Contacts of the helix formed by residues 77 - 87 (chain C) in PDB entry 2KI4
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 TRP 77 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B TRP* 4.7 23.6 - + - -
80B ILE* 4.4 2.2 - - + -
81B GLY* 3.4 31.2 - - - -
84B ALA* 3.4 36.6 - - + +
85B LYS* 5.9 3.8 - - - -
73C PHE* 6.4 0.4 - - + -
74C ASN* 4.0 42.5 - - + +
75C GLU 3.0 0.4 + - - -
76C TYR* 1.3 91.5 - + + +
78C ARG* 1.3 82.8 + - + +
80C ILE* 2.9 41.5 + - + +
81C GLY* 3.5 6.1 + - - -
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Residues in contact with ARG 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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62C SER 2.6 29.9 + - - -
63C LEU* 3.2 34.4 + - + +
65C VAL* 3.6 24.2 - - - +
74C ASN* 5.2 5.6 + - - +
75C GLU* 3.1 26.1 + - - +
77C TRP* 1.3 91.6 - - + +
79C LEU* 1.3 53.6 + - - +
81C GLY* 2.7 23.9 + - - +
82C GLU* 2.9 21.9 + - + +
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Residues in contact with LEU 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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38C PHE* 3.7 36.3 - - + -
41C LEU* 4.5 8.1 - - + -
42C VAL* 4.3 13.2 - - + -
46C LEU* 4.7 5.4 - - + -
50C LEU* 3.9 17.7 - - + -
56C LEU* 5.6 0.4 - - + -
59C LYS* 4.8 14.8 - - + -
63C LEU* 3.8 14.6 - - + +
76C TYR* 2.8 36.4 + - + +
78C ARG* 1.3 72.0 - - - +
80C ILE* 1.3 63.9 + - + +
82C GLU* 2.9 12.8 + - + +
83C LEU* 2.9 40.5 + - + +
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Residues in contact with ILE 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 4.2 27.8 - - + -
12B SER* 6.1 1.1 - - - +
13B ILE* 5.3 5.3 - - + +
77B TRP* 5.7 0.2 - - - -
16C VAL* 4.8 23.8 - - + +
17C VAL* 6.2 2.2 - - + -
20C PHE* 5.9 0.9 - - + -
76C TYR* 3.5 39.9 - - + +
77C TRP* 2.9 33.5 + - + +
79C LEU* 1.3 72.3 - - + +
81C GLY* 1.3 51.8 + - - +
83C LEU* 3.5 11.4 - - + +
84C ALA* 2.8 35.7 + - + +
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Residues in contact with GLY 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TRP* 4.2 19.9 - - - -
77C TRP* 3.5 8.1 + - - -
78C ARG* 2.7 13.2 + - - -
80C ILE* 1.3 75.7 - - - +
82C GLU* 1.3 60.1 + - - -
84C ALA* 3.4 7.2 - - - +
85C LYS* 2.8 39.8 + - - +
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Residues in contact with GLU 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU* 5.2 4.7 - - + -
59C LYS* 5.9 3.7 - - + +
63C LEU* 5.8 2.5 - - + -
78C ARG* 2.9 20.8 + - + +
79C LEU* 3.5 11.9 - - + +
81C GLY* 1.3 74.8 - - - +
83C LEU* 1.3 60.4 + - + +
85C LYS* 2.6 40.5 + - + +
86C GLU* 2.7 38.7 + - + +
93C LEU* 5.1 13.3 - - - +
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Residues in contact with LEU 83 (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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9B LEU* 3.6 34.3 - - + -
13B ILE* 6.3 0.2 - - - -
46C LEU* 3.9 19.7 - - + -
49C LEU* 3.6 30.5 - - + +
50C LEU* 3.5 36.1 - - + +
79C LEU* 2.9 38.7 + - + +
80C ILE* 3.5 16.6 - - + +
82C GLU* 1.3 75.1 - - - +
84C ALA* 1.3 61.9 + - - +
86C GLU* 3.1 19.3 + - - +
87C ILE* 3.3 13.0 + - - +
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Residues in contact with ALA 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ILE* 3.6 33.2 - - + +
77B TRP* 4.2 20.4 - - + -
80C ILE* 2.8 23.2 + - + +
81C GLY* 3.2 9.8 + - - +
83C LEU* 1.3 74.1 - - - +
85C LYS* 1.3 62.1 + - - +
87C ILE* 3.3 18.7 - - - +
88C ARG* 5.1 0.9 - - - +
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Residues in contact with LYS 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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74B ASN* 5.3 10.5 - - - +
77B TRP* 5.0 18.6 - - + +
81C GLY* 2.8 21.8 + - - +
82C GLU* 2.6 39.2 + - + +
84C ALA* 1.3 71.2 - - - +
86C GLU* 1.3 57.5 + - + +
88C ARG* 2.7 19.0 + - + +
89C LYS* 2.7 60.2 + - + +
93C LEU* 5.8 8.5 - - + -
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Residues in contact with GLU 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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49C LEU* 4.9 10.8 - - + +
50C LEU* 3.7 20.5 - - + +
51C LYS* 2.9 35.7 + - - +
82C GLU* 2.7 37.0 + - + +
83C LEU* 3.1 10.7 + - - +
85C LYS* 1.3 72.6 - - + +
87C ILE* 1.3 64.6 + - - +
88C ARG 3.6 0.2 - - - -
89C LYS 2.9 28.2 + - - +
90C LYS* 3.4 15.4 + - - +
91C LYS* 5.2 0.5 - - - -
93C LEU* 6.2 4.0 - - - -
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Residues in contact with ILE 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLU* 4.7 19.7 - - + +
13B ILE* 3.9 31.2 - - + -
49C LEU* 4.9 16.9 - - + +
83C LEU 3.3 6.2 + - - +
84C ALA 3.3 18.6 - - - +
85C LYS 3.0 0.8 + - - -
86C GLU* 1.3 77.5 - - - +
88C ARG* 1.3 64.3 + - + +
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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