Contacts of the helix formed by residues 869 - 878 (chain B) in PDB entry 1Z00
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 SER 869 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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867B ALA 5.3 0.2 + - - -
868B LEU* 1.3 93.7 - - - +
870B GLN* 1.3 65.9 + - - +
871B ASP* 3.0 13.9 - - - -
872B GLU* 3.0 26.5 + - - +
873B LEU 3.4 1.2 + - - -
887B TYR* 4.0 8.3 - - - -
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Residues in contact with GLN 870 (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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869B SER* 1.3 73.6 - - - +
871B ASP* 1.3 55.6 + - - +
873B LEU* 2.9 17.1 - - - +
874B THR* 2.6 54.4 + - - -
880B ALA* 3.7 5.2 + - - +
883B ALA* 3.3 4.8 - - - +
884B LYS* 3.1 43.7 - - + +
887B TYR* 3.7 39.8 - - + -
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Residues in contact with ASP 871 (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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869B SER* 3.0 12.3 - - - -
870B GLN* 1.3 81.4 + - - +
872B GLU* 1.3 62.2 + - - +
874B THR* 3.3 6.6 + - - +
875B SER* 2.7 39.3 + - - +
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Residues in contact with GLU 872 (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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868B LEU* 3.8 24.4 - - + +
869B SER* 3.0 32.7 + - - +
871B ASP* 1.3 82.0 - - - +
873B LEU* 1.3 63.1 + - - +
875B SER* 3.1 17.8 + - - -
876B ILE* 3.2 22.0 + - + +
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Residues in contact with LEU 873 (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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855B LEU* 5.7 3.4 - - + -
865B LEU* 4.1 9.0 - - + +
868B LEU* 3.4 28.0 - - + +
869B SER 3.5 1.3 - - - +
870B GLN* 2.9 39.0 - - + +
872B GLU* 1.3 77.6 - - - +
874B THR* 1.3 58.9 + - - +
876B ILE* 4.4 9.2 - - + +
877B LEU* 2.8 37.2 + - + +
883B ALA* 3.3 30.3 - - + +
886B LEU* 3.5 37.5 - - + -
887B TYR* 3.8 15.9 - - + -
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Residues in contact with THR 874 (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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870B GLN* 2.6 44.1 + - - -
871B ASP* 3.4 8.1 - - - +
872B GLU 3.2 0.6 - - - -
873B LEU* 1.3 76.6 - - - +
875B SER* 1.3 57.9 + - - +
878B GLY* 2.8 32.9 + - - +
879B ASN 4.5 1.1 - - - -
880B ALA* 3.8 27.5 - - + +
883B ALA* 3.2 10.7 - - - +
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Residues in contact with SER 875 (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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871B ASP* 2.7 20.4 + - - +
872B GLU* 3.1 12.6 + - - -
874B THR* 1.3 78.5 - - - +
876B ILE* 1.3 64.1 + - - +
878B GLY* 4.0 5.4 + - - -
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Residues in contact with ILE 876 (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 ASN* 5.0 1.2 - - - +
854B SER* 4.1 14.1 - - - +
855B LEU* 3.4 28.3 - - + -
858B HIS* 3.7 45.3 - - + +
859B VAL* 4.9 8.7 - - + +
868B LEU* 4.6 14.1 - - + -
872B GLU* 3.2 20.8 + - + +
873B LEU* 3.9 7.2 - - - +
875B SER* 1.3 81.7 - - - +
877B LEU* 1.3 62.4 + - - +
878B GLY* 4.6 0.2 - - - -
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Residues in contact with LEU 877 (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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847B VAL* 4.5 5.6 - - + -
851B ASN* 3.3 53.7 + - + +
855B LEU* 3.5 31.0 - - + -
873B LEU* 2.8 19.6 + - + +
876B ILE* 1.3 73.2 - - - +
878B GLY* 1.3 57.4 + - - +
879B ASN* 3.0 17.8 + - - +
882B ASN* 3.8 10.1 - - + +
883B ALA* 3.4 35.0 - - - +
886B LEU* 3.9 18.2 - - + -
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Residues in contact with GLY 878 (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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874B THR* 2.8 18.6 + - - +
875B SER 4.4 5.2 - - - -
876B ILE 3.3 2.2 - - - -
877B LEU* 1.3 77.0 - - - +
879B ASN* 1.3 58.4 + - - +
880B ALA 3.8 2.3 + - - -
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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