Contacts of the helix formed by residues 122 - 133 (chain A) in PDB entry 4O6M
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 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A ILE* 3.5 22.8 - - - +
117A LYS 3.1 22.6 + - - +
118A LEU* 4.0 2.9 - - - +
119A SER* 3.1 31.5 + - - +
121A ASP* 1.3 76.9 - - + +
123A LEU* 1.3 59.1 + - - +
124A LYS 3.3 2.5 - - - +
125A THR* 3.2 20.6 + - + +
126A ALA* 2.8 25.2 + - - +
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Residues in contact with LEU 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 ILE* 4.0 26.5 - - + -
14A GLU* 4.3 19.7 - - + +
15A LYS 6.1 0.4 - - - +
16A LEU* 4.0 11.9 - - + +
21A LEU* 4.3 10.8 - - + -
118A LEU* 4.1 24.7 - - + -
119A SER 3.5 20.6 - - - +
120A ASN* 4.3 11.2 - - - +
121A ASP 3.5 3.0 + - - -
122A ASN* 1.3 75.2 - - - +
124A LYS* 1.3 60.5 + - - +
126A ALA* 3.4 5.7 - - + +
127A GLU* 2.9 28.1 + - - +
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Residues in contact with LYS 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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121A ASP 4.8 3.7 + - - +
122A ASN 3.3 0.4 - - - -
123A LEU* 1.3 77.7 - - - +
125A THR* 1.3 63.2 + - - +
127A GLU* 3.4 9.4 + - - +
128A LYS* 3.2 21.5 + - - +
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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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116A ILE* 4.4 6.3 - - + -
122A ASN* 3.2 24.5 + - + +
123A LEU 3.2 0.4 - - - -
124A LYS* 1.3 76.9 - - - +
126A ALA* 1.3 59.9 + - - +
128A LYS* 3.3 7.5 + - + +
129A LEU* 3.0 46.4 + - + +
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Residues in contact with ALA 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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16A LEU* 4.0 16.6 - - + -
58A LEU* 4.0 14.5 - - + +
116A ILE* 4.6 10.5 - - + +
118A LEU* 4.2 17.7 - - + -
122A ASN 2.8 14.6 + - - +
123A LEU* 3.2 14.8 + - + +
125A THR* 1.3 77.2 - - - +
127A GLU* 1.3 56.9 + - - +
129A LEU* 3.4 4.7 + - - +
130A LEU* 2.9 31.4 + - - +
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Residues in contact with GLU 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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16A LEU* 3.7 20.1 - - + +
17A LEU* 3.8 32.6 + - + +
123A LEU 2.9 12.9 + - - +
124A LYS* 3.5 12.1 - - - +
125A THR 3.3 0.2 - - - -
126A ALA* 1.3 77.1 - - - +
128A LYS* 1.3 57.8 + - - +
130A LEU* 3.3 3.8 + - - +
131A LEU* 2.9 39.2 + - + +
165A ARG* 2.8 37.3 + - - -
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Residues in contact with LYS 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 LYS 3.2 10.6 + - - +
125A THR* 3.6 11.4 - - + +
126A ALA 3.3 0.2 - - - -
127A GLU* 1.3 80.4 - - - +
129A LEU* 1.3 58.3 + - + +
131A LEU* 3.4 10.6 + - - +
132A SER* 2.9 28.9 + - - -
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Residues in contact with LEU 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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60A LEU* 4.0 17.3 - - + -
114A TRP* 4.2 18.3 - - + +
116A ILE* 3.5 39.3 - - + -
125A THR* 3.0 26.8 + - + +
126A ALA* 3.9 3.6 - - - +
128A LYS* 1.3 78.0 - - + +
130A LEU* 1.3 57.5 + - - +
132A SER* 2.6 27.3 + - - +
133A SER* 3.0 16.3 + - - -
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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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16A LEU* 3.9 17.7 - - + -
17A LEU* 4.0 6.5 - - + -
24A ARG* 3.6 40.8 - - - +
58A LEU* 4.2 8.1 - - + -
59A ILE 5.4 1.8 - - - +
60A LEU* 3.8 21.5 - - + +
126A ALA 2.9 19.6 + - - +
127A GLU 3.7 4.5 - - - +
129A LEU* 1.3 76.6 - - - +
131A LEU* 1.3 62.0 + - - +
133A SER* 2.5 32.0 + - - +
134A LEU* 3.5 11.4 - - + +
223A LEU* 3.8 20.0 - - + -
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Residues in contact with LEU 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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17A LEU* 3.8 17.7 - - + -
127A GLU* 2.9 31.3 + - + +
128A LYS* 3.7 8.3 - - - +
130A LEU* 1.3 75.9 - - - +
132A SER* 1.3 62.6 + - - +
134A LEU* 3.2 37.9 + - + +
161A LEU* 3.6 44.7 - - + +
162A ARG* 6.2 0.2 - - - -
164A SER* 5.1 1.1 - - - -
165A ARG* 4.1 33.7 - - + +
223A LEU* 4.3 7.9 - - + -
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Residues in contact with SER 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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114A TRP* 3.8 14.7 - - - -
128A LYS 2.9 15.4 + - - -
129A LEU* 2.6 28.4 + - - +
131A LEU* 1.3 76.4 - - - +
133A SER* 1.3 59.1 + - - +
134A LEU 3.2 1.9 + - - -
135A ILE 3.7 12.8 - - - +
161A LEU* 5.0 6.7 - - - -
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Residues in contact with SER 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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60A LEU* 4.1 19.5 + - - -
62A ARG* 4.6 15.9 + - - +
114A TRP* 3.6 28.1 - - - -
129A LEU 3.0 12.5 + - - -
130A LEU* 2.5 35.7 + - - +
132A SER* 1.3 73.8 - - - +
134A LEU* 1.3 61.2 + - - +
135A ILE* 2.8 10.5 + - - -
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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