Contacts of the helix formed by residues 113 - 124 (chain B) in PDB entry 1KO1
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 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111B LYS* 6.0 1.7 - - - -
112B GLY* 1.3 78.2 - - - -
114B PHE* 1.3 66.9 + - - +
115B ASP* 3.8 19.7 - - - +
116B VAL* 3.1 20.1 + - + +
117B ILE* 3.2 11.6 + - - +
138B PHE* 4.0 2.7 - - - -
157B ASP* 6.3 0.2 - - - +
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Residues in contact with PHE 114 (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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113B ASP* 1.3 75.0 - - - +
115B ASP* 1.3 63.6 + - + +
117B ILE 3.4 0.2 + - - -
118B GLU* 2.8 56.4 + - + +
131B THR* 4.9 8.1 - - + -
134B LEU* 3.6 33.4 - - + +
135B VAL* 3.7 31.6 - - + -
138B PHE* 3.7 33.0 - + + -
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Residues in contact with ASP 115 (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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113B ASP* 3.8 13.2 - - - +
114B PHE* 1.3 84.1 - - + +
116B VAL* 1.3 85.3 + - - +
118B GLU* 3.8 10.1 - - - +
119B SER* 3.0 26.0 + - - -
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Residues in contact with VAL 116 (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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112B GLY 5.2 0.2 - - - -
113B ASP* 3.1 19.2 + - + +
115B ASP* 1.3 88.9 + - - +
117B ILE* 1.3 63.8 + - + +
119B SER* 3.2 18.6 + - - +
120B ARG* 3.3 18.0 + - - +
156B ILE* 4.5 16.6 - - + +
157B ASP* 3.8 45.8 - - + +
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Residues in contact with ILE 117 (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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16B VAL* 3.1 26.5 - - + -
17B SER 3.4 24.5 - - - +
18B GLY* 3.5 17.5 - - - +
19B SER* 4.2 13.0 - - - -
110B LEU 5.6 0.2 - - - +
112B GLY* 4.0 10.1 - - - +
113B ASP 3.2 9.9 + - - +
114B PHE 4.0 4.0 - - - +
116B VAL* 1.3 72.4 - - - +
118B GLU* 1.3 68.2 + - - +
120B ARG* 3.0 4.4 + - - +
121B LEU* 2.9 22.5 + - + +
134B LEU* 3.8 15.0 - - + -
138B PHE* 3.7 16.4 - - + -
156B ILE* 4.0 19.3 - - + -
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Residues in contact with GLU 118 (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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114B PHE* 2.8 47.0 + - + +
115B ASP* 3.8 10.1 - - - +
117B ILE* 1.3 73.1 - - - +
119B SER* 1.3 58.4 + - - +
121B LEU* 3.2 6.2 + - - +
122B LYS* 2.8 57.9 + - + +
131B THR* 4.2 18.9 + - - +
134B LEU* 3.6 18.3 - - + +
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Residues in contact with SER 119 (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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115B ASP 3.0 14.8 + - - -
116B VAL* 3.2 12.5 + - - +
118B GLU* 1.3 76.5 - - - +
120B ARG* 1.3 65.3 + - - +
122B LYS* 3.4 10.7 + - - +
123B ALA* 3.1 23.2 + - - +
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Residues in contact with ARG 120 (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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18B GLY* 3.1 34.0 + - - +
19B SER 3.8 9.8 + - - -
20B GLY* 4.0 14.5 - - - +
116B VAL* 3.3 16.5 + - - +
117B ILE* 3.0 9.3 + - - +
119B SER* 1.3 76.9 + - - +
121B LEU* 1.3 66.4 + - - +
123B ALA* 3.1 15.9 + - + +
124B ARG* 3.2 23.4 + - + +
156B ILE* 3.8 38.2 + - - +
158B GLN 5.1 3.8 + - - -
160B LEU* 6.0 5.9 - - - +
163B VAL* 5.3 4.9 - - - +
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Residues in contact with LEU 121 (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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17B SER* 3.6 20.2 - - - +
18B GLY* 3.8 12.8 - - - +
117B ILE* 2.9 12.5 + - + +
118B GLU* 3.5 7.9 - - + +
120B ARG* 1.3 78.8 - - - +
122B LYS* 1.3 62.5 + - - +
123B ALA 3.2 0.9 + - - -
124B ARG* 3.3 55.1 + - - +
130B LYS* 4.6 25.1 - - + +
134B LEU* 3.9 36.6 - - + -
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Residues in contact with LYS 122 (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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118B GLU* 2.8 47.6 + - + +
119B SER* 3.7 10.3 - - - +
120B ARG 3.3 0.2 - - - -
121B LEU* 1.3 75.7 - - - +
123B ALA* 1.3 59.6 + - - +
124B ARG 4.3 3.5 - - - +
131B THR* 5.5 7.0 - - - +
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Residues in contact with ALA 123 (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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119B SER 3.1 17.0 + - - +
120B ARG* 3.1 9.3 + - + +
122B LYS* 1.3 76.4 - - - +
124B ARG* 1.3 68.7 + - - +
125B LYS* 3.6 0.7 + - - -
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Residues in contact with ARG 124 (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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17B SER* 3.8 12.5 + - - -
18B GLY* 3.5 24.4 - - - +
20B GLY* 5.3 2.4 - - - +
120B ARG* 3.2 20.6 + - + +
121B LEU* 3.3 44.4 + - - +
122B LYS 4.3 3.8 - - - +
123B ALA* 1.3 83.8 - - - +
125B LYS* 1.3 69.6 + - + +
130B LYS* 5.1 2.0 - - - +
176B CL 3.9 11.5 - - - +
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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
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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