Contacts of the helix formed by residues 848 - 855 (chain B) in PDB entry 6ZGI
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 ASP 848 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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835B LYS* 4.1 9.7 + - - +
844B ILE* 3.1 24.6 + - + +
846B ALA 4.3 0.3 + - - -
847B ARG* 1.3 86.0 + - - +
849B LEU* 1.3 69.4 + - - +
850B ILE* 3.7 17.0 + - - +
851B CYS* 3.5 31.0 + - + +
852B ALA* 3.2 20.3 + - - +
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Residues in contact with LEU 849 (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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846B ALA 5.8 1.3 - - - +
847B ARG 3.6 15.3 - - - +
848B ASP* 1.3 75.1 + - - +
850B ILE* 1.3 64.1 + - + +
852B ALA* 3.4 8.8 + - + +
853B GLN* 3.0 35.7 + - - +
960B ASN* 3.6 37.2 - - - +
964B LYS* 5.9 3.1 - - - +
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Residues in contact with ILE 850 (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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829B ALA* 5.0 13.7 - - + +
830B ASP* 4.2 31.0 - - + +
835B LYS* 3.7 23.3 - - + -
848B ASP* 3.3 16.2 + - - +
849B LEU* 1.3 81.1 - - + +
851B CYS* 1.3 56.8 + - - +
853B GLN* 3.2 23.6 + - - +
854B LYS* 2.9 45.1 + - + +
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Residues in contact with CYS 851 (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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592A PHE* 5.1 2.9 - - - -
835B LYS* 3.4 25.4 - - - -
840B CYS* 2.0 53.2 - - + -
845B ALA* 4.5 8.1 - - - -
846B ALA 5.2 0.2 - - - -
848B ASP* 3.5 17.8 + - + +
850B ILE* 1.3 76.0 - - - +
852B ALA* 1.3 60.2 + - - +
854B LYS* 3.7 5.7 - - - +
855B PHE* 2.9 43.0 + - + -
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Residues in contact with ALA 852 (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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569A ILE* 5.8 4.9 - - + -
846B ALA* 4.3 22.1 - - - +
848B ASP 3.2 13.1 + - - +
849B LEU* 3.6 12.8 - - + +
850B ILE 3.3 0.2 - - - -
851B CYS* 1.3 79.6 - - - +
853B GLN* 1.3 59.8 + - + +
855B PHE* 3.8 6.9 + - - +
856B ASN* 2.8 27.1 - - - +
963B VAL* 4.4 17.3 - - + +
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Residues in contact with GLN 853 (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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849B LEU* 3.0 20.9 + - - +
850B ILE* 3.4 29.6 - - - +
852B ALA* 1.3 76.5 - - + +
854B LYS* 1.3 58.4 + - + +
856B ASN* 3.1 17.0 + - - +
857B GLY 3.6 0.2 + - - -
858B LEU* 3.3 35.6 + - + +
860B VAL* 5.4 3.6 - - - +
956B ALA* 4.5 3.6 + - - +
959B LEU* 3.3 39.1 - - + +
960B ASN* 3.3 25.6 + - - +
963B VAL* 4.0 22.4 - - + -
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Residues in contact with LYS 854 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317A ASN* 4.5 9.2 + - - -
591A SER 5.2 0.5 - - - +
592A PHE* 3.6 46.2 - - + -
593A GLY* 5.2 2.7 + - - +
614A ASP* 3.5 32.2 + - - -
740B MET* 5.4 0.5 - - - +
835B LYS* 4.5 13.2 - - + -
850B ILE* 2.9 37.9 + - + +
851B CYS* 3.2 3.3 + - - +
853B GLN* 1.3 72.3 - - + +
855B PHE* 1.3 60.0 + - - +
856B ASN 3.1 6.7 + - - -
857B GLY* 3.6 8.1 + - - -
858B LEU 4.0 13.7 - - - +
859B THR* 3.9 27.1 - - - +
860B VAL 5.3 1.6 - - - +
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Residues in contact with PHE 855 (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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588A THR* 3.9 19.3 - - + -
589A PRO* 3.9 46.4 - - + +
591A SER 4.3 9.3 - - - +
592A PHE* 3.6 26.2 - + + -
740B MET* 4.0 14.9 - - - +
837B TYR* 4.0 10.1 - + - -
840B CYS* 4.0 22.2 - - - -
845B ALA* 3.6 28.9 - - + -
846B ALA 5.5 0.4 - - - -
851B CYS* 2.9 27.3 + - + +
852B ALA* 3.8 6.7 + - - +
853B GLN 3.3 0.2 - - - -
854B LYS* 1.3 76.2 - - - +
856B ASN* 1.3 65.8 + - - +
857B GLY 3.6 0.7 - - - -
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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