Contacts of the helix formed by residues 106 - 115 (chain A) in PDB entry 1AX8
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 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A LEU* 3.6 11.3 - - - +
105A GLU* 1.3 99.4 - - + +
107A LEU* 1.3 66.1 + - - +
108A ASP* 3.2 27.6 + - - +
109A SER* 3.1 21.8 + - - -
110A LEU* 4.2 0.3 - - - +
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Residues in contact with LEU 107 (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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63A GLN* 3.5 41.3 - - + +
64A ILE* 4.1 13.2 - - + +
67A SER* 3.4 36.6 - - - +
104A LEU* 4.7 5.6 - - + +
105A GLU 5.6 0.4 - - - +
106A THR* 1.3 77.1 - - - +
108A ASP* 1.3 64.7 + - - +
109A SER 3.2 2.7 - - - -
110A LEU* 3.1 32.8 + - + +
111A GLY* 3.8 3.3 + - - -
114A LEU* 6.3 0.7 - - + -
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Residues in contact with ASP 108 (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 THR* 3.2 21.3 - - - +
107A LEU* 1.3 80.3 - - - +
109A SER* 1.3 61.0 + - - +
110A LEU 3.3 0.2 - - - -
111A GLY* 3.5 12.1 + - - -
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Residues in contact with SER 109 (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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104A LEU* 4.3 8.6 - - - +
106A THR* 3.1 22.5 + - - -
108A ASP* 1.3 72.1 - - - +
110A LEU* 1.3 63.4 + - - +
111A GLY 3.1 8.7 + - - -
112A GLY* 4.1 6.4 + - - -
113A VAL* 5.0 1.9 - - - +
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Residues in contact with LEU 110 (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* 4.6 6.7 - - + -
60A VAL* 4.6 10.5 - - + -
64A ILE* 4.3 20.6 - - + -
104A LEU* 3.3 40.4 - - + -
107A LEU* 3.1 29.4 + - + +
109A SER* 1.3 77.7 - - - +
111A GLY* 1.3 65.9 + - - +
112A GLY 3.4 0.7 - - - -
113A VAL* 3.1 25.7 - - + +
114A LEU* 3.0 39.3 + - + +
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Residues in contact with GLY 111 (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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107A LEU 3.8 3.9 + - - -
108A ASP* 3.5 11.6 + - - -
109A SER 3.1 3.8 - - - -
110A LEU* 1.3 75.0 - - - +
112A GLY* 1.3 63.8 + - - +
114A LEU* 3.0 3.3 + - - -
115A GLU* 2.8 45.4 + - - +
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Residues in contact with GLY 112 (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 SER 4.1 5.4 + - - -
110A LEU 3.4 0.6 - - - -
111A GLY* 1.3 74.7 - - - +
113A VAL* 1.3 61.5 + - - +
114A LEU 3.4 0.2 + - - -
115A GLU* 3.6 17.4 + - - +
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Residues in contact with VAL 113 (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* 4.0 20.9 - - + -
109A SER 5.0 1.9 + - - +
110A LEU* 3.1 44.6 - - + +
112A GLY* 1.3 75.0 - - - +
114A LEU* 1.3 61.5 + - + +
115A GLU 3.5 1.7 - - - +
124A VAL* 3.7 3.5 - - - +
128A ARG* 2.8 45.1 + - - +
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Residues in contact with LEU 114 (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* 5.1 1.6 - - + -
64A ILE* 4.1 31.6 - - + -
68A MET* 5.5 2.2 - - + -
107A LEU* 6.3 1.6 - - + -
110A LEU* 3.0 36.8 + - + +
111A GLY* 3.0 3.4 + - - +
113A VAL* 1.3 89.0 - - + +
115A GLU* 1.3 64.6 + - - +
116A ALA 3.9 0.3 + - - -
121A THR* 3.5 38.0 - - + +
124A VAL* 3.6 12.7 - - - +
125A ALA* 4.1 33.2 - - + +
128A ARG* 4.4 12.1 - - - +
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Residues in contact with GLU 115 (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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111A GLY* 2.8 37.6 + - - +
112A GLY* 3.6 13.3 + - - +
113A VAL 3.5 3.0 - - - +
114A LEU* 1.3 81.7 - - - +
116A ALA* 1.3 66.3 + - - +
119A TYR 5.6 0.9 - - - +
121A THR* 3.0 31.3 - - - +
124A VAL* 5.2 0.9 - - - +
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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