Contacts of the helix formed by residues 112 - 121 (chain A) in PDB entry 1JEQ
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 GLY 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A TYR* 5.0 0.4 - - - -
75A ILE* 4.2 7.1 - - - +
110A ASN 3.6 2.6 + - - -
111A PRO* 1.3 75.6 - - - +
113A ALA* 1.3 67.9 + - - -
114A LYS* 3.3 2.9 - - - -
115A ARG* 3.1 21.8 + - - +
116A ILE* 3.1 15.1 + - - +
316B TYR 4.3 4.3 - - - -
318B SER* 4.1 12.1 - - - -
319B ASP* 4.0 6.1 - - - -
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Residues in contact with ALA 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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112A GLY* 1.3 71.7 - - - +
114A LYS* 1.3 58.7 + - + +
116A ILE* 3.2 5.4 + - - +
117A LEU* 2.9 27.0 + - - +
491A GLU* 4.6 1.7 - - + +
494A ALA* 3.9 14.1 - - + +
495A LEU* 3.4 33.9 - - + +
316B TYR* 3.9 21.1 - - + -
319B ASP* 2.8 25.8 + - - +
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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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112A GLY 3.3 0.6 - - - -
113A ALA* 1.3 74.2 - - + +
115A ARG* 1.3 67.0 + - + +
117A LEU* 3.6 9.3 - - + +
118A GLU* 2.9 24.4 + - - +
494A ALA 5.2 8.5 - - - +
495A LEU* 4.0 17.9 - - + -
319B ASP* 4.3 8.5 + - - +
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Residues in contact with ARG 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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71A TYR* 4.0 16.5 + - + -
83A LEU 3.0 18.0 + - - -
106A GLN* 3.1 48.4 + - - +
107A GLU* 2.8 41.6 + - - +
109A ASP* 3.3 33.1 + - - +
110A ASN 3.9 14.1 - - - -
112A GLY* 3.1 15.6 + - - +
114A LYS* 1.3 77.9 - - + +
116A ILE* 1.3 63.9 + - - +
118A GLU* 3.2 4.3 + - - +
119A LEU* 3.0 22.9 + - - +
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Residues in contact with ILE 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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68A GLN* 3.5 20.3 - - + +
71A TYR* 3.9 25.8 - - + -
72A ILE* 3.5 40.4 - - + -
75A ILE* 3.6 28.9 - - + -
112A GLY 3.1 9.5 + - - +
113A ALA* 3.6 6.7 - - - +
115A ARG* 1.3 76.1 - - - +
117A LEU* 1.3 64.7 + - - +
119A LEU* 3.2 7.5 + - - +
120A ASP* 2.8 25.2 + - + +
491A GLU* 4.4 12.3 - - - +
316B TYR* 4.1 11.4 - - + +
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Residues in contact with LEU 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 ALA 2.9 14.2 + - - +
114A LYS* 3.6 13.5 - - + +
116A ILE* 1.3 76.3 - - - +
118A GLU* 1.3 65.9 + - - +
120A ASP* 3.1 21.0 + - - +
121A GLN* 3.2 31.8 + - + +
491A GLU* 5.4 1.1 + - - -
495A LEU* 4.4 28.9 - - + +
497A LEU* 6.4 2.5 - - + -
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Residues in contact with GLU 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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105A LEU* 3.6 37.2 - - + +
106A GLN* 2.9 31.9 + - - +
114A LYS 2.9 14.0 + - - +
115A ARG* 3.3 8.1 - - - +
117A LEU* 1.3 77.1 - - - +
119A LEU* 1.3 64.4 + - - +
121A GLN* 2.9 27.0 + - - +
122A PHE* 4.2 9.6 + - + -
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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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64A ILE* 3.5 30.4 - - + +
67A ILE* 3.4 32.3 - - + -
68A GLN* 4.1 15.7 - - + +
71A TYR* 4.0 28.9 - - + -
85A VAL* 3.9 29.8 - - + -
87A PHE* 4.6 0.9 - - + -
105A LEU* 3.9 12.1 - - + -
106A GLN* 4.5 2.9 - - - +
115A ARG 3.0 13.7 + - - +
116A ILE* 3.7 7.9 - - - +
118A GLU* 1.3 75.7 - - - +
120A ASP* 1.3 64.4 + - - +
122A PHE* 3.0 25.8 + - + +
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Residues in contact with ASP 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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68A GLN* 3.1 34.5 + - - +
116A ILE* 2.8 11.3 + - + +
117A LEU* 3.2 20.8 - - - +
118A GLU 3.1 0.2 - - - -
119A LEU* 1.3 77.1 - - - +
121A GLN* 1.3 64.3 + - - +
122A PHE 3.0 5.8 + - - -
123A LYS* 3.1 30.2 + - - +
130A ARG* 5.5 1.0 + - - -
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Residues in contact with GLN 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 LEU* 3.2 35.7 + - + +
118A GLU* 2.9 17.6 + - + +
120A ASP* 1.3 84.3 + - - +
122A PHE* 1.3 71.4 - - + +
123A LYS 3.5 0.4 - - - -
127A GLY* 3.1 18.4 - - - +
130A ARG* 2.5 46.5 + - - +
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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