Contacts of the helix formed by residues 124 - 143 (chain J) 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 SER 124 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125J GLN* 3.8 28.7 - - - +
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Residues in contact with GLN 125 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124J SER* 3.8 28.9 - - - +
126J SER* 3.8 27.1 - - - +
128J ILE* 4.6 13.5 - - - +
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Residues in contact with SER 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125J GLN* 3.8 25.1 - - - +
127J SER* 3.8 28.3 - - - +
129J LYS* 4.3 18.6 - - - +
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Residues in contact with SER 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126J SER* 3.8 24.9 - - - +
128J ILE* 3.7 29.6 - - - +
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Residues in contact with ILE 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125J GLN* 4.6 14.1 - - - +
127J SER* 3.7 29.2 - - - +
129J LYS* 3.8 26.7 - - - +
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Residues in contact with LYS 129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126J SER* 4.3 15.9 - - - +
128J ILE* 3.8 25.1 - - - +
130J SER* 3.8 29.6 - - - +
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Residues in contact with SER 130 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129J LYS* 3.8 29.2 - - - +
131J SER* 3.8 29.2 - - - +
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Residues in contact with SER 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J SER* 3.8 26.9 - - - +
132J ILE* 3.7 29.4 - - - +
134J LEU* 4.4 18.4 - - - +
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Residues in contact with ILE 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131J SER* 3.7 29.6 - - - +
133J CYS* 3.8 25.4 - - - +
135J LEU* 4.6 13.9 - - - +
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Residues in contact with CYS 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132J ILE* 3.8 29.4 - - - +
134J LEU* 3.8 25.8 - - - +
136J ARG* 4.6 15.0 - - - +
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Residues in contact with LEU 134 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131J SER* 4.4 15.3 - - - +
133J CYS* 3.8 25.6 - - - +
135J LEU* 3.7 30.1 - - - +
137J GLY* 4.5 15.5 - - - +
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Residues in contact with LEU 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132J ILE* 4.6 14.8 - - - +
134J LEU* 3.7 29.6 - - - +
136J ARG* 3.8 25.1 - - - +
138J LYS* 4.3 19.1 - - - +
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Residues in contact with ARG 136 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133J CYS* 4.6 15.5 - - - +
135J LEU* 3.8 24.5 - - - +
137J GLY* 3.7 29.2 - - - +
139J ILE* 4.4 15.0 - - - +
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Residues in contact with GLY 137 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134J LEU* 4.5 16.6 - - - +
136J ARG* 3.7 29.2 - - - +
138J LYS* 3.8 24.9 - - - +
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Residues in contact with LYS 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135J LEU* 4.3 15.9 - - - +
137J GLY* 3.8 23.3 - - - +
139J ILE* 3.7 30.1 - - - +
141J ASP* 4.5 13.7 - - - +
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Residues in contact with ILE 139 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136J ARG* 4.4 17.3 - - - +
138J LYS* 3.7 29.4 - - - +
140J TYR* 3.8 27.6 - - - +
142J ALA* 4.6 15.0 - - - +
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Residues in contact with TYR 140 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139J ILE* 3.8 23.8 - - - +
141J ASP* 3.8 28.7 - - - +
143J LEU* 4.2 18.2 - - - +
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Residues in contact with ASP 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138J LYS* 4.5 17.3 - - - +
140J TYR* 3.8 25.8 - - - +
142J ALA* 3.8 29.6 - - - +
144J ASP* 4.5 14.6 - - - +
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Residues in contact with ALA 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139J ILE* 4.6 13.0 - - - +
141J ASP* 3.8 28.5 - - - +
143J LEU* 3.8 24.7 - - - +
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Residues in contact with LEU 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140J TYR* 4.2 18.8 - - - +
142J ALA* 3.8 29.2 - - - +
144J ASP* 3.8 25.4 - - - +
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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