Contacts of the helix formed by residues 77 - 106 (chain C) 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 THR 77 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76C ILE* 3.8 29.6 - - - +
78C GLU* 3.8 29.2 - - - +
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Residues in contact with GLU 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C THR* 3.8 29.2 - - - +
79C GLU* 3.8 28.9 - - - +
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Residues in contact with GLU 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C GLU* 3.8 24.2 - - - +
80C ASP* 3.8 29.2 - - - +
82C GLN* 4.1 19.3 - - - +
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Residues in contact with ASP 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C GLU* 3.8 25.6 - - - +
81C ALA* 3.7 29.6 - - - +
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Residues in contact with ALA 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ASP* 3.7 29.6 - - - +
82C GLN* 3.8 25.4 - - - +
84C MET* 4.4 16.2 - - - +
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Residues in contact with GLN 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C GLU* 4.1 19.3 - - - +
81C ALA* 3.8 28.9 - - - +
83C ASP* 3.8 26.5 - - - +
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Residues in contact with ASP 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C GLN* 3.8 29.8 - - - +
84C MET* 3.8 26.0 - - - +
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Residues in contact with MET 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C ALA* 4.4 19.3 - - - +
83C ASP* 3.8 27.6 - - - +
85C ASP* 3.8 29.2 - - - +
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Residues in contact with ASP 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C MET* 3.8 27.8 - - - +
86C ALA* 3.8 28.9 - - - +
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Residues in contact with ALA 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C ASP* 3.8 29.2 - - - +
87C TYR* 3.8 26.0 - - - +
89C LEU* 4.4 18.8 - - - +
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Residues in contact with TYR 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ALA* 3.8 24.9 - - - +
88C THR* 3.7 30.1 - - - +
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Residues in contact with THR 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C TYR* 3.7 29.8 - - - +
89C LEU* 3.8 25.8 - - - +
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Residues in contact with LEU 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ALA* 4.4 15.3 - - - +
88C THR* 3.8 26.0 - - - +
90C ALA* 3.7 28.7 - - - +
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Residues in contact with ALA 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C LEU* 3.7 29.8 - - - +
91C LYS* 3.8 27.4 - - - +
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Residues in contact with LYS 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C ALA* 3.8 24.9 - - - +
92C ALA* 3.7 29.8 - - - +
94C PHE* 4.4 15.3 - - - +
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Residues in contact with ALA 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C LYS* 3.7 29.4 - - - +
93C TYR* 3.8 26.2 - - - +
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Residues in contact with TYR 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ALA* 3.8 24.7 - - - +
94C PHE* 3.8 29.8 - - - +
96C VAL* 4.6 17.7 - - - +
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Residues in contact with PHE 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C LYS* 4.4 19.5 - - - +
93C TYR* 3.8 29.8 - - - +
95C ASP* 3.8 24.0 - - - +
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Residues in contact with ASP 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C PHE* 3.8 29.2 - - - +
96C VAL* 3.8 26.9 - - - +
97C LYS* 4.4 6.7 - - - +
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Residues in contact with VAL 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C TYR* 4.6 15.5 - - - +
95C ASP* 3.8 21.1 - - - +
97C LYS* 3.0 37.2 - - - +
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Residues in contact with LYS 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ASP* 4.4 10.8 - - - +
96C VAL* 3.0 38.1 - - - +
98C GLU* 3.8 24.5 - - - +
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Residues in contact with GLU 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C LYS* 3.8 28.7 - - - +
99C TYR* 3.7 29.8 - - - +
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Residues in contact with TYR 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C GLU* 3.7 29.8 - - - +
100C ASP* 3.8 29.2 - - - +
102C ALA* 4.3 19.3 - - - +
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Residues in contact with ASP 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C TYR* 3.8 25.8 - - - +
101C ARG* 3.8 29.2 - - - +
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Residues in contact with ARG 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C ASP* 3.8 29.4 - - - +
102C ALA* 3.8 24.7 - - - +
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Residues in contact with ALA 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C TYR* 4.3 20.6 - - - +
101C ARG* 3.8 27.4 - - - +
103C ALA* 3.8 30.1 - - - +
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Residues in contact with ALA 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C ALA* 3.8 30.5 - - - +
104C HIS* 3.8 26.0 - - - +
106C LEU* 4.2 21.3 - - - +
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Residues in contact with HIS 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ALA* 3.8 26.0 - - - +
105C PHE* 3.7 29.8 - - - +
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Residues in contact with PHE 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C HIS* 3.7 29.4 - - - +
106C LEU* 3.8 27.6 - - - +
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Residues in contact with LEU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C ALA* 4.2 20.0 - - - +
105C PHE* 3.8 28.9 - - - +
107C HIS* 3.8 25.6 - - - +
109C CYS* 4.6 16.8 - - - +
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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