Contacts of the helix formed by residues 107 - 124 (chain B) in PDB entry 1KAF
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 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B GLU* 5.1 14.8 - - + +
106B ILE* 1.3 81.0 - - - +
108B SER* 1.3 63.5 + - - +
109B ASP* 2.6 34.8 + - - +
110B MET* 3.1 27.5 + - - +
111B GLU* 3.2 13.3 + - - +
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Residues in contact with SER 108 (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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107B THR* 1.3 73.6 - - - +
109B ASP* 1.3 63.9 + - - +
111B GLU* 3.3 11.7 + - - +
112B GLU* 3.1 24.5 + - - +
150C ARG* 4.4 20.2 - - - -
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Residues in contact with ASP 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B THR* 2.6 33.3 + - - +
108B SER* 1.3 78.8 + - - +
110B MET* 1.3 60.7 + - - +
112B GLU* 3.4 6.0 + - - +
113B ASP* 3.1 30.2 + - - +
196B ARG* 2.9 28.3 + - - +
150C ARG* 4.1 11.1 + - - +
165C TYR* 3.3 45.1 + - + +
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Residues in contact with MET 110 (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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105B GLU 4.5 1.8 - - - +
106B ILE* 3.7 22.4 - - + -
107B THR* 3.1 35.7 + - - +
109B ASP* 1.3 77.3 - - - +
111B GLU* 1.3 59.9 + - - +
113B ASP* 3.3 1.7 + - - +
114B LYS* 2.9 31.2 + - - +
136B SER 3.2 24.9 - - - +
137B ASN* 4.0 2.9 - - - -
138B TYR* 3.8 11.7 - - + -
154B ILE* 3.7 27.0 - - + +
156B ASN* 3.8 25.6 - - - +
196B ARG* 3.5 26.0 - - - +
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Residues in contact with GLU 111 (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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106B ILE* 3.7 21.6 - - + +
107B THR 3.2 8.8 + - - +
108B SER* 3.3 12.0 + - - +
110B MET* 1.3 78.7 - - - +
112B GLU* 1.3 61.1 + - - +
114B LYS* 3.3 4.3 + - + +
115B ASP* 3.0 32.8 + - - +
138B TYR* 3.4 26.7 + - - +
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Residues in contact with GLU 112 (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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108B SER 3.1 15.8 + - - +
109B ASP* 3.8 6.4 - - - +
110B MET 3.3 0.2 - - - -
111B GLU* 1.3 77.1 - - - +
113B ASP* 1.3 67.7 + - - +
115B ASP* 3.3 11.1 + - + +
116B LEU* 3.1 21.9 + - + +
144C LYS* 4.3 21.5 + - + +
145C ARG* 2.7 58.3 + - - +
150C ARG* 4.6 6.9 + - - -
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Residues in contact with ASP 113 (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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109B ASP* 3.1 18.4 + - - +
110B MET 3.7 3.4 - - - +
112B GLU* 1.3 80.8 - - - +
114B LYS* 1.3 60.4 + - - +
116B LEU* 3.4 6.2 + - - +
117B MET* 2.9 28.4 + - - +
154B ILE* 4.1 13.4 - - + +
196B ARG* 2.8 42.5 + - - +
197B SER* 5.4 1.5 - - - -
198B ALA* 5.4 4.0 + - - -
201B ILE* 3.5 27.8 - - + +
145C ARG* 5.2 4.3 + - - -
165C TYR* 6.1 0.6 - - - -
166C LYS* 5.1 5.4 + - - +
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Residues in contact with LYS 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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110B MET 2.9 18.5 + - - +
111B GLU* 3.6 4.9 - - + +
113B ASP* 1.3 74.6 - - - +
115B ASP* 1.3 83.0 + - - +
117B MET* 3.2 3.3 + - - +
118B LEU* 2.8 56.7 + - + +
131B VAL* 4.4 16.6 - - + -
138B TYR* 3.7 48.6 + - + +
154B ILE* 4.2 9.4 - - + +
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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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111B GLU* 3.0 23.0 + - - +
112B GLU* 3.3 11.8 + - + +
114B LYS* 1.3 100.2 + - - +
116B LEU* 1.3 60.7 + - - +
118B LEU* 3.5 4.8 + - - +
119B LYS* 3.0 33.1 + - + +
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Residues in contact with LEU 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 GLU* 3.1 13.4 + - + +
113B ASP* 3.6 9.9 - - - +
114B LYS 3.2 0.2 - - - -
115B ASP* 1.3 78.0 - - - +
117B MET* 1.3 63.7 - - - +
119B LYS* 3.2 17.9 + - + +
120B LEU* 3.0 43.5 + - + +
198B ALA* 3.9 37.0 - - + +
201B ILE* 3.9 22.2 - - + -
202B GLU* 4.2 7.9 - - - +
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Residues in contact with MET 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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113B ASP 2.9 18.3 + - - +
114B LYS* 3.2 6.0 + - - +
116B LEU* 1.3 78.1 - - - +
118B LEU* 1.3 63.8 + - + +
120B LEU* 3.3 4.3 + - - +
121B LEU* 2.9 48.7 + - + +
138B TYR* 5.5 2.0 - - - +
140B ALA* 4.2 8.5 - - - -
152B PHE* 3.7 30.5 - - + +
153B GLU* 4.0 7.6 - - - +
154B ILE* 3.6 29.6 - - + -
160B MET* 3.2 34.1 - - + -
201B ILE* 4.2 11.6 - - + +
205B ILE* 4.7 4.6 - - + +
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Residues in contact with LEU 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 LYS* 2.8 56.7 + - + +
115B ASP* 3.9 5.2 - - - +
117B MET* 1.3 88.3 - - + +
119B LYS* 1.3 57.9 + - + +
121B LEU* 3.3 5.0 + - + +
122B ASP* 2.9 42.5 + - - +
128B LEU* 3.4 32.8 - - + -
131B VAL* 3.4 22.7 - - + -
140B ALA* 4.9 3.4 - - + -
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Residues in contact with LYS 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 25.8 + - + +
116B LEU* 3.2 18.0 + - + +
118B LEU* 1.3 79.9 - - + +
120B LEU* 1.3 61.1 + - - +
122B ASP* 3.8 6.6 - - - +
123B LYS* 3.0 28.8 + - - +
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Residues in contact with LEU 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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116B LEU* 3.0 35.0 + - + +
117B MET 3.8 2.2 - - - +
119B LYS* 1.3 79.1 - - + +
121B LEU* 1.3 64.9 + - - +
123B LYS* 3.4 20.3 + - + +
124B ASN* 2.9 35.1 + - - +
201B ILE* 4.0 11.0 - - + +
202B GLU* 3.0 59.9 - - - +
205B ILE* 3.6 20.0 - - + -
206B THR* 5.3 4.0 - - - +
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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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117B MET* 2.9 40.3 + - + +
118B LEU* 3.3 6.5 + - - +
120B LEU* 1.3 77.4 - - - +
122B ASP* 1.3 61.8 + - - +
124B ASN 3.4 1.7 + - - -
125B GLY 3.2 3.5 + - - -
126B PHE* 2.9 62.0 + - + +
128B LEU* 4.3 17.9 - - + -
140B ALA* 3.8 22.9 - - + -
152B PHE* 3.8 26.5 - - + -
205B ILE* 3.8 19.3 - - + -
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Residues in contact with ASP 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 LEU* 2.9 27.7 + - - +
119B LYS* 3.8 6.1 - - - +
121B LEU* 1.3 75.3 - - - +
123B LYS* 1.3 67.5 + - - +
125B GLY* 3.1 13.7 + - - -
126B PHE 4.7 8.5 - - - +
128B LEU* 5.0 8.7 - - - +
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Residues in contact with LYS 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 LYS 3.0 18.0 + - - +
120B LEU* 3.6 24.0 - - + +
121B LEU 3.3 0.2 - - - -
122B ASP* 1.3 78.3 - - - +
124B ASN* 1.3 76.9 + - - +
125B GLY 3.5 0.5 + - - -
202B GLU* 5.9 1.6 - - - -
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Residues in contact with ASN 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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120B LEU* 2.9 29.8 + - - +
122B ASP 3.2 0.4 - - - -
123B LYS* 1.3 99.4 + - - +
125B GLY* 1.3 63.4 + - - +
126B PHE* 3.5 17.1 + - + -
205B ILE* 3.8 17.6 + - - +
206B THR* 4.8 4.2 + - - +
209B SER* 3.5 34.8 + - - -
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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