Contacts of the helix formed by residues 886 - 898 (chain B) in PDB entry 4BIC
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 886 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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884B LEU 4.2 0.4 + - - -
885B GLY* 1.4 67.6 - - - +
887B PRO* 1.4 73.5 - - + +
888B GLN* 3.1 26.3 + - - +
889B ALA* 3.1 32.4 + - + +
890B ALA 2.8 31.4 + - - -
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Residues in contact with PRO 887 (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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843B LEU* 3.9 14.4 - - + -
844B GLN* 3.4 42.4 - - + +
881B PHE 5.9 0.2 - - - +
885B GLY 3.5 3.1 - - - +
886B GLU* 1.4 95.0 - - + +
888B GLN* 1.4 55.6 + - - +
890B ALA* 3.6 5.1 - - + +
891B MET* 2.9 35.9 + - - +
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Residues in contact with GLN 888 (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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843B LEU* 3.9 15.8 - - + +
886B GLU* 3.1 21.4 + - - +
887B PRO* 1.4 74.3 - - - +
889B ALA* 1.4 61.1 + - - +
891B MET* 3.8 1.5 + - - +
892B PHE* 3.3 22.9 + - - +
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Residues in contact with ALA 889 (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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884B LEU 4.6 5.2 - - - +
885B GLY* 5.7 0.2 - - - -
886B GLU* 3.1 24.6 + - + +
888B GLN* 1.4 75.0 - - - +
890B ALA* 1.4 57.7 + - - +
892B PHE* 3.3 8.0 + - - +
893B LYS* 3.1 42.1 + - + +
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Residues in contact with ALA 890 (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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844B GLN* 6.0 0.4 - - + -
881B PHE* 3.7 22.0 - - + +
884B LEU* 3.5 21.7 + - + +
885B GLY 3.4 14.6 - - - +
886B GLU 2.8 20.3 + - - +
887B PRO* 3.6 7.0 - - + +
889B ALA* 1.4 72.9 - - - +
891B MET* 1.4 58.4 + - - +
893B LYS* 3.4 5.2 - - - +
894B VAL* 2.9 32.8 + - - +
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Residues in contact with MET 891 (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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843B LEU* 3.5 50.7 - - + +
844B GLN* 3.8 13.0 - - + +
846B MET* 4.4 12.8 - - + +
851B ILE* 3.8 30.0 - - + +
881B PHE* 3.5 43.3 - - + -
887B PRO 2.9 23.9 + - - +
888B GLN 4.6 1.8 - - - +
890B ALA* 1.4 69.6 - - + +
892B PHE* 1.4 60.0 + - - +
894B VAL* 3.7 21.9 - - + +
895B GLY 3.1 20.4 + - - -
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Residues in contact with PHE 892 (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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851B ILE* 5.7 1.3 - - - -
888B GLN 3.3 18.9 + - - +
889B ALA* 3.3 8.7 + - - +
891B MET* 1.4 73.2 - - - +
893B LYS* 1.4 63.6 + - - +
895B GLY* 3.3 11.4 + - - -
896B MET* 3.3 28.0 + - + +
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Residues in contact with LYS 893 (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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884B LEU* 3.5 46.3 + - + +
889B ALA* 3.1 23.7 + - + +
890B ALA* 3.4 9.0 - - - +
892B PHE* 1.4 75.5 - - + +
894B VAL* 1.3 53.8 - - - +
896B MET* 3.3 19.2 + - + +
897B PHE* 2.8 63.5 + - + -
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Residues in contact with VAL 894 (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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851B ILE* 5.7 4.3 - - + -
865B TRP* 6.0 1.6 - - + -
881B PHE* 3.6 40.4 - - + -
884B LEU* 3.6 8.1 - - + -
890B ALA 2.9 28.4 + - - +
891B MET* 3.7 26.7 - - + +
892B PHE 3.4 0.2 - - - -
893B LYS* 1.3 72.6 - - - +
895B GLY* 1.3 56.0 - - - +
898B LYS* 2.7 33.4 + - - -
899B VAL* 3.4 30.0 + - + +
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Residues in contact with GLY 895 (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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851B ILE* 4.7 22.4 - - - -
891B MET 3.1 15.2 + - - -
892B PHE 3.3 4.7 + - - -
893B LYS 3.3 0.6 - - - -
894B VAL* 1.3 78.2 - - - +
896B MET* 1.4 58.4 + - - +
898B LYS* 3.7 9.9 + - - +
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Residues in contact with MET 896 (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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892B PHE* 3.3 32.0 + - + +
893B LYS* 3.3 27.8 - - + +
895B GLY* 1.4 75.6 - - - +
897B PHE* 1.4 76.1 + - + +
898B LYS* 3.7 1.7 + - - +
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Residues in contact with PHE 897 (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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884B LEU* 4.8 13.5 - - + -
893B LYS* 2.8 53.0 + - + +
896B MET* 1.4 85.5 - - + +
898B LYS* 1.4 69.6 + - - +
899B VAL* 3.5 27.9 + - + +
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Residues in contact with LYS 898 (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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894B VAL 2.7 17.3 + - - -
895B GLY 3.7 8.4 + - - +
896B MET 3.4 3.5 - - - +
897B PHE* 1.4 74.9 - - - +
899B VAL* 1.4 56.9 + - - +
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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