Contacts of the helix formed by residues 79 - 87 (chain B) in PDB entry 6B0Z
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 79 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77B THR 3.5 2.9 + - - +
78B PRO* 1.3 74.0 - - - +
80B GLU* 1.3 64.2 + - - +
81B LYS* 3.1 35.0 + - - +
82B ARG* 3.1 28.4 + - - +
83B VAL* 3.0 23.7 + - - +
91B MET* 3.6 16.4 - - - -
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Residues in contact with GLU 80 (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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79B ASP* 1.3 77.0 - - - +
81B LYS* 1.3 74.8 + - + +
83B VAL* 3.3 8.1 + - + +
84B GLU* 3.2 19.6 + - - +
91B MET* 3.4 18.2 - - + +
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Residues in contact with LYS 81 (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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79B ASP* 3.1 36.4 + - - +
80B GLU* 1.3 90.5 - - + +
82B ARG* 1.3 57.1 + - + +
84B GLU* 3.1 8.1 + - - +
85B GLU* 2.7 37.2 + - - +
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Residues in contact with ARG 82 (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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17B GLU* 3.1 26.4 + - - -
76B ILE* 3.3 34.2 - - + +
77B THR 4.0 2.9 + - - +
78B PRO* 3.7 10.3 - - + -
79B ASP* 3.1 33.1 + - - +
81B LYS* 1.3 77.2 - - - +
83B VAL* 1.3 64.1 + - - +
85B GLU* 2.8 39.3 + - - -
86B PHE* 3.0 33.5 + - + +
88B LEU* 3.8 4.7 - - + +
313B THR* 3.3 25.0 + - - +
317B ARG* 3.7 6.0 - - - +
501B NDP 3.1 23.8 + - - -
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Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B PRO* 4.9 0.9 - - + -
79B ASP 3.0 18.7 + - - +
80B GLU* 3.4 8.7 - - + +
81B LYS 3.2 0.2 - - - -
82B ARG* 1.3 75.5 - - - +
84B GLU* 1.3 58.1 + - - +
87B LYS* 2.8 26.9 + - - +
88B LEU* 3.1 37.4 + - + +
90B GLN* 4.5 6.1 - - - +
91B MET* 4.1 34.3 - - + +
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Residues in contact with GLU 84 (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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80B GLU 3.2 8.7 + - - +
81B LYS* 3.1 10.4 + - - +
83B VAL* 1.3 79.2 - - - +
85B GLU* 1.3 67.2 + - - +
86B PHE 3.2 0.7 + - - -
87B LYS* 3.4 42.0 + - - +
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Residues in contact with GLU 85 (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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17B GLU* 4.6 0.3 - - - +
81B LYS 2.7 19.4 + - - +
82B ARG* 2.8 35.7 + - - +
84B GLU* 1.3 74.7 - - - +
86B PHE* 1.3 85.3 + - + +
87B LYS* 5.2 1.2 - - - +
317B ARG* 2.8 34.1 + - - -
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Residues in contact with PHE 86 (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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17B GLU* 5.0 2.9 - - + -
46B ILE* 3.7 35.7 - - + -
47B GLU* 3.7 32.3 - - + +
50B ASP* 5.1 1.2 - - - +
76B ILE* 3.9 24.7 - - + -
82B ARG* 3.0 24.1 + - + +
85B GLU* 1.3 113.2 - - + +
87B LYS* 1.3 73.1 + - - +
88B LEU* 3.6 22.1 - - + +
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Residues in contact with LYS 87 (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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50B ASP* 4.0 6.6 - - - +
83B VAL 2.8 11.1 + - - +
84B GLU* 3.4 35.1 + - - +
85B GLU 5.2 1.3 - - - +
86B PHE* 1.3 81.2 - - - +
88B LEU* 1.3 62.8 + - - +
89B LYS* 3.8 1.7 + - - +
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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