Contacts of the helix formed by residues 113 - 126 (chain A) in PDB entry 1J75
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 ASN 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A LEU* 1.3 66.8 + - - +
115A GLU* 3.0 23.2 + - - +
116A GLN* 2.8 47.7 + - + +
117A LYS* 3.3 20.3 + - - +
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Residues in contact with LEU 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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113A ASN* 1.3 71.2 - - - +
115A GLU* 1.3 60.9 + - - +
117A LYS* 3.1 7.6 + - + +
118A ILE* 2.8 44.9 + - + +
138A CYS* 4.2 11.9 - - + +
140A VAL* 4.0 22.0 - - + -
144A THR* 3.6 34.1 - - + +
145A LEU* 3.9 20.0 - - + -
148A VAL* 3.8 21.5 - - + -
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Residues in contact with GLU 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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113A ASN* 3.0 19.0 + - - +
114A LEU* 1.3 78.9 - - - +
116A GLN* 1.3 68.7 + - - +
118A ILE* 3.3 3.3 + - - +
119A LEU* 3.0 30.7 + - + +
148A VAL* 4.1 18.0 - - + +
151A ARG* 3.0 28.1 + - - +
152A LEU* 3.7 29.6 - - + +
155A GLU* 5.6 0.2 - - - -
157A ARG* 3.0 23.9 + - - +
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Residues in contact with GLN 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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113A ASN* 2.8 31.8 + - + +
114A LEU 3.3 0.2 - - - -
115A GLU* 1.3 83.1 + - - +
117A LYS* 1.3 58.5 + - - +
119A LEU* 3.3 24.2 + - - +
120A GLN* 2.9 29.9 + - - +
157A ARG* 5.0 2.2 - - - +
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Residues in contact with LYS 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 ASN 3.3 11.1 + - - +
114A LEU* 3.1 12.7 + - + +
116A GLN* 1.3 79.8 - - - +
118A ILE* 1.3 61.4 + - - +
120A GLN* 2.6 35.1 + - - +
121A VAL* 3.0 42.9 + - - +
137A LYS* 3.1 27.5 + - - +
138A CYS* 4.1 20.0 - - + +
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Residues in contact with ILE 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 LEU* 2.8 23.1 + - + +
115A GLU* 3.6 4.5 - - - +
117A LYS* 1.3 77.2 - - - +
119A LEU* 1.3 62.7 + - - +
121A VAL* 3.3 4.2 + - - +
122A LEU* 3.0 35.8 + - + +
134A LEU* 4.7 6.9 - - + +
138A CYS* 4.1 12.8 - - - -
145A LEU* 3.8 34.1 - - + +
148A VAL* 3.7 35.9 - - + -
149A LEU* 3.9 26.0 - - + -
152A LEU* 4.2 10.8 - - + -
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Residues in contact with LEU 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 GLU* 3.0 22.1 + - + +
116A GLN* 3.7 26.5 - - - +
117A LYS 3.3 0.2 - - - -
118A ILE* 1.3 81.9 - - - +
120A GLN* 1.3 56.4 + - - +
122A LEU* 3.5 3.6 + - - +
123A SER* 2.8 36.0 + - - +
152A LEU* 4.1 11.7 - - + -
157A ARG* 3.8 39.9 - - - +
158A VAL* 4.0 27.1 - - + -
168A ILE* 4.0 15.8 - - + +
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Residues in contact with GLN 120 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A GLN 2.9 17.5 + - - +
117A LYS* 2.6 39.7 - - + +
119A LEU* 1.3 74.3 - - - +
121A VAL* 1.3 73.9 + - - +
123A SER* 3.3 4.2 + - - -
124A ASP* 2.9 58.3 + - - +
137A LYS* 5.8 4.9 - - - +
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Residues in contact with VAL 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 LYS* 3.0 38.2 + - - +
118A ILE 3.6 4.3 - - - +
120A GLN* 1.3 86.1 - - - +
122A LEU* 1.3 55.6 + - - +
124A ASP* 3.8 2.1 - - - +
125A ASP* 3.0 30.2 + - + +
129A VAL* 4.9 8.7 - - + -
134A LEU* 3.6 24.7 - - + -
137A LYS* 3.9 38.1 - - + -
138A CYS* 4.1 8.1 - - - -
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Residues in contact with LEU 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 ILE* 3.0 33.5 + - + +
119A LEU* 3.8 5.2 - - - +
121A VAL* 1.3 75.2 - - - +
123A SER* 1.3 57.8 + - - +
125A ASP* 3.7 4.5 - - - +
126A GLY* 2.9 27.7 + - - -
127A GLY 4.5 2.4 + - - +
129A VAL* 3.8 18.8 - - + -
134A LEU* 4.0 12.6 - - + -
149A LEU* 4.5 1.8 - - + -
158A VAL* 3.7 31.6 - - + -
166A TRP* 3.5 38.4 - - + +
167A SER* 4.2 8.1 - - - +
168A ILE* 3.9 19.6 + - + +
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Residues in contact with SER 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 LEU* 2.8 24.5 + - - +
120A GLN* 3.7 5.4 - - - -
122A LEU* 1.3 73.7 - - - +
124A ASP* 1.3 68.2 + - - +
126A GLY* 3.3 12.7 + - - -
168A ILE* 3.3 23.1 - - - +
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Residues in contact with ASP 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 GLN* 2.9 47.0 + - - +
121A VAL* 3.8 3.8 - - - +
123A SER* 1.3 79.2 - - - +
125A ASP* 1.3 64.8 + - - +
126A GLY* 4.4 0.2 - - - -
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Residues in contact with ASP 125 (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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121A VAL* 3.0 17.9 + - + +
122A LEU 3.7 1.3 - - - +
124A ASP* 1.3 80.1 - - - +
126A GLY* 1.3 57.9 + - - +
127A GLY* 2.9 31.9 + - - +
128A PRO 4.4 3.5 - - - +
129A VAL* 3.4 30.3 - - + +
133A GLN* 5.3 2.8 - - - +
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Residues in contact with GLY 126 (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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122A LEU 2.9 16.3 + - - -
123A SER* 3.3 10.8 + - - -
125A ASP* 1.3 75.2 - - - +
127A GLY* 1.3 56.0 + - - +
167A SER* 5.5 2.7 - - - -
168A ILE* 6.1 3.1 - - - -
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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