Contacts of the strand formed by residues 73 - 81 (chain B) in PDB entry 5KOQ
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 LYS 73 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71B SER 3.7 1.8 + - - +
72B TYR* 1.3 82.8 - - - +
74B HIS* 1.3 64.3 + - - +
75B ASN 3.8 0.2 + - - -
94B GLN* 2.8 60.5 + - + +
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Residues in contact with HIS 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LYS* 6.0 2.7 - - - -
72B TYR* 2.9 35.5 + - + +
73B LYS* 1.3 76.6 - - - +
75B ASN* 1.3 75.9 + - - +
76B GLY* 4.4 13.2 + - - -
91B PHE* 5.1 7.6 - + - -
94B GLN* 5.9 0.3 - - - +
401B NAG 4.8 3.5 - - - +
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Residues in contact with ASN 75 (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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72B TYR* 4.4 0.6 + - - -
73B LYS 3.8 1.4 + - - +
74B HIS* 1.3 86.6 + - - +
76B GLY* 1.3 61.6 + - - +
77B THR* 2.7 33.8 + - - -
92B LEU* 3.2 26.4 + - + +
93B SER* 4.6 4.9 - - - +
94B GLN* 6.0 2.2 - - + -
107B MET* 5.1 4.3 - - + +
401B NAG 1.5 73.9 + - - +
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Residues in contact with GLY 76 (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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74B HIS* 4.4 12.3 - - - -
75B ASN* 1.3 72.8 - - - +
77B THR* 1.3 62.6 + - - +
78B GLU* 3.4 9.7 + - - +
91B PHE* 3.7 24.8 - - - +
92B LEU 2.8 17.0 + - - -
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Residues in contact with THR 77 (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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75B ASN* 2.7 24.1 + - - -
76B GLY* 1.3 73.9 - - - +
78B GLU* 1.3 69.9 + - - +
79B LEU* 3.4 2.9 + - + +
91B PHE* 3.3 1.3 - - - -
92B LEU* 2.8 39.5 + - + +
401B NAG 4.2 16.3 + - - +
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Residues in contact with GLU 78 (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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76B GLY 3.4 8.0 + - - +
77B THR* 1.3 78.7 - - - +
79B LEU* 1.3 59.2 + - - +
80B THR* 4.3 1.6 + - - +
90B GLY 3.5 15.0 - - - +
91B PHE* 4.3 3.1 - - + +
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Residues in contact with LEU 79 (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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43B ASN* 5.8 2.7 - - - +
77B THR* 3.4 3.3 + - + +
78B GLU* 1.3 73.6 - - - +
80B THR* 1.3 62.5 + - - +
81B LEU* 4.2 17.0 + - + +
89B SER* 3.7 2.1 - - - -
90B GLY 3.0 33.8 + - - +
91B PHE* 5.3 1.8 - - - -
92B LEU* 4.5 21.3 - - + -
137B ILE* 4.8 16.2 - - + +
138B GLY* 6.5 0.2 - - - -
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Residues in contact with THR 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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78B GLU* 4.3 2.0 + - - +
79B LEU* 1.3 75.1 - - - +
81B LEU* 1.3 63.2 + - - +
82B ARG* 4.0 5.7 + - + +
87B THR* 4.3 13.0 - - - +
88B VAL 3.4 14.6 - - - +
89B SER* 3.5 16.5 + - - +
137B ILE* 3.4 25.1 - - - +
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Residues in contact with LEU 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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41B SER* 5.9 5.4 - - - +
43B ASN* 3.8 29.6 - - + +
45B TRP* 3.6 37.0 - - + +
79B LEU* 4.4 20.9 - - + +
80B THR* 1.3 76.3 - - - +
82B ARG* 1.3 58.2 + - - +
87B THR* 3.6 1.6 - - - -
88B VAL* 2.8 61.2 + - + +
89B SER* 5.6 0.2 - - - -
90B GLY 5.6 0.7 - - - +
109B GLY* 5.9 3.8 - - - -
111B VAL* 5.0 4.7 - - + -
137B ILE* 3.8 17.0 - - + -
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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