Contacts of the helix formed by residues 118 - 130 (chain A) in PDB entry 2R28
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 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A ARG* 4.2 1.1 - - - +
117A LEU* 1.3 76.6 - - - +
119A ASP* 1.3 69.1 + - - +
120A GLU* 3.3 13.2 + - + +
121A GLU* 2.7 47.1 + - + +
122A VAL* 2.9 23.3 + - - +
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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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103A ALA* 6.5 0.2 - - + -
107A ARG* 3.1 30.5 + - - +
118A THR* 1.3 75.7 + - - +
120A GLU* 1.3 63.3 + - - +
122A VAL* 3.1 11.5 - - + +
123A ASP* 3.0 32.6 + - - +
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Residues in contact with GLU 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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118A THR* 3.2 12.5 + - + +
119A ASP* 1.3 79.0 - - - +
121A GLU* 1.3 56.8 + - + +
123A ASP* 3.3 11.7 + - + +
124A GLU* 2.9 28.4 + - + +
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Residues in contact with GLU 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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116A LYS 4.2 2.4 - - - +
117A LEU* 3.3 26.8 - - + +
118A THR* 2.7 49.4 + - + +
120A GLU* 1.3 74.9 - - + +
122A VAL* 1.3 64.4 + - - +
124A GLU* 3.4 7.9 + - - +
125A MET* 3.0 23.9 + - - +
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Residues in contact with VAL 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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103A ALA* 4.1 27.1 - - + +
106A LEU* 4.1 8.9 - - + +
107A ARG* 3.7 40.2 - - + +
117A LEU* 3.6 28.5 - - + -
118A THR 2.9 13.0 + - - +
119A ASP* 3.1 27.1 - - + +
121A GLU* 1.3 73.2 - - - +
123A ASP* 1.3 62.7 + - - +
125A MET* 3.1 8.8 + - - +
126A ILE* 3.0 27.7 + - - +
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Residues in contact with ASP 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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103A ALA* 3.3 21.8 - - - +
119A ASP* 3.0 30.7 + - - +
120A GLU* 3.6 11.8 - - + +
122A VAL* 1.3 75.0 - - - +
124A GLU* 1.3 53.2 + - - +
126A ILE* 3.4 8.5 + - - +
127A ARG* 2.7 34.4 + - - +
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Residues in contact with GLU 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 GLU* 2.9 18.0 + - + +
121A GLU* 3.6 8.5 - - - +
122A VAL 3.2 0.2 - - - -
123A ASP* 1.3 73.5 - - - +
125A MET* 1.3 64.9 + - - +
127A ARG* 3.0 44.2 + - - -
128A GLU* 2.8 47.5 + - - +
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Residues in contact with MET 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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106A LEU* 3.9 23.8 - - + -
110A MET* 4.0 21.1 - - - +
117A LEU* 3.8 26.0 - - + -
121A GLU 3.0 15.6 + - - +
122A VAL 3.1 8.7 + - - +
124A GLU* 1.3 77.3 - - + +
126A ILE* 1.3 62.9 + - - +
128A GLU* 3.5 15.6 + - - +
129A ALA* 3.5 17.7 + - - +
145A MET* 5.7 7.0 - - + -
396C ILE* 4.1 28.3 - - + -
400C ILE* 5.1 8.1 - - + -
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Residues in contact with ILE 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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101A ILE* 4.1 15.0 - - + +
102A SER 4.3 1.6 - - - +
103A ALA* 4.2 24.5 - - + +
106A LEU* 3.4 26.2 - - + -
122A VAL 3.0 18.6 + - - +
123A ASP* 3.6 7.9 - - - +
125A MET* 1.3 70.8 - - - +
127A ARG* 1.3 69.8 + - - +
129A ALA* 2.9 13.9 + - - +
130A ASP* 3.0 18.1 + - + +
135A GLY* 3.2 35.2 - - - +
136A GLN* 3.7 11.7 - - - -
137A VAL* 3.8 21.0 - - + +
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Residues in contact with ARG 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 ASP 2.7 21.5 + - - +
124A GLU* 3.0 44.2 + - - +
126A ILE* 1.3 76.9 - - - +
128A GLU* 1.3 76.8 + - - +
130A ASP* 3.1 22.0 + - + +
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Residues in contact with GLU 128 (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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124A GLU* 2.8 47.5 + - - +
125A MET* 3.7 15.4 - - - +
126A ILE 3.2 0.2 - - - -
127A ARG* 1.3 88.7 - - - +
129A ALA* 1.3 55.9 + - - +
130A ASP 3.5 0.2 - - - -
131A ILE* 4.9 5.5 - - - +
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Residues in contact with ALA 129 (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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125A MET 3.5 8.4 + - - +
126A ILE 2.9 5.8 + - - +
128A GLU* 1.3 73.6 - - - +
130A ASP* 1.3 58.5 + - - +
131A ILE* 3.0 19.3 + - - +
137A VAL* 3.8 27.8 - - + -
141A GLU* 3.2 21.2 - - - +
144A GLN* 5.7 1.5 + - - +
145A MET* 4.4 32.8 - - + -
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Residues in contact with ASP 130 (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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126A ILE* 3.0 24.1 + - + +
127A ARG* 3.1 16.2 + - + +
128A GLU 3.5 0.4 - - - -
129A ALA* 1.3 73.3 - - - +
131A ILE* 1.3 66.0 + - - +
132A ASP* 3.1 1.0 - - - +
133A GLY* 3.0 26.6 + - - +
134A ASP 3.3 0.7 + - - -
135A GLY* 2.8 30.2 + - - -
136A GLN 3.8 4.3 - - - +
137A VAL* 5.1 0.4 - - - -
141A GLU* 3.9 4.7 - - - -
1004A CA 2.3 30.5 - - - -
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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