Contacts of the helix formed by residues 105 - 117 (chain A) in PDB entry 1XO1
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 PHE 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A THR* 5.5 2.9 - - + -
32A PHE* 4.1 22.0 - + - -
104A PHE* 1.3 104.5 - + + +
106A GLU* 1.3 61.4 + - - +
108A LEU* 3.8 16.0 - - + +
109A LYS* 3.0 30.4 + - - +
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Residues in contact with GLU 106 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A PHE 3.2 3.4 - - - +
105A PHE* 1.3 76.7 - - - +
107A TYR* 1.3 66.3 + - + +
108A LEU 3.2 0.4 - - - -
109A LYS* 3.2 27.8 + - + +
110A ASP* 2.9 37.6 + - - +
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Residues in contact with TYR 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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42A PRO* 3.6 51.3 - - + +
43A PHE* 3.4 31.3 - + + +
44A ALA* 4.7 2.6 + - - +
104A PHE* 3.2 16.7 + - - +
106A GLU* 1.3 82.7 - - + +
108A LEU* 1.3 58.4 + - - +
110A ASP* 3.2 20.0 + - + +
111A ALA* 2.9 27.5 + - - +
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Residues in contact with LEU 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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27A GLY 4.3 1.8 - - - +
28A THR* 4.1 26.2 - - + +
31A GLY* 3.9 24.0 - - - -
43A PHE* 3.6 12.3 - - + -
47A TYR* 4.2 11.7 - - + -
104A PHE* 2.7 37.5 + - + +
105A PHE* 3.9 16.6 - - + +
106A GLU 3.2 0.2 - - - -
107A TYR* 1.3 73.9 - - - +
109A LYS* 1.3 61.5 + - + +
111A ALA* 3.2 2.9 + - + +
112A PHE* 3.0 58.3 + - + -
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Residues in contact with LYS 109 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A PHE 3.0 18.8 + - - +
106A GLU* 3.2 32.9 + - + +
108A LEU* 1.3 75.7 - - + +
110A ASP* 1.3 65.9 + - - +
112A PHE* 3.2 9.7 + - - +
113A GLU* 3.0 32.1 + - + +
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Residues in contact with ASP 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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42A PRO* 5.9 1.5 - - + +
44A ALA* 4.0 11.4 - - + +
106A GLU* 2.9 23.9 + - - +
107A TYR* 3.4 26.1 - - + +
109A LYS* 1.3 76.1 - - - +
111A ALA* 1.3 59.4 + - - +
113A GLU* 3.1 10.9 + - - +
114A LEU* 2.9 30.5 + - - +
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Residues in contact with ALA 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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43A PHE* 3.9 12.6 - - + -
44A ALA* 3.6 18.6 - - - +
47A TYR* 3.9 31.0 - - + -
48A VAL* 4.1 4.5 - - - +
107A TYR 2.9 13.2 + - - +
108A LEU* 3.3 12.6 - - + +
110A ASP* 1.3 77.4 - - - +
112A PHE* 1.3 57.0 + - - +
114A LEU* 3.5 2.4 + - - +
115A CYS* 2.9 28.9 + - - +
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Residues in contact with PHE 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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27A GLY 3.7 10.1 - - - -
28A THR* 3.7 6.5 - - - -
47A TYR* 3.6 20.4 - - - -
65A VAL* 4.0 10.8 - - + -
66A LEU 3.6 15.3 - - - -
67A GLY* 3.6 25.4 - - - -
68A ASP 5.5 0.2 - - - -
108A LEU* 3.0 52.0 + - + +
109A LYS* 3.2 10.1 + - - +
111A ALA* 1.3 74.7 - - - +
113A GLU* 1.3 67.7 + - - +
115A CYS* 3.4 4.6 - - + +
116A LYS* 3.1 29.9 + - + +
121A THR* 3.6 22.0 - - + +
123A THR* 4.6 8.5 - - + -
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Residues in contact with GLU 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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109A LYS* 3.0 25.0 + - + +
110A ASP* 3.1 12.8 + - - +
112A PHE* 1.3 77.5 - - - +
114A LEU* 1.3 65.2 + - - +
116A LYS* 3.2 51.7 + - - +
117A THR* 3.8 10.7 + - - +
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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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44A ALA* 3.5 36.6 - - + +
45A SER* 3.9 13.7 - - - +
48A VAL* 3.7 13.2 - - + -
110A ASP 2.9 16.1 + - - +
111A ALA 3.8 3.8 - - - +
113A GLU* 1.3 76.2 - - - +
115A CYS* 1.3 62.8 + - - +
117A THR* 2.6 35.7 + - + +
118A THR* 3.6 7.4 + - - +
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Residues in contact with CYS 115 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A TYR* 4.3 5.6 - - + -
48A VAL* 3.8 13.7 - - + +
51A ILE* 4.1 13.5 - - - -
65A VAL* 3.4 43.3 - - - -
111A ALA 2.9 19.1 + - - +
112A PHE* 3.4 12.1 - - - +
113A GLU 3.2 0.2 - - - -
114A LEU* 1.3 77.8 - - - +
116A LYS* 1.3 57.8 + - - +
118A THR* 3.1 2.9 + - - -
119A PHE* 2.9 36.4 + - - +
121A THR* 3.5 10.4 + - + +
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Residues in contact with LYS 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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112A PHE* 3.1 16.5 + - + +
113A GLU* 3.2 47.0 + - - +
114A LEU 3.2 0.6 - - - -
115A CYS* 1.3 77.0 - - - +
117A THR* 1.3 60.4 + - + +
118A THR 3.2 1.3 + - - -
119A PHE 3.5 9.9 + - - +
120A PRO* 5.4 0.3 - - - +
121A THR* 3.6 31.8 + - + +
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Residues in contact with THR 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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113A GLU 3.9 13.5 - - - +
114A LEU* 2.6 29.8 + - + +
116A LYS* 1.3 76.8 - - + +
118A THR* 1.3 62.3 + - - +
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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