Contacts of the helix formed by residues 108 - 120 (chain B) in PDB entry 1TU8
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 ALA 108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B ARG 3.8 2.4 + - - +
104B MET* 3.2 9.5 + - - +
106B TYR 3.8 0.2 - - - -
107B MET* 1.3 84.4 - - + +
109B TYR* 1.3 60.5 + - - +
110B GLU* 3.2 6.5 + - - -
111B THR* 4.1 8.1 - - - +
112B GLU* 2.9 63.0 + - + +
113B LYS 4.0 0.3 + - - -
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Residues in contact with TYR 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B MET* 3.0 24.1 + - - -
105B ILE* 3.6 25.1 + - + +
108B ALA* 1.3 76.0 - - - +
110B GLU* 1.3 77.3 + - + +
111B THR 3.3 0.7 + - - -
113B LYS* 3.0 60.0 + - + +
164B LEU* 4.4 2.2 - - + -
207B LYS* 3.5 45.0 - - + +
208B GLN 2.9 32.4 + - - -
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Residues in contact with GLU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B MET 5.7 0.3 - - - -
108B ALA* 3.2 3.5 + - - -
109B TYR* 1.3 89.1 + - + +
111B THR* 1.3 68.8 + - + +
113B LYS* 5.7 0.2 - - - -
207B LYS* 2.5 41.7 + - - +
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Residues in contact with THR 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ALA* 3.5 9.4 + - - +
110B GLU* 1.3 91.0 - - + +
112B GLU* 1.3 71.7 + - - +
113B LYS 3.7 1.3 - - - -
114B ASP 5.2 0.4 - - - -
115B PRO* 3.5 17.5 - - - +
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Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B MET* 3.8 16.0 - - + +
108B ALA* 2.9 35.2 + - + +
111B THR* 1.3 85.7 - - - +
113B LYS* 1.3 59.9 + - - +
114B ASP 3.5 2.0 - - - -
115B PRO* 3.6 11.2 - - + +
116B TYR* 2.9 31.6 + - + +
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Residues in contact with LYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B MET* 3.8 18.2 - - + +
109B TYR* 3.0 56.3 + - + +
111B THR 3.7 0.6 - - - -
112B GLU* 1.3 77.0 - - - +
114B ASP* 1.3 67.9 + - - +
116B TYR* 3.3 2.8 + - - +
117B ILE* 3.0 49.6 + - + +
164B LEU* 4.1 26.3 + - + -
208B GLN 4.4 3.6 + - - -
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Residues in contact with ASP 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B THR 5.1 0.6 + - - -
113B LYS* 1.3 82.4 - - - +
115B PRO* 1.3 71.6 - - + +
117B ILE* 3.1 12.1 + - - +
118B LYS* 3.0 32.1 + - - +
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Residues in contact with PRO 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B THR 3.5 20.9 - - - +
112B GLU* 3.5 17.0 - - + +
114B ASP* 1.3 95.4 - - + +
116B TYR* 1.3 55.6 + - - +
118B LYS* 4.7 5.8 - - + +
119B SER* 2.8 42.4 + - - +
120B ILE* 3.6 5.6 + - + +
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Residues in contact with TYR 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LEU* 3.3 16.8 - - + +
100B LYS* 3.9 31.9 - - + -
101B TYR* 3.5 13.2 + + - +
104B MET* 4.0 20.0 - - + -
112B GLU* 2.9 21.6 + - + +
113B LYS 3.5 3.4 - - - +
115B PRO* 1.3 76.2 - - - +
117B ILE* 1.3 63.7 + - - +
120B ILE* 3.3 37.8 + - + +
121B LEU* 2.9 39.9 + - + +
161B HIS* 2.7 40.8 + + - -
164B LEU* 3.8 22.2 - - + -
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Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LYS* 3.0 40.1 + - + +
114B ASP* 3.1 13.4 + - - +
116B TYR* 1.3 76.3 - - + +
118B LYS* 1.3 60.5 + - + +
121B LEU* 4.0 10.2 - - + +
122B PRO* 3.3 22.5 - - - +
164B LEU* 3.9 41.1 - - + +
165B ASP* 3.4 34.1 - - + +
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Residues in contact with LYS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ASP* 3.0 20.4 + - - +
115B PRO* 4.3 5.3 - - + +
117B ILE* 1.3 80.8 - - + +
119B SER* 1.3 71.4 + - - +
122B PRO* 3.6 15.5 - - - +
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Residues in contact with SER 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B PRO* 2.8 23.1 + - - +
118B LYS* 1.3 89.7 + - - +
120B ILE* 1.3 64.8 + - - +
122B PRO* 4.4 2.5 - - - -
123B GLY* 5.4 1.7 + - - -
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Residues in contact with ILE 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B LYS* 4.2 20.6 - - + -
115B PRO* 3.6 4.7 + - + +
116B TYR* 3.3 48.4 + - + +
119B SER* 1.3 86.3 - - - +
121B LEU* 1.3 66.2 + - - +
122B PRO* 3.4 1.4 - - - -
123B GLY* 3.4 5.0 + - - -
124B GLU* 3.4 27.7 + - + +
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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