S PHE* 3.8 52.3 - + + -
649S GLU* 5.6 2.0 - - + -
689S VAL* 4.2 5.6 - - + -
690S LEU* 4.2 12.8 - - + -
693S CYS* 3.8 29.6 - - - -
713S ARG 3.0 20.1 + - - +
714S MET* 3.7 13.0 - - - +
716S GLU* 1.3 75.0 - - - +
718S ILE* 1.3 68.9 + - + +
720S THR* 3.0 28.6 + - + -
721S VAL* 3.8 5.7 + - + +
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Residues in contact with ILE 718 (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* 4.3 15.3 - - + -
693S CYS* 4.9 2.5 - - + -
714S MET* 2.9 41.4 + - + +
715S GLU* 3.9 7.6 - - - +
717S PHE* 1.3 79.3 - - + +
719S GLY* 1.3 59.5 + - - +
720S THR 3.1 4.9 + - - -
721S VAL* 3.2 24.3 + - - +
730S VAL* 3.5 23.3 - - + +
733S ILE* 3.8 36.3 - - + -
734S THR* 3.6 19.3 - - - +
737S ILE* 5.0 3.6 - - + -
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Residues in contact with GLY 719 (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 3.1 15.4 + - - -
716S GLU* 3.3 7.6 + - - -
717S PHE 3.2 0.4 - - - -
718S ILE* 1.3 76.2 - - - +
720S THR* 1.3 57.8 + - - +
721S VAL 3.4 3.9 + - - +
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Residues in contact with THR 720 (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* 5.4 5.1 - - + -
649S GLU* 4.9 11.7 - - + +
716S GLU 3.2 13.1 + - - -
717S PHE* 3.0 27.5 + - + +
719S GLY* 1.3 76.1 + - - +
721S VAL* 1.3 64.8 + - - +
722S ARG* 3.3 30.8 + - - +
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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