Contacts of the helix formed by residues 108 - 120 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103D ARG 3.7 2.2 + - - +
104D MET* 3.0 9.1 + - - +
107D MET* 1.3 83.9 - - + +
109D TYR* 1.3 60.8 + - - +
110D GLU* 3.3 5.6 - - - -
111D THR* 3.5 8.4 + - - +
112D GLU* 2.9 63.1 + - + +
113D LYS 4.0 0.2 + - - -
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Residues in contact with TYR 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D MET* 2.9 23.9 + - - -
105D ILE* 3.5 28.0 + - + +
107D MET 4.0 0.2 - - - -
108D ALA* 1.3 76.2 - - - +
110D GLU* 1.3 77.1 + - + +
111D THR 3.5 0.5 + - - -
113D LYS* 3.0 59.9 + - + +
164D LEU* 4.4 1.3 - - + -
207D LYS* 3.5 38.3 - - + +
208D GLN 2.8 35.8 + - - -
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Residues in contact with GLU 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D MET 5.8 0.5 - - - -
108D ALA* 3.3 3.0 - - - -
109D TYR* 1.3 91.5 + - + +
111D THR* 1.3 68.1 + - + +
113D LYS* 5.7 0.3 - - - +
207D LYS* 2.6 41.4 + - - +
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Residues in contact with THR 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D ALA* 3.5 9.9 + - - +
110D GLU* 1.3 90.7 - - + +
112D GLU* 1.3 68.6 + - - +
113D LYS 3.7 1.1 - - - -
114D ASP 5.2 0.4 - - - -
115D PRO* 3.7 16.5 - - - +
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Residues in contact with GLU 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D ARG 5.7 0.5 - - - -
104D MET* 4.0 16.9 - - + +
108D ALA* 2.9 36.8 + - + +
111D THR* 1.3 83.3 - - - +
113D LYS* 1.3 66.6 + - - +
114D ASP 3.4 2.5 - - - -
115D PRO* 3.5 10.0 - - + +
116D TYR* 2.9 25.5 + - + +
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Residues in contact with LYS 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D MET* 3.8 16.1 - - - +
108D ALA 4.0 1.0 + - - -
109D TYR* 3.0 55.7 + - + +
110D GLU 5.0 1.1 - - - +
111D THR 3.7 0.6 - - - -
112D GLU* 1.3 78.0 - - - +
114D ASP* 1.3 68.1 + - - +
116D TYR* 3.3 1.9 + - - +
117D ILE* 2.9 55.5 + - + +
164D LEU* 4.0 29.8 + - + -
208D GLN 4.4 3.0 + - - -
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Residues in contact with ASP 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D THR 5.1 0.6 + - - -
113D LYS* 1.3 94.3 - - - +
115D PRO* 1.3 65.2 - - + +
117D ILE* 3.3 13.9 + - - +
118D LYS* 2.9 31.2 + - - +
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Residues in contact with PRO 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D THR 3.7 18.4 - - - +
112D GLU* 3.5 15.9 - - + +
114D ASP* 1.3 93.4 - - + +
116D TYR* 1.3 57.3 + - - +
118D LYS* 4.4 5.2 - - + +
119D SER* 2.7 41.3 + - - +
120D ILE* 3.4 6.1 + - + +
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Residues in contact with TYR 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D LEU* 3.4 16.5 - - + +
100D LYS* 4.0 26.7 - - + -
101D TYR* 3.6 14.0 + + - +
104D MET* 3.9 20.9 - - + -
112D GLU* 2.9 21.6 + - + +
113D LYS 3.5 4.0 - - - +
115D PRO* 1.3 75.0 - - - +
117D ILE* 1.3 64.3 + - - +
120D ILE* 3.2 42.5 + - + +
121D LEU* 2.8 41.6 + - + +
161D HIS* 2.7 37.0 + + - -
164D LEU* 3.8 26.0 - - + -
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Residues in contact with ILE 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D LYS* 2.9 43.2 + - + +
114D ASP* 3.6 11.7 - - - +
116D TYR* 1.3 76.4 - - - +
118D LYS* 1.3 61.3 + - + +
121D LEU* 4.1 10.8 - - + +
122D PRO* 3.4 18.7 - - - +
164D LEU* 3.9 35.9 - - + +
165D ASP* 3.3 37.1 - - + +
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Residues in contact with LYS 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D ASP 2.9 17.5 + - - +
115D PRO* 4.3 2.5 - - + +
117D ILE* 1.3 80.8 - - + +
119D SER* 1.3 70.7 + - - +
120D ILE 3.8 0.2 - - - -
122D PRO* 3.5 16.7 - - - +
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Residues in contact with SER 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D PRO* 2.7 25.0 + - - +
118D LYS* 1.3 90.3 - - - +
120D ILE* 1.3 64.5 + - - +
122D PRO* 4.3 2.5 - - - -
123D GLY* 5.4 1.7 + - - -
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Residues in contact with ILE 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D LYS* 4.4 12.3 - - + -
112D GLU* 6.0 1.8 - - - +
115D PRO* 4.2 6.1 - - + +
116D TYR* 3.2 45.5 + - + +
119D SER* 1.3 85.2 - - - +
121D LEU* 1.3 66.1 + - - +
122D PRO* 3.5 0.7 - - - -
123D GLY* 3.5 4.7 + - - -
124D GLU* 3.3 34.5 + - + +
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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