Contacts of the helix formed by residues 52 - 96 (chain E) in PDB entry 5KHU
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 ARG 52 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E PHE* 3.8 28.9 - - - +
55E CYS* 4.7 15.0 - - - +
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Residues in contact with PHE 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E ARG* 3.8 28.9 - - - +
54E LEU* 3.8 27.1 - - - +
56E GLU* 4.6 15.7 - - - +
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Residues in contact with LEU 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E PHE* 3.8 24.5 - - - +
55E CYS* 3.8 28.7 - - - +
57E SER* 4.5 15.0 - - - +
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Residues in contact with CYS 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E ARG* 4.7 14.4 - - - +
54E LEU* 3.8 26.0 - - - +
56E GLU* 3.8 29.4 - - - +
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Residues in contact with GLU 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E PHE* 4.6 13.7 - - - +
55E CYS* 3.8 29.6 - - - +
57E SER* 3.8 24.5 - - - +
----------------------------------------------------------
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Residues in contact with SER 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E LEU* 4.5 18.6 - - - +
56E GLU* 3.8 28.0 - - - +
58E VAL* 3.8 28.7 - - - +
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Residues in contact with VAL 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E SER* 3.8 25.6 - - - +
59E PHE* 3.8 28.7 - - - +
61E TYR* 4.6 15.9 - - - +
----------------------------------------------------------
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Residues in contact with PHE 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E VAL* 3.8 28.3 - - - +
60E SER* 3.8 27.1 - - - +
----------------------------------------------------------
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Residues in contact with SER 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E PHE* 3.8 24.5 - - - +
61E TYR* 3.8 29.6 - - - +
----------------------------------------------------------
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Residues in contact with TYR 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E VAL* 4.6 16.6 - - - +
60E SER* 3.8 29.6 - - - +
62E GLN* 3.8 26.9 - - - +
----------------------------------------------------------
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Residues in contact with GLN 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E TYR* 3.8 26.5 - - - +
63E VAL* 3.8 28.5 - - - +
----------------------------------------------------------
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Residues in contact with VAL 63 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E GLN* 3.8 26.5 - - - +
64E ALA* 3.8 28.7 - - - +
----------------------------------------------------------
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Residues in contact with ALA 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E VAL* 3.8 28.3 - - - +
65E SER* 3.8 25.4 - - - +
----------------------------------------------------------
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Residues in contact with SER 65 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E ALA* 3.8 29.2 - - - +
66E THR* 3.9 26.2 - - - +
----------------------------------------------------------
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Residues in contact with THR 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E SER* 3.9 27.8 - - - +
67E LEU* 3.8 28.3 - - - +
----------------------------------------------------------
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Residues in contact with LEU 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E THR* 3.8 25.6 - - - +
68E LYS* 3.8 29.2 - - - +
----------------------------------------------------------
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Residues in contact with LYS 68 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E LEU* 3.8 26.5 - - - +
69E GLN* 3.8 28.9 - - - +
----------------------------------------------------------
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Residues in contact with GLN 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E LYS* 3.8 29.2 - - - +
70E VAL* 3.8 26.0 - - - +
----------------------------------------------------------
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Residues in contact with VAL 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E GLN* 3.8 27.1 - - - +
71E LYS* 3.8 29.2 - - - +
----------------------------------------------------------
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Residues in contact with LYS 71 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E VAL* 3.8 28.3 - - - +
72E HIS* 3.8 27.4 - - - +
----------------------------------------------------------
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Residues in contact with HIS 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E LYS* 3.8 27.4 - - - +
73E ASP* 3.8 28.9 - - - +
----------------------------------------------------------
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Residues in contact with ASP 73 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E HIS* 3.8 26.5 - - - +
74E GLN* 3.8 29.8 - - - +
----------------------------------------------------------
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Residues in contact with GLN 74 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E ASP* 3.8 26.9 - - - +
75E GLN* 3.8 29.4 - - - +
----------------------------------------------------------
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Residues in contact with GLN 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E GLN* 3.8 29.6 - - - +
76E VAL* 3.8 25.6 - - - +
----------------------------------------------------------
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Residues in contact with VAL 76 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E GLN* 3.8 26.5 - - - +
77E ALA* 3.8 29.2 - - - +
----------------------------------------------------------
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Residues in contact with ALA 77 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E VAL* 3.8 28.9 - - - +
78E ARG* 3.8 26.0 - - - +
----------------------------------------------------------
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Residues in contact with ARG 78 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E ALA* 3.8 29.2 - - - +
79E MET* 3.8 26.7 - - - +
----------------------------------------------------------
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Residues in contact with MET 79 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E ARG* 3.8 28.7 - - - +
80E GLU* 3.9 26.9 - - - +
----------------------------------------------------------
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Residues in contact with GLU 80 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E MET* 3.9 27.8 - - - +
81E LYS* 3.8 28.0 - - - +
----------------------------------------------------------
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Residues in contact with LYS 81 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E GLU* 3.8 26.2 - - - +
82E LEU* 3.8 28.9 - - - +
----------------------------------------------------------
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Residues in contact with LEU 82 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E LYS* 3.8 26.5 - - - +
83E ALA* 3.8 28.9 - - - +
----------------------------------------------------------
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Residues in contact with ALA 83 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E LEU* 3.8 29.2 - - - +
84E GLY* 3.8 25.6 - - - +
----------------------------------------------------------
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Residues in contact with GLY 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E ALA* 3.8 28.0 - - - +
85E LEU* 3.8 28.0 - - - +
----------------------------------------------------------
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Residues in contact with LEU 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E GLY* 3.8 28.5 - - - +
86E VAL* 3.8 26.2 - - - +
----------------------------------------------------------
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Residues in contact with VAL 86 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E LEU* 3.8 29.2 - - - +
87E GLU* 3.8 27.6 - - - +
----------------------------------------------------------
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Residues in contact with GLU 87 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E VAL* 3.8 25.6 - - - +
88E GLU* 3.8 29.8 - - - +
----------------------------------------------------------
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Residues in contact with GLU 88 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E GLU* 3.8 29.6 - - - +
89E LEU* 3.8 25.6 - - - +
----------------------------------------------------------
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Residues in contact with LEU 89 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E GLU* 3.8 29.6 - - - +
90E GLU* 3.8 24.7 - - - +
----------------------------------------------------------
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Residues in contact with GLU 90 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E LEU* 3.8 28.9 - - - +
91E ALA* 3.8 27.4 - - - +
----------------------------------------------------------
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Residues in contact with ALA 91 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E GLU* 3.8 24.5 - - - +
92E ASP* 3.8 30.1 - - - +
----------------------------------------------------------
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Residues in contact with ASP 92 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E ALA* 3.8 26.9 - - - +
93E GLU* 3.8 28.9 - - - +
----------------------------------------------------------
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Residues in contact with GLU 93 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E ASP* 3.8 28.7 - - - +
94E TRP* 3.8 27.6 - - - +
----------------------------------------------------------
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Residues in contact with TRP 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E GLU* 3.8 27.1 - - - +
95E ARG* 3.8 30.3 - - - +
----------------------------------------------------------
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Residues in contact with ARG 95 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E TRP* 3.8 29.8 - - - +
96E PHE* 3.8 27.6 - - - +
----------------------------------------------------------
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Residues in contact with PHE 96 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E ARG* 3.8 28.9 - - - +
97E LYS* 3.8 28.5 - - - +
----------------------------------------------------------
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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