Contacts of the helix formed by residues 107 - 124 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A GLU* 4.7 9.9 - - + +
106A ILE* 1.3 78.7 - - - +
108A SER* 1.3 64.0 + - - +
109A ASP* 3.5 10.1 + - - +
110A MET* 3.1 36.7 + - - +
111A GLU* 3.2 24.4 + - - +
156A ASN* 6.2 0.9 - - + -
196A ARG* 4.3 0.9 + - - -
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Residues in contact with SER 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A THR* 1.3 73.7 - - - +
109A ASP* 1.3 65.8 + - - +
111A GLU* 3.3 15.8 + - - +
112A GLU* 3.0 33.9 + - - +
129B LYS* 3.6 24.8 + - - -
143B GLU 6.0 0.2 - - - -
150B ARG* 5.5 4.7 - - - -
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Residues in contact with ASP 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A THR* 3.2 7.2 + - - +
108A SER* 1.3 79.7 - - - +
110A MET* 1.3 56.9 + - - +
112A GLU* 3.2 15.2 + - - +
113A ASP* 2.8 35.1 + - - +
196A ARG* 3.6 15.9 - - - +
145B ARG* 2.9 30.4 + - - +
150B ARG* 2.7 39.2 + - - -
165B TYR* 3.3 19.1 - - + -
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Residues in contact with MET 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A GLU 4.3 2.2 - - - +
106A ILE* 3.6 24.2 - - + -
107A THR* 3.1 44.3 + - - +
109A ASP* 1.3 77.0 - - - +
111A GLU* 1.3 56.9 + - - +
113A ASP* 3.3 1.8 + - - +
114A LYS* 2.8 31.7 + - - +
136A SER 3.2 24.5 - - - +
137A ASN* 4.1 2.2 - - - -
138A TYR* 3.8 9.9 - - + -
154A ILE* 3.6 29.6 - - + +
156A ASN* 3.7 28.0 - - - +
196A ARG* 3.4 24.0 - - - +
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Residues in contact with GLU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ILE* 3.8 12.4 - - + +
107A THR 3.2 15.8 + - - +
108A SER* 3.6 14.9 + - - +
109A ASP 3.2 0.2 - - - -
110A MET* 1.3 77.3 - - - +
112A GLU* 1.3 57.3 + - + +
114A LYS* 3.4 3.0 + - - +
115A ASP* 2.9 39.2 + - - +
138A TYR* 3.7 25.8 + - - +
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Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A SER* 3.0 26.9 + - - +
109A ASP* 3.5 13.5 - - - +
111A GLU* 1.3 78.1 - - + +
113A ASP* 1.3 65.6 + - - +
115A ASP* 3.3 10.2 + - - +
116A LEU* 3.1 21.7 + - - +
129B LYS* 5.6 0.3 + - - -
143B GLU 4.1 3.5 - - - +
144B LYS* 3.2 25.7 - - + -
145B ARG* 2.9 49.3 + - - +
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Residues in contact with ASP 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ASP* 2.8 21.9 + - - +
110A MET 3.7 3.6 - - - +
112A GLU* 1.3 75.9 - - - +
114A LYS* 1.3 57.7 + - - +
116A LEU* 3.3 6.4 + - - +
117A MET* 2.9 27.7 + - - +
154A ILE* 3.9 15.5 - - + -
196A ARG* 2.8 39.4 + - - +
197A SER* 5.1 6.3 + - - -
198A ALA* 5.1 2.1 + - - -
201A ILE* 3.7 28.4 - - + +
145B ARG* 5.0 9.7 + - - -
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Residues in contact with LYS 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A MET 2.8 17.6 + - - +
111A GLU* 3.7 4.0 - - - +
113A ASP* 1.3 73.7 - - - +
115A ASP* 1.3 76.5 + - - +
117A MET* 3.2 3.8 + - - -
118A LEU* 2.9 70.5 + - + +
131A VAL* 4.4 11.4 - - + -
138A TYR* 3.7 49.5 + - + +
154A ILE* 4.1 12.3 - - + +
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Residues in contact with ASP 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A GLU* 2.9 27.1 + - - +
112A GLU* 3.5 8.8 - - - +
113A ASP 3.3 0.2 - - - -
114A LYS* 1.3 97.4 + - - +
116A LEU* 1.3 56.5 + - - +
118A LEU* 3.5 4.8 + - - +
119A LYS* 3.0 29.2 + - - +
144B LYS* 5.9 3.1 - - - -
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLU 3.1 12.4 + - - +
113A ASP* 3.6 8.1 - - - +
115A ASP* 1.3 73.9 - - - +
117A MET* 1.3 68.1 + - - +
119A LYS* 3.2 20.3 + - + +
120A LEU* 3.0 51.7 + - + +
198A ALA* 3.8 40.2 - - + +
201A ILE* 4.0 17.0 - - + -
202A GLU* 4.3 8.1 - - - +
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Residues in contact with MET 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ASP 2.9 17.5 + - - +
114A LYS* 3.5 7.2 - - - +
116A LEU* 1.3 77.1 - - - +
118A LEU* 1.3 65.4 + - + +
120A LEU* 3.7 3.6 - - - +
121A LEU* 2.8 48.4 + - + +
138A TYR* 5.8 2.0 - - - +
140A ALA* 4.3 8.3 - - - -
152A PHE* 3.6 33.4 - - + +
153A GLU 4.1 7.0 - - - +
154A ILE* 3.9 27.6 - - + -
160A MET* 3.2 33.9 - - + -
201A ILE* 4.1 12.9 - - + +
205A ILE* 5.0 2.4 - - + +
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Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A LYS* 2.9 62.8 + - + +
115A ASP* 3.9 4.9 - - - +
117A MET* 1.3 88.8 - - + +
119A LYS* 1.3 62.7 + - - +
121A LEU* 3.8 6.1 - - - +
122A ASP* 3.0 34.8 + - - +
128A LEU* 4.5 10.1 - - + -
131A VAL* 4.1 26.2 - - + -
140A ALA* 4.7 7.0 - - + -
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Residues in contact with LYS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ASP 3.0 18.8 + - - +
116A LEU* 3.4 22.5 - - + +
118A LEU* 1.3 76.6 - - - +
120A LEU* 1.3 66.5 + - + +
122A ASP* 3.7 6.4 - - - +
123A LYS* 3.0 27.4 + - + +
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU* 3.0 37.2 + - + +
117A MET 3.8 2.7 - - - +
119A LYS* 1.3 83.9 - - + +
121A LEU* 1.3 65.9 + - - +
123A LYS* 4.1 21.1 - - + +
124A ASN* 2.9 32.6 + - - +
201A ILE* 4.2 9.0 - - + +
202A GLU* 3.5 57.4 - - - +
205A ILE* 3.8 19.6 - - + +
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Residues in contact with LEU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A MET* 2.8 42.3 + - + +
118A LEU* 3.8 6.3 - - - +
120A LEU* 1.3 75.5 - - - +
122A ASP* 1.3 62.0 + - - +
124A ASN 3.4 2.3 + - - -
125A GLY 3.3 3.1 + - - -
126A PHE* 2.9 55.0 + - + +
128A LEU* 4.3 18.2 - - + -
140A ALA* 4.0 22.0 - - + -
152A PHE* 3.8 27.4 - - + -
205A ILE* 3.7 24.9 - - + -
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Residues in contact with ASP 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU* 3.0 25.4 + - - +
119A LYS* 3.7 5.8 - - - +
121A LEU* 1.3 76.3 - - - +
123A LYS* 1.3 66.8 + - - +
125A GLY* 3.1 13.4 + - - +
126A PHE 4.4 10.2 - - - +
128A LEU* 4.9 8.7 - - - +
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Residues in contact with LYS 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A LYS* 3.0 19.8 + - + +
120A LEU* 3.6 19.8 - - + +
122A ASP* 1.3 80.0 - - - +
124A ASN* 1.3 76.8 + - - +
125A GLY 3.5 1.9 + - - -
202A GLU* 4.5 13.3 + - - -
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Residues in contact with ASN 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LEU* 2.9 27.7 + - - +
121A LEU 3.4 0.2 + - - -
122A ASP 3.2 0.2 - - - -
123A LYS* 1.3 100.7 - - - +
125A GLY* 1.3 60.8 + - - +
126A PHE* 3.4 15.4 + - + -
205A ILE* 3.7 11.5 + - - +
206A THR* 5.4 1.8 - - - +
209A SER* 3.0 39.0 + - - +
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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