Contacts of the helix formed by residues 829 - 843 (chain F) in PDB entry 5ZCS
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 829 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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820F GLU 4.6 2.7 - - - +
821F ARG* 3.7 36.7 - - + +
825F ALA 3.3 17.9 + - - +
826F LYS* 3.9 5.3 + - - +
827F GLN 3.5 1.0 - - - -
828F LEU* 1.3 77.1 - - - +
830F LYS* 1.3 54.2 + - - +
831F TRP 3.3 2.9 - - - -
832F HIS* 2.9 12.8 + - + +
833F ARG* 2.7 32.0 + - - +
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Residues in contact with LYS 830 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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826F LYS 4.2 10.0 + - - +
827F GLN 4.7 5.8 + - - +
828F LEU* 3.7 0.6 - - - +
829F GLU* 1.3 77.6 - - - +
831F TRP* 1.3 51.3 + - - +
833F ARG* 3.0 13.1 + - + +
834F GLU* 2.6 32.6 + - - +
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Residues in contact with TRP 831 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828F LEU 5.1 5.3 - - - +
829F GLU 3.3 0.8 - - - +
830F LYS* 1.3 77.8 - - - +
832F HIS* 1.3 57.8 + - - +
834F GLU* 3.0 14.0 + - + +
835F TYR* 2.8 23.9 + - - +
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Residues in contact with HIS 832 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794F LEU 6.0 2.5 - - - +
821F ARG* 5.1 7.0 - - + -
828F LEU 5.0 2.8 + - - +
829F GLU* 2.9 22.1 + - + +
831F TRP* 1.3 75.0 - - - +
833F ARG* 1.3 57.1 + - - +
835F TYR* 3.0 14.1 + - + +
836F ASN* 2.9 22.3 + - - +
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Residues in contact with ARG 833 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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821F ARG* 5.1 10.0 - - + +
829F GLU 2.7 14.9 + - - +
830F LYS* 3.0 17.2 + - + +
832F HIS* 1.3 68.1 - - - +
834F GLU* 1.3 52.5 + - - +
836F ASN* 3.0 13.0 + - + +
837F SER* 2.7 31.6 + - - -
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Residues in contact with GLU 834 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830F LYS 2.6 16.0 + - - +
831F TRP* 3.0 18.4 - - - +
833F ARG* 1.3 70.9 - - - +
835F TYR* 1.3 52.1 + - - +
837F SER* 3.0 13.5 + - - -
838F LYS* 2.6 32.4 + - - +
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Residues in contact with TYR 835 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797F LEU 5.5 5.2 - - - +
798F GLY* 5.3 10.8 - - - +
831F TRP 2.8 10.1 + - - +
832F HIS* 3.0 18.8 + - + +
834F GLU* 1.3 75.7 - - - +
836F ASN* 1.3 55.8 + - - +
838F LYS* 3.0 13.6 + - + +
839F TYR* 2.8 24.1 + - - +
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Residues in contact with ASN 836 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832F HIS 2.9 8.1 + - - +
833F ARG* 3.0 20.4 + - + +
835F TYR* 1.3 73.1 - - - +
837F SER* 1.3 56.4 + - - +
839F TYR* 3.0 13.5 + - + +
840F VAL* 2.8 24.7 + - - +
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Residues in contact with SER 837 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833F ARG 2.7 15.6 + - - -
834F GLU* 3.0 17.7 + - - -
836F ASN* 1.3 68.5 - - - +
838F LYS* 1.3 58.3 + - - +
840F VAL* 3.0 14.6 + - - +
841F ASP* 2.8 25.6 + - - +
870F ARG* 6.4 2.2 - - - -
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Residues in contact with LYS 838 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834F GLU 2.6 15.7 + - - +
835F TYR* 3.0 17.9 - - - +
837F SER* 1.3 72.9 - - - +
839F TYR* 1.3 49.3 + - - +
841F ASP* 3.0 11.0 + - - +
842F LEU* 2.7 34.9 + - - +
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Residues in contact with TYR 839 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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808F PHE* 5.8 6.3 - - + -
835F TYR 2.8 9.5 + - - +
836F ASN* 3.0 18.6 + - + +
838F LYS* 1.3 75.9 - - - +
840F VAL* 1.3 55.6 + - - +
842F LEU* 3.0 21.9 + - + +
843F ILE* 3.0 21.3 + - - +
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Residues in contact with VAL 840 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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836F ASN 2.8 11.2 + - - +
837F SER* 3.0 17.4 + - - +
839F TYR* 1.3 76.8 - - - +
841F ASP* 1.3 56.7 + - - +
843F ILE 4.6 8.6 - - - +
844F GLU* 4.7 9.0 - - - +
870F ARG* 6.0 6.3 - - + -
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Residues in contact with ASP 841 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837F SER 2.8 11.7 + - - +
838F LYS* 3.0 11.8 + - - +
840F VAL* 1.3 77.2 - - - +
842F LEU* 1.3 63.6 + - - +
843F ILE 5.2 0.2 - - - -
844F GLU* 5.3 1.4 + - - +
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Residues in contact with LEU 842 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804F LEU* 5.7 5.6 - - + +
805F LEU* 6.0 3.6 - - - -
808F PHE* 5.0 11.7 - - + -
838F LYS 2.7 17.8 + - - +
839F TYR* 3.0 12.9 + - - +
841F ASP* 1.3 78.3 - - - +
843F ILE* 1.3 60.6 + - + +
844F GLU 3.8 2.9 + - - -
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Residues in contact with ILE 843 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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808F PHE* 4.8 17.3 - - + +
839F TYR 3.0 15.4 + - - +
840F VAL* 4.6 4.0 - - - +
842F LEU* 1.3 76.3 - - + +
844F GLU* 1.3 64.4 + - - +
845F GLU 3.4 6.2 + - - +
846F GLN* 4.0 20.8 + - + +
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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