Contacts of the helix formed by residues 104 - 115 (chain A) in PDB entry 3TAU
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 GLU 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A SER* 3.4 1.0 + - - -
18A LYS* 4.3 13.9 - - - +
102A GLU* 5.9 1.6 - - - -
103A ILE* 1.3 88.6 - - - +
105A VAL* 1.4 66.2 + - - +
106A GLN* 3.3 6.5 - - + +
107A GLY* 3.2 7.0 + - - +
108A ALA 3.0 18.4 + - - -
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Residues in contact with VAL 105 (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 SER* 3.4 10.7 + - - +
12A GLY* 3.5 34.6 + - - +
13A PRO* 4.2 5.8 - - + -
104A GLU* 1.4 72.2 - - - +
106A GLN* 1.4 76.8 + - + +
108A ALA* 3.4 4.1 + - - +
109A MSE 3.3 28.6 + - - +
122A PHE* 4.4 2.5 - - + -
159A MSE 3.5 33.4 - - + -
163A TYR* 4.3 3.3 + - - +
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Residues in contact with GLN 106 (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 GLU* 3.3 3.6 - - + +
105A VAL* 1.4 85.3 - - + +
107A GLY* 1.3 64.8 + - - +
109A MSE 3.5 40.5 + - - +
110A GLN* 3.6 18.6 + - - +
159A MSE 5.1 4.0 - - - +
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Residues in contact with GLY 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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73A GLU* 4.0 2.8 - - - +
103A ILE* 3.8 22.7 - - - +
104A GLU* 3.2 11.4 + - - +
106A GLN* 1.3 77.4 - - - +
108A ALA* 1.4 61.9 + - - +
110A GLN* 3.1 27.6 + - - +
111A VAL* 3.2 16.3 + - - +
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Residues in contact with ALA 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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9A VAL* 4.5 7.2 - - + -
11A SER* 3.7 13.2 - - - +
103A ILE* 3.8 13.1 - - + +
104A GLU 3.0 13.2 + - - +
105A VAL 3.6 6.1 - - - +
106A GLN 3.4 0.2 - - - -
107A GLY* 1.4 75.3 - - - +
109A MSE 1.3 57.8 + - - +
111A VAL* 3.3 6.4 + - - +
112A ARG* 2.8 31.8 + - - +
120A PHE* 3.9 3.8 - - + -
163A TYR* 3.3 28.9 - - + +
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Residues in contact with MSE 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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105A VAL 3.3 16.0 + - - +
106A GLN* 3.5 31.9 - - - +
107A GLY 3.3 0.2 - - - -
108A ALA* 1.3 72.9 - - + +
110A GLN* 1.4 64.4 + - - +
112A ARG* 3.4 38.9 + - - +
113A LYS* 3.1 24.1 + - - +
159A MSE 3.9 27.4 - - + -
163A TYR* 5.4 1.1 - - + +
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Residues in contact with GLN 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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72A LEU 3.3 10.8 - - - +
73A GLU* 3.6 12.4 + - + +
74A TYR* 3.2 47.6 + - - +
75A ALA* 5.5 1.8 - - - +
106A GLN* 3.6 16.9 + - - +
107A GLY* 3.1 16.9 + - - +
109A MSE 1.4 77.3 - - - +
111A VAL* 1.3 60.2 + - - +
113A LYS* 3.3 8.6 + - - +
114A ALA* 3.0 18.5 + - - +
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Residues in contact with VAL 111 (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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7A LEU* 4.0 17.0 - - + -
9A VAL* 3.9 26.7 - - + -
72A LEU* 3.8 15.7 - - + +
73A GLU* 3.7 25.1 - - + -
84A THR* 5.6 0.2 - - - -
101A LEU* 4.2 17.7 - - + -
103A ILE* 4.2 4.3 - - + -
107A GLY 3.2 14.5 + - - +
108A ALA* 3.3 8.7 + - - +
110A GLN* 1.3 74.6 - - - +
112A ARG* 1.4 52.5 + - - +
114A ALA* 3.3 1.0 + - - +
115A MSE 2.6 37.1 + - + +
120A PHE* 3.9 7.0 - - + -
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Residues in contact with ARG 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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108A ALA 2.8 18.6 + - - +
109A MSE 3.4 53.1 + - - +
111A VAL* 1.4 74.1 - - - +
113A LYS* 1.3 60.9 + - - +
116A PRO* 3.3 28.0 - - + +
120A PHE* 3.4 32.2 - - + -
159A MSE 6.1 0.4 - - - +
162A SER* 3.0 55.4 + - - -
163A TYR* 4.4 12.3 - - - -
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Residues in contact with LYS 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 MSE 3.1 16.6 + - - +
110A GLN* 3.6 6.5 - - - +
112A ARG* 1.3 77.3 - - - +
114A ALA* 1.3 61.1 + - - +
115A MSE 3.8 0.2 + - - -
116A PRO* 4.0 6.9 - - - +
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Residues in contact with ALA 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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71A MSE 4.5 4.5 - - - +
72A LEU* 3.6 38.2 - - + +
86A LEU* 5.7 0.7 - - - +
110A GLN 3.0 16.8 + - - +
111A VAL 3.9 1.6 - - - +
113A LYS* 1.3 77.6 - - - +
115A MSE 1.3 61.8 + - - +
116A PRO* 3.7 4.8 - - - +
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Residues in contact with MSE 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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7A LEU* 3.7 32.1 - - + -
72A LEU* 3.9 14.1 - - + -
86A LEU* 3.4 33.2 - - + -
89A VAL* 4.3 7.2 - - + -
90A GLU* 5.1 7.2 - - - +
93A LEU* 4.1 22.2 - - + -
111A VAL* 2.6 15.7 + - + +
112A ARG 3.5 2.9 - - - -
114A ALA* 1.3 76.7 - - - +
116A PRO* 1.4 66.6 - - - +
117A GLU* 3.1 35.3 + - + +
118A GLY 3.1 12.0 + - - +
120A PHE* 3.4 13.7 - - - -
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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