Contacts of the helix formed by residues 113 - 126 (chain J) in PDB entry 3J7Y
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 113 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112J VAL* 1.3 75.6 - - - +
114J LEU* 1.3 63.0 + - - +
115J LYS* 3.5 14.9 + - - +
116J HIS* 3.1 25.1 + - - +
117J VAL* 3.2 23.9 + - - +
155J VAL* 4.0 0.9 - - - -
156J VAL* 3.1 35.9 - - + -
157J LYS* 3.8 16.2 - - - +
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Residues in contact with LEU 114 (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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113J THR* 1.3 71.8 - - - +
115J LYS* 1.3 61.0 + - + +
117J VAL* 3.2 9.2 + - + +
118J TYR* 2.9 57.6 + - + +
141J VAL* 5.3 6.5 - - + -
145J ILE* 4.2 25.8 - - + -
155J VAL* 4.9 0.7 - - + -
156J VAL 2.8 7.4 + - - +
157J LYS* 3.6 42.2 - - + +
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Residues in contact with LYS 115 (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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113J THR* 3.3 13.3 + - - +
114J LEU* 1.3 78.4 - - + +
116J HIS* 1.3 56.9 + - - +
118J TYR* 3.2 14.8 + - + +
119J GLU* 2.9 38.7 + - + +
157J LYS* 5.8 6.3 - - + +
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Residues in contact with HIS 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94J ALA* 3.3 44.2 + - + +
112J VAL* 3.4 32.5 - - + -
113J THR* 3.1 17.4 + - - +
114J LEU 3.2 0.2 - - - -
115J LYS* 1.3 77.3 - - - +
117J VAL* 1.3 57.4 + - - +
119J GLU* 3.2 20.9 + - - +
120J ILE* 2.9 38.2 + - + +
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Residues in contact with VAL 117 (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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91J LEU* 5.3 7.2 - - + -
112J VAL* 4.1 11.0 - - + -
113J THR 3.2 15.2 + - - +
114J LEU* 3.2 10.2 + - + +
116J HIS* 1.3 77.5 - - - +
118J TYR* 1.3 55.9 - - - +
120J ILE* 3.2 8.1 - - - +
121J ALA 2.9 24.4 + - - -
141J VAL* 3.6 15.9 - - + -
144J ILE* 3.1 41.6 - - + +
145J ILE* 4.2 16.2 - - + +
148J ALA* 5.6 4.3 - - + -
155J VAL* 3.8 22.7 - - + -
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Residues in contact with TYR 118 (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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114J LEU* 2.9 50.2 + - + +
115J LYS* 3.4 13.5 - - + +
117J VAL* 1.3 76.1 - - - +
119J GLU* 1.3 56.9 + - + +
121J ALA* 3.2 7.1 + - - +
122J ARG* 2.9 36.2 + - + +
137J LEU* 3.7 32.8 - - + -
138J SER* 5.6 4.7 + - - -
141J VAL* 3.7 28.6 - - + +
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Residues in contact with GLU 119 (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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115J LYS* 2.9 18.1 + - + +
116J HIS* 3.4 33.5 + - - +
118J TYR* 1.3 77.3 - - + +
120J ILE* 1.3 58.0 - - + +
122J ARG* 3.2 9.9 + - + +
123J ILE* 2.9 36.0 + - + +
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Residues in contact with ILE 120 (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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87J VAL* 3.6 19.5 - - + -
90J PHE* 3.4 30.3 - - + -
91J LEU* 4.2 20.4 - - + -
94J ALA* 5.0 4.5 - - + -
116J HIS* 2.9 30.3 + - + +
117J VAL* 3.2 19.1 - - - +
119J GLU* 1.3 76.3 - - + +
121J ALA* 1.3 57.2 + - - +
123J ILE* 3.1 12.1 - - - +
124J LYS* 2.9 36.8 + - + +
144J ILE* 3.5 36.1 - - + -
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Residues in contact with ALA 121 (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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117J VAL 2.9 6.8 + - - +
118J TYR* 3.3 10.5 - - - +
120J ILE* 1.3 78.3 - - - +
122J ARG* 1.3 53.3 + - - +
124J LYS* 3.2 6.4 + - - +
125J ALA* 2.8 35.5 + - - +
137J LEU* 3.6 24.0 - - + -
140J VAL* 3.9 18.0 - - + +
141J VAL* 5.0 1.1 - - + -
144J ILE* 3.4 26.0 - - + -
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Residues in contact with ARG 122 (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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118J TYR* 2.9 26.6 + - + +
119J GLU* 3.4 10.3 - - + +
121J ALA* 1.3 76.3 - - - +
123J ILE* 1.3 65.3 + - + +
125J ALA* 3.3 27.2 + - - +
126J GLN* 4.2 7.1 + - - +
137J LEU* 3.7 47.2 - - - +
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Residues in contact with ILE 123 (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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84J GLN* 2.8 43.6 + - - +
85J PRO* 5.3 4.5 - - + -
90J PHE* 3.3 46.4 - - + -
119J GLU* 2.9 24.0 + - + +
120J ILE* 3.1 16.1 + - - +
122J ARG* 1.3 77.5 - - + +
124J LYS* 1.3 55.6 + - - +
125J ALA 3.6 0.5 + - - -
126J GLN* 4.0 21.8 + - - +
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Residues in contact with LYS 124 (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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2170A G 4.2 4.5 - - - +
84J GLN* 3.3 26.7 + - - +
85J PRO 3.8 4.2 + - - -
87J VAL* 3.5 40.6 - - + +
90J PHE* 4.1 12.3 - - - -
120J ILE* 2.9 28.3 + - + +
121J ALA* 3.2 6.7 + - - +
123J ILE* 1.3 74.1 - - - +
125J ALA* 1.3 61.7 + - - +
126J GLN 3.3 2.5 - - - -
127J ASP* 2.9 23.8 + - - +
130J PHE* 3.3 45.7 - - + -
132J LEU* 4.0 25.1 - - + +
140J VAL* 6.0 1.1 - - + -
144J ILE* 4.9 2.9 - - + -
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Residues in contact with ALA 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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121J ALA 2.8 18.7 + - - +
122J ARG* 3.3 23.6 + - - +
124J LYS* 1.3 74.2 - - - +
126J GLN* 1.3 61.5 + - - +
127J ASP 3.2 8.0 + - - +
132J LEU* 4.4 15.2 - - - +
140J VAL* 5.9 7.6 - - + -
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Residues in contact with GLN 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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84J GLN* 5.7 0.4 - - - +
122J ARG 4.2 6.0 + - - +
123J ILE* 4.0 19.4 + - - +
124J LYS 3.3 0.6 - - - -
125J ALA* 1.3 78.1 - - - +
127J ASP* 1.3 65.8 + - - +
128J GLU* 4.0 4.3 + - - +
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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