Contacts of the helix formed by residues 101 - 113 (chain J) in PDB entry 4UJ3
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 101 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19J ASP* 2.7 41.7 + - - +
97J LEU* 3.1 34.1 + - - +
98J THR 3.8 1.8 + - - +
99J TYR 3.2 0.6 - - - -
100J GLU* 1.3 73.6 - - - +
102J VAL* 1.3 59.7 + - - +
103J GLU 3.1 3.1 - - - -
104J ARG* 2.8 33.0 + - + +
105J TRP* 3.1 16.1 + - + +
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Residues in contact with VAL 102 (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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89J LEU* 3.9 28.5 - - + -
91J TYR* 4.0 20.6 - - + -
98J THR 3.7 13.1 + - - +
99J TYR* 2.9 33.4 + - + +
101J ASN* 1.3 76.1 - - - +
103J GLU* 1.3 62.8 + - - +
105J TRP* 3.1 11.3 + - - +
106J LEU* 3.0 24.8 + - + +
121J LEU* 4.0 9.4 - - + -
142J PHE* 3.9 28.3 - - + -
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Residues in contact with GLU 103 (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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100J GLU 3.8 9.6 + - - +
101J ASN 3.1 0.6 - - - -
102J VAL* 1.3 79.5 - - - +
104J ARG* 1.3 63.2 + - - +
106J LEU* 3.3 11.8 + - - +
107J LYS* 3.1 22.0 + - - +
142J PHE* 5.3 10.0 - - + -
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Residues in contact with ARG 104 (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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100J GLU 4.7 0.4 + - - -
101J ASN* 2.8 26.8 + - + +
103J GLU* 1.3 80.0 - - - +
105J TRP* 1.3 59.8 + - + +
107J LYS* 3.3 9.4 - - - +
108J GLU* 3.3 18.9 + - - +
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Residues in contact with TRP 105 (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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17J ILE* 4.1 24.1 - - + +
18J GLY* 3.1 31.0 - - - -
19J ASP* 2.9 32.3 + - - +
69J GLY* 3.1 29.2 - - - -
71J GLU* 3.8 24.5 - - + -
81J TYR* 4.3 0.2 - - - -
89J LEU* 4.1 19.7 - - + -
90J VAL 5.3 0.4 - - - -
98J THR 5.4 1.6 - - - -
101J ASN* 3.1 27.2 + - + +
102J VAL* 3.5 10.3 - - - +
104J ARG* 1.3 75.0 - - + +
106J LEU* 1.3 58.8 + - - +
107J LYS 3.1 1.8 - - - -
108J GLU* 3.1 38.2 + - + +
109J LEU* 2.8 30.5 + - - +
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Residues in contact with LEU 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89J LEU* 3.7 18.8 - - + -
102J VAL* 3.0 13.4 + - + +
103J GLU* 3.3 11.4 + - - +
105J TRP* 1.3 76.8 - - - +
107J LYS* 1.3 56.0 + - - +
109J LEU* 3.5 4.6 - - + +
110J ARG* 2.8 30.5 + - - +
119J ILE* 3.6 31.4 - - + -
142J PHE* 4.0 22.7 - - + -
146J ASN* 4.0 15.7 - - + +
148J LEU* 3.8 30.1 - - + -
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Residues in contact with LYS 107 (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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103J GLU 3.1 11.7 + - - +
104J ARG* 3.3 13.9 - - - +
106J LEU* 1.3 74.7 - - - +
108J GLU* 1.3 65.2 - - - +
110J ARG* 3.0 6.9 + - - -
111J ASP* 2.9 34.2 + - - +
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Residues in contact with GLU 108 (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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71J GLU* 3.9 22.8 - - - +
72J ARG* 4.1 15.3 - - - +
77J THR* 5.0 5.8 - - - -
81J TYR* 2.6 37.2 + - + +
104J ARG 3.3 8.5 + - - +
105J TRP* 3.1 33.3 + - + +
107J LYS* 1.3 78.3 - - - +
109J LEU* 1.3 57.7 + - - +
111J ASP* 4.4 5.2 - - - -
112J HIS* 2.9 45.6 + - + +
113J ALA 4.0 0.3 + - - -
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Residues in contact with LEU 109 (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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17J ILE* 3.7 21.8 - - + -
81J TYR* 3.3 34.3 + - + -
87J ALA* 4.1 17.3 - - + -
89J LEU* 4.8 2.2 - - + -
105J TRP 2.8 14.2 + - - +
106J LEU* 3.5 13.7 - - + +
108J GLU* 1.3 77.7 - - - +
110J ARG* 1.3 58.1 + - - +
113J ALA* 3.1 40.7 + - + +
114J ASP 4.7 1.4 - - - +
117J ILE* 4.4 9.7 - - + +
119J ILE* 3.1 45.5 - - + -
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Residues in contact with ARG 110 (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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103A GLU* 4.4 22.3 - - + +
145A LYS* 5.0 2.6 + - - +
146A ASN* 5.7 2.8 + - - +
106J LEU 2.8 17.3 + - - +
107J LYS* 3.0 7.4 + - - +
109J LEU* 1.3 75.9 - - - +
111J ASP* 1.3 65.3 + - - +
113J ALA 4.6 4.6 - - - +
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Residues in contact with ASP 111 (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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103A GLU* 5.5 1.2 - - - +
145A LYS* 2.4 37.1 + - - +
107J LYS* 2.9 22.9 + - - +
108J GLU* 3.8 2.8 - - - +
110J ARG* 1.3 87.7 - - - +
112J HIS* 1.3 83.7 + - + +
113J ALA 3.4 1.5 - - - +
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Residues in contact with HIS 112 (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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145A LYS* 4.7 2.2 - - - +
77J THR* 3.3 24.0 + - - +
78J SER* 4.7 17.2 + - - +
81J TYR* 3.6 27.8 - - + +
82J ARG 5.4 0.2 + - - -
108J GLU* 2.9 25.7 + - + +
111J ASP* 1.3 94.2 - - + +
113J ALA* 1.3 60.0 + - - +
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Residues in contact with ALA 113 (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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145A LYS* 5.2 2.5 + - - -
81J TYR* 3.6 33.7 - - + +
108J GLU 4.0 0.6 + - - -
109J LEU* 3.1 32.3 + - + +
110J ARG* 4.6 4.3 - - - +
111J ASP 4.5 4.9 - - - +
112J HIS* 1.3 82.1 - - - +
114J ASP* 1.3 71.3 + - - +
115J SER 3.6 0.9 + - - -
117J ILE* 4.5 9.0 - - + -
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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