Contacts of the helix formed by residues 122 - 133 (chain A) in PDB entry 1V8O
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 ASP 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A VAL* 3.7 10.0 - - - +
108A THR 3.1 11.7 - - - +
109A GLN* 3.4 15.9 - - - +
111A ARG* 3.5 21.3 + - - +
114A LEU* 3.8 10.2 - - + +
121A ILE* 1.3 76.1 - - - +
123A VAL* 1.3 65.0 + - - +
124A GLU* 3.9 16.1 - - - +
125A THR* 2.7 34.2 + - - -
126A LEU 3.3 15.1 + - - -
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Residues in contact with VAL 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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11A ALA* 3.5 37.2 - - + +
14A ALA* 4.0 19.5 - - + +
15A LEU* 4.1 19.7 - - + -
18A HIS* 4.9 1.1 - - + -
107A VAL* 4.2 6.9 - - + +
109A GLN* 2.8 30.0 + - - +
122A ASP* 1.3 74.5 - - - +
124A GLU* 1.3 68.8 + - - +
126A LEU* 3.4 2.2 + - - +
127A LEU* 3.0 38.8 + - + +
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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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109A GLN* 4.7 2.4 - - - +
122A ASP* 3.4 16.2 + - - +
123A VAL* 1.3 80.4 - - - +
125A THR* 1.3 68.3 + - - +
127A LEU* 3.2 8.3 + - - +
128A VAL* 3.2 28.0 + - + +
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Residues in contact with THR 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 ILE* 3.8 28.0 - - + +
122A ASP* 2.7 25.5 + - - -
124A GLU* 1.3 78.9 + - - +
126A LEU* 1.3 68.0 + - - +
128A VAL* 2.8 26.1 + - + +
129A ARG* 3.0 28.4 + - + +
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Residues in contact with LEU 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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5A TYR* 3.5 48.9 - - + -
7A VAL* 4.8 0.9 - - + -
15A LEU* 4.2 28.9 - - + -
29A LEU* 4.6 10.1 - - + -
107A VAL* 3.8 26.2 - - + -
121A ILE* 3.7 9.1 - - + +
122A ASP 3.3 11.8 + - - +
123A VAL* 3.4 6.5 + - - +
125A THR* 1.3 79.1 - - - +
127A LEU* 1.3 57.3 + - - +
129A ARG* 3.4 3.6 + - - +
130A LEU* 2.9 50.4 + - + +
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Residues in contact with LEU 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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15A LEU* 4.1 20.9 - - + -
18A HIS* 3.4 35.7 - - + +
21A LYS* 4.5 23.3 - - + +
22A TRP* 4.3 13.9 - - + -
123A VAL* 3.0 27.2 + - + +
124A GLU* 3.5 11.4 - - - +
125A THR 3.0 0.8 - - - -
126A LEU* 1.3 78.6 - - - +
128A VAL* 1.3 59.5 + - + +
130A LEU* 3.3 12.9 + - + +
131A ALA* 3.0 28.1 + - - +
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Residues in contact with VAL 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* 3.3 22.0 - - + +
125A THR* 2.8 25.5 + - + +
127A LEU* 1.3 75.0 - - + +
129A ARG* 1.3 70.2 + - + +
131A ALA* 3.5 8.1 + - - +
132A ALA* 3.2 20.4 + - - +
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Residues in contact with ARG 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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5A TYR* 3.5 38.0 + - - +
105A VAL* 4.0 14.6 - - - +
119A GLY 5.4 1.0 + - - -
121A ILE* 3.7 33.9 - - - +
125A THR* 3.0 27.7 + - + +
126A LEU 3.6 7.4 - - - +
128A VAL* 1.3 81.9 - - + +
130A LEU* 1.3 66.2 + - - +
132A ALA* 2.9 9.6 + - - +
133A GLN* 2.9 28.4 + - + +
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Residues in contact with LEU 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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5A TYR* 4.4 6.7 - - + +
21A LYS 4.7 7.0 - - - +
22A TRP* 3.9 26.5 - - + -
25A HIS* 3.2 54.0 + - + -
28A LYS* 4.3 2.2 - - + +
29A LEU* 4.4 9.2 - - + -
126A LEU* 2.9 51.5 + - + +
127A LEU* 3.8 9.2 - - + +
129A ARG* 1.3 77.5 - - - +
131A ALA* 1.3 61.6 + - - +
133A GLN* 3.2 33.3 + - - +
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Residues in contact with ALA 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 LEU 3.0 16.6 + - - +
128A VAL* 3.6 9.4 - - - +
129A ARG 3.0 0.2 - - - -
130A LEU* 1.3 75.2 - - - +
132A ALA* 1.3 63.7 + - - +
133A GLN* 3.0 9.7 + - - +
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Residues in contact with ALA 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 VAL 3.2 10.3 + - - +
129A ARG* 2.9 12.2 + - - +
131A ALA* 1.3 78.7 - - - +
133A GLN* 1.3 63.7 + - + +
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Residues in contact with GLN 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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4A GLU* 3.9 10.2 + - - +
5A TYR* 3.6 17.8 + - - -
24A LYS* 4.0 10.7 + - - -
25A HIS* 3.1 24.2 - - + -
28A LYS* 3.1 29.1 + - - +
129A ARG* 2.9 19.0 + - + +
130A LEU* 3.4 39.0 - - - +
131A ALA 3.0 7.3 - - - +
132A ALA* 1.3 86.4 - - + +
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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