Contacts of the helix formed by residues 115 - 134 (chain A) in PDB entry 2OQ1
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 115 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A SER* 3.5 23.5 - - - -
40A GLN* 4.0 10.6 + - - -
113A GLN 3.6 2.4 + - - -
114A PRO* 1.3 73.5 - - - +
116A VAL* 1.3 65.8 + - - -
117A PHE 3.3 2.9 - - - -
118A ASP* 3.4 13.4 + - - +
119A CYS* 3.1 23.0 + - - +
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Residues in contact with VAL 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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16A SER* 4.8 1.8 + - - -
114A PRO 3.8 3.6 + - - +
115A GLY* 1.3 71.0 - - - -
117A PHE* 1.3 59.4 + - - +
119A CYS* 3.1 9.3 + - + +
120A LEU* 2.9 38.7 + - + +
235A TRP* 3.9 23.1 - - + -
239A GLU* 5.7 2.9 - - + +
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Residues in contact with PHE 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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45A LEU* 3.9 9.6 - - + -
115A GLY* 3.3 1.2 - - - -
116A VAL* 1.3 78.2 - - - +
118A ASP* 1.3 58.6 + - - +
120A LEU* 3.2 5.4 + - + +
121A ARG* 2.8 74.8 + - + +
124A MSE 5.7 0.2 - - + -
156A ALA* 3.7 22.2 - - - -
159A ALA* 3.8 13.0 - - + -
233A THR* 3.7 8.3 - - - -
235A TRP* 3.5 49.1 - + + -
236A GLN* 3.6 40.2 - - + -
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Residues in contact with ASP 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASP* 4.8 5.0 - - - +
40A GLN* 3.0 34.1 + - - +
115A GLY* 3.4 13.9 + - - +
116A VAL 3.3 0.2 - - - -
117A PHE* 1.3 76.1 - - - +
119A CYS* 1.3 63.7 + - - +
121A ARG* 3.1 34.7 + - - +
122A ASP* 3.1 23.0 + - - +
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Residues in contact with CYS 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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114A PRO* 6.1 2.7 - - + -
115A GLY 3.1 13.8 + - - +
116A VAL* 3.1 10.1 + - - +
118A ASP* 1.3 77.7 - - - +
120A LEU* 1.3 67.0 + - + +
122A ASP* 3.5 18.1 - - - +
123A ALA* 3.8 5.9 + - - +
1119A PB 2.6 30.5 - - - -
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Residues in contact with LEU 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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116A VAL* 2.9 28.8 + - + +
117A PHE* 3.8 7.2 - - + +
119A CYS* 1.3 80.2 - - + +
121A ARG* 1.3 65.6 + - - +
122A ASP 3.1 2.3 + - - -
123A ALA* 3.3 8.6 + - + +
124A MSE 3.2 41.2 + - + +
163A MSE 4.4 17.0 - - + -
235A TRP* 3.6 34.8 - - + +
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Residues in contact with ARG 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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45A LEU* 3.8 14.7 - - - +
46A GLY 5.7 3.8 - - - +
117A PHE* 2.8 65.6 + - + +
118A ASP* 3.1 36.2 + - - +
120A LEU* 1.3 73.2 - - - +
122A ASP* 1.3 65.8 + - - +
124A MSE 3.7 10.1 - - - +
125A VAL* 2.9 34.1 + - + +
152A GLU* 4.3 28.0 + - - +
155A ILE* 4.5 9.6 - - + -
156A ALA* 3.7 31.4 - - - +
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Residues in contact with ASP 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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118A ASP 3.1 12.3 + - - +
119A CYS* 3.5 13.4 - - - +
120A LEU 3.1 0.2 - - - -
121A ARG* 1.3 76.7 - - - +
123A ALA* 1.3 65.0 + - - +
125A VAL* 3.2 5.3 + - - +
126A ARG* 3.0 47.8 + - - +
144A ILE* 5.7 2.4 - - - +
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Residues in contact with ALA 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 CYS 3.8 6.1 + - - +
120A LEU* 3.3 10.9 + - + +
122A ASP* 1.3 80.9 + - - +
124A MSE 1.3 58.6 + - + +
126A ARG* 3.4 12.6 + - - +
127A ASP* 3.0 28.9 + - - +
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Residues in contact with MSE 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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117A PHE* 5.7 0.4 - - + -
120A LEU* 3.2 38.9 + - + +
121A ARG* 3.7 6.3 - - - +
122A ASP 3.2 0.4 - - - -
123A ALA* 1.3 76.3 - - + +
125A VAL* 1.3 60.7 + - - +
127A ASP* 3.4 5.7 + - - +
128A TYR* 2.9 29.6 + - - +
155A ILE* 3.5 28.6 - - + +
158A THR* 6.3 0.2 - - - -
159A ALA* 3.6 42.4 - - + +
162A ARG* 4.1 36.8 - - + +
163A MSE 5.1 5.2 - - - -
235A TRP* 5.3 0.7 - - - +
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Residues in contact with VAL 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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121A ARG* 2.9 24.8 + - + +
122A ASP* 3.7 5.8 - - - +
124A MSE 1.3 72.1 - - - +
126A ARG* 1.3 68.2 + - + +
128A TYR* 3.3 6.3 + - - +
129A VAL* 2.9 36.8 + - + +
144A ILE* 4.8 8.3 - - + -
148A ALA* 4.0 28.9 - - + +
151A VAL* 4.1 13.0 - - + -
152A GLU* 4.1 18.8 - - - +
155A ILE* 4.2 20.9 - - + -
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Residues in contact with ARG 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 ASP* 3.0 38.7 + - - +
123A ALA* 3.6 9.9 - - - +
125A VAL* 1.3 78.8 - - + +
127A ASP* 1.3 56.7 + - - +
129A VAL* 3.3 1.7 + - - +
130A ARG* 2.8 50.5 + - - +
140A LEU* 4.1 19.0 - - + +
141A GLU* 2.9 38.0 + - - -
144A ILE* 3.3 38.4 - - + +
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Residues in contact with ASP 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 ALA 3.0 17.0 + - - +
124A MSE 3.8 5.6 - - - +
126A ARG* 1.3 78.4 - - - +
128A TYR* 1.3 61.3 + - - +
130A ARG* 3.7 18.4 + - - +
131A GLN* 2.9 57.8 + - - +
162A ARG* 4.4 20.5 + - - +
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Residues in contact with TYR 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 MSE 2.9 18.5 + - - +
125A VAL 3.6 4.3 - - - +
127A ASP* 1.3 79.2 + - - +
129A VAL* 1.3 64.2 + - + +
131A GLN* 3.9 3.8 - - - +
132A THR* 2.9 58.5 + - + +
133A TRP* 5.7 3.1 - - - -
151A VAL* 3.9 29.3 - - + +
154A LEU* 3.8 24.1 - - + +
155A ILE* 4.0 20.9 - - + -
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Residues in contact with VAL 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 VAL* 2.9 29.6 + - + +
126A ARG 3.8 3.4 - - - +
128A TYR* 1.3 83.8 - - + +
130A ARG* 1.3 58.9 + - - +
133A TRP* 2.9 46.5 + - + +
134A LYS 4.0 0.2 + - - -
135A LEU* 4.7 1.0 + - + -
140A LEU* 3.6 17.0 - - + -
143A ALA* 3.8 25.8 - - + -
144A ILE* 3.9 15.9 - - + -
147A GLN* 4.2 24.2 - - + -
151A VAL* 5.2 0.9 - - + -
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Residues in contact with ARG 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 ARG* 2.8 36.5 + - - +
127A ASP* 3.7 29.9 + - - +
129A VAL* 1.3 76.7 - - - +
131A GLN* 1.3 69.1 + - - +
134A LYS* 2.9 31.4 + - - +
135A LEU 3.6 9.6 - - - +
136A GLU* 3.4 35.8 + - - +
140A LEU* 3.8 27.8 - - + +
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Residues in contact with GLN 131 (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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127A ASP* 2.9 50.8 + - - +
128A TYR* 4.0 4.3 - - - +
130A ARG* 1.3 89.5 - - - +
132A THR* 1.3 59.8 + - - +
134A LYS* 2.9 37.2 + - - +
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Residues in contact with THR 132 (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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128A TYR* 2.9 45.7 + - + +
131A GLN* 1.3 81.1 - - - +
133A TRP* 1.3 84.0 + - + +
134A LYS* 3.7 8.0 - - - +
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Residues in contact with TRP 133 (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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128A TYR* 5.7 3.6 - - - -
129A VAL* 2.9 39.2 + - + +
132A THR* 1.3 93.2 - - + +
134A LYS* 1.3 69.9 + - - +
135A LEU* 3.2 31.6 + - + +
143A ALA* 5.4 2.7 - - + -
147A GLN* 4.1 37.1 + - + +
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Residues in contact with LYS 134 (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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130A ARG* 2.9 17.0 + - - +
131A GLN* 2.9 32.5 + - - +
132A THR 3.7 10.5 - - - +
133A TRP* 1.3 78.9 - - - +
135A LEU* 1.3 63.1 + - - +
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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
------------------------------------------------------------
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