Contacts of the helix formed by residues 115 - 127 (chain A) in PDB entry 1R28
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 GLU 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A GLN 3.6 4.2 + - - -
114A MET* 1.3 70.8 - - - +
116A HIS* 1.3 71.0 - - + +
118A VAL* 3.0 17.5 + - - +
119A ASP* 2.9 45.8 + - - +
122A ARG* 3.5 11.4 + - - -
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Residues in contact with HIS 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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89A PHE* 6.5 0.2 - - + -
114A MET 3.4 0.4 - - - -
115A GLU* 1.3 80.2 - - + +
117A VAL* 1.3 63.2 + - + +
119A ASP* 3.4 12.7 + - - +
120A THR* 2.9 25.7 + - - -
11B PHE* 4.6 16.6 - + + -
13B ARG* 4.9 20.9 + - + -
17B ASP* 5.1 8.9 + - - -
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Residues in contact with VAL 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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86A LEU* 3.8 25.4 - - + -
89A PHE* 3.4 39.3 - - + -
95A LEU* 3.9 17.9 - - + -
109A ALA* 3.9 10.3 - - + -
114A MET* 3.2 25.0 + - + +
116A HIS* 1.3 77.4 - - + +
118A VAL* 1.3 68.0 + - - +
120A THR* 3.0 7.9 + - - -
121A CYS* 2.9 27.0 + - - -
11B PHE* 4.6 6.1 - - + -
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Residues in contact with VAL 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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106A MET* 4.4 8.2 - - + +
109A ALA* 3.7 8.1 - - + -
110A MET* 3.7 45.3 - - + +
114A MET 3.0 25.0 + - - +
115A GLU* 3.3 17.7 - - - +
117A VAL* 1.3 77.3 - - - +
119A ASP* 1.3 62.6 + - - +
121A CYS* 3.3 6.7 + - - +
122A ARG* 3.1 56.1 + - - +
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Residues in contact with ASP 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* 2.9 43.9 + - - +
116A HIS* 3.6 11.8 + - - +
117A VAL 3.1 0.2 - - - -
118A VAL* 1.3 76.4 - - - +
120A THR* 1.3 58.2 + - - +
122A ARG* 3.1 21.7 + - - +
123A LYS* 2.9 40.7 + - + +
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Residues in contact with THR 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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95A LEU* 4.3 13.7 - - + -
97A LEU* 4.5 6.3 - - + -
116A HIS 2.9 13.4 + - - -
117A VAL* 3.0 8.4 + - - -
119A ASP* 1.3 77.1 - - - +
121A CYS* 1.3 59.0 + - - +
123A LYS* 3.2 24.9 + - + +
124A PHE* 2.9 28.2 + - + +
9B ILE* 4.5 15.9 - - + -
11B PHE* 3.3 30.5 - - + -
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Residues in contact with CYS 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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95A LEU* 4.8 0.4 - - - -
97A LEU* 4.1 20.9 - - - -
102A ILE* 4.1 7.0 - - + -
105A VAL* 3.8 29.6 - - - -
106A MET* 3.9 31.6 - - + -
117A VAL* 2.9 26.2 + - - -
118A VAL* 3.5 8.1 - - - +
120A THR* 1.3 74.1 - - - +
122A ARG* 1.3 64.9 + - - +
124A PHE* 3.2 2.6 + - - +
125A ILE* 2.9 30.3 + - - +
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Residues in contact with ARG 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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106A MET* 4.2 15.3 - - + +
110A MET* 5.2 12.7 - - - +
115A GLU* 3.5 10.9 + - - -
118A VAL* 3.1 39.4 + - - +
119A ASP* 3.2 31.9 + - - +
121A CYS* 1.3 76.3 - - - +
123A LYS* 1.3 58.2 + - + +
125A ILE* 3.2 9.8 + - + +
126A LYS* 2.8 47.9 + - - +
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Residues in contact with LYS 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 ASP* 2.9 20.1 + - + +
120A THR* 3.5 35.6 + - + +
122A ARG* 1.3 75.9 - - + +
124A PHE* 1.3 62.4 + - - +
126A LYS* 3.4 8.0 + - - +
127A ALA* 3.0 26.7 + - - +
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Residues in contact with PHE 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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97A LEU* 3.6 39.7 - - + -
98A ARG* 3.8 33.2 - - - -
99A GLU* 3.9 27.6 - - - -
102A ILE* 3.3 23.1 - - + -
120A THR* 2.9 14.0 + - + +
121A CYS 3.4 7.6 - - - +
123A LYS* 1.3 75.9 - - - +
125A ILE* 1.3 62.0 + - - +
127A ALA* 3.9 2.6 - - - +
128A SER 3.3 27.8 + - - -
7B SER* 4.9 3.4 - - - -
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Residues in contact with ILE 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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99A GLU* 5.5 2.6 - - - +
102A ILE* 3.1 37.5 - - + -
103A MET* 4.1 15.0 - - - -
106A MET* 3.8 28.5 - - + -
121A CYS 2.9 18.3 + - - +
122A ARG* 3.6 8.1 - - + +
124A PHE* 1.3 78.7 - - - +
126A LYS* 1.3 65.2 + - + +
127A ALA 3.2 1.6 + - - -
128A SER 4.2 8.4 + - - +
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Residues in contact with LYS 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 ARG* 2.8 30.3 + - + +
123A LYS* 3.4 7.4 + - - +
125A ILE* 1.3 78.0 - - + +
127A ALA* 1.3 59.7 + - - +
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Residues in contact with ALA 127 (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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123A LYS 3.0 17.4 + - - +
124A PHE* 3.9 4.0 - - - +
125A ILE 3.2 2.2 - - - -
126A LYS* 1.3 79.6 - - - +
128A SER* 1.3 70.5 + - - +
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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