Contacts of the strand formed by residues 81 - 87 (chain B) in PDB entry 2CKH
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 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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511A ARG* 3.6 17.8 + - - -
18B ASN 3.8 0.8 + - - -
19B LEU* 3.4 15.9 - - + +
20B LYS 3.0 22.9 + - - -
61B PHE* 3.5 31.2 - - + -
76B GLU 4.6 1.4 - - - +
77B MET* 3.8 0.9 - - - -
78B GLU* 2.9 43.8 + - - +
79B ASP 3.0 5.4 + - - +
80B GLU* 1.3 79.1 - - - +
82B THR* 1.3 59.4 + - - +
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Residues in contact with THR 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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20B LYS* 3.3 33.1 - - + +
22B ALA* 4.1 17.3 - - + -
28B VAL* 5.8 2.0 - - + -
61B PHE* 3.3 22.9 - - - -
62B ASP* 4.6 5.7 + - - +
80B GLU 4.1 2.8 + - - -
81B ASP* 1.3 78.3 + - - +
83B ILE* 1.3 74.6 + - - +
84B ASP* 4.2 9.2 + - - +
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Residues in contact with ILE 83 (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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19B LEU* 4.3 22.2 - - + -
20B LYS 2.7 12.6 + - - +
21B VAL* 3.4 19.8 - - + +
22B ALA 2.9 25.8 + - - -
39B LEU* 4.2 25.1 - - + -
42B LEU* 5.0 6.3 - - + -
59B PHE* 4.1 17.0 - - + -
60B ARG 3.9 2.5 - - - -
61B PHE* 4.6 4.5 - - + -
66B ILE* 3.5 28.3 - - + -
77B MET* 4.2 15.9 - - + -
82B THR* 1.3 79.0 - - - +
84B ASP* 1.3 73.7 + - - +
85B VAL 3.9 0.2 + - - -
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Residues in contact with ASP 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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500A LYS* 4.3 14.1 + - - +
508A ALA* 4.9 6.5 - - - +
512A TRP* 3.7 25.7 + - + -
22B ALA* 3.8 14.3 - - - +
58B ARG 3.9 0.3 - - - +
59B PHE* 3.5 3.1 - - - -
60B ARG 2.8 41.0 + - - +
62B ASP* 4.8 3.8 + - - +
82B THR* 5.0 8.3 - - - +
83B ILE* 1.3 75.7 - - - +
85B VAL* 1.3 59.9 + - - +
86B PHE* 3.4 29.2 - - + -
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Residues in contact with VAL 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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500A LYS* 5.4 0.2 + - - -
21B VAL* 4.2 5.2 - - + -
22B ALA 3.2 16.4 + - - +
23B GLY* 3.8 5.2 - - - -
24B GLN* 3.6 21.1 + - - +
46B TYR* 3.7 30.5 - - + +
52B LEU* 6.0 2.0 - - + -
57B ILE* 3.9 26.2 - - + -
58B ARG 3.4 12.6 - - - +
59B PHE* 3.7 28.5 - - + -
84B ASP* 1.3 75.3 - - - +
86B PHE* 1.3 70.0 + - - +
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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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496A PHE* 3.5 51.1 - + + -
500A LYS* 3.3 34.5 - - + -
512A TRP* 3.8 20.0 - + - -
24B GLN* 3.3 20.0 - - - +
57B ILE* 3.2 12.0 - - - +
58B ARG 3.0 38.7 + - - +
60B ARG* 4.1 20.0 - - + -
84B ASP* 3.4 36.1 - - + -
85B VAL* 1.3 78.0 - - - +
87B GLN* 1.3 62.5 + - - +
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Residues in contact with GLN 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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496A PHE* 3.5 16.2 - - - -
24B GLN* 2.9 23.9 + - - +
56B GLN* 3.9 13.2 - - + +
57B ILE* 4.6 5.2 - - + -
86B PHE* 1.3 75.8 - - - +
88B GLN* 1.3 68.7 + - - +
89B GLN* 3.2 11.4 + - + +
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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