Contacts of the helix formed by residues 118 - 131 (chain A) in PDB entry 1TAU
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 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ASP* 4.4 2.0 - - - +
20A HIS* 3.3 44.1 - - + -
65A VAL* 3.5 16.8 - - + +
66A PHE 4.0 16.4 - - - +
67A ASP* 3.2 10.7 + - - +
116A TYR 3.7 1.4 + - - -
117A GLU* 1.3 71.5 - - - +
119A ASP* 1.3 59.9 + - - +
121A VAL* 3.5 1.7 + - - -
122A LEU* 3.0 32.8 + - - +
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Residues in contact with ASP 119 (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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18A ASP* 3.9 1.7 - - - +
20A HIS* 4.1 1.5 - - - -
21A HIS* 3.2 20.5 + - - -
117A GLU* 3.2 8.4 - - + +
118A ALA* 1.3 82.4 - - - +
120A ASP* 1.3 61.1 + - - +
122A LEU* 3.4 8.9 + - + +
123A ALA* 3.0 29.3 + - - +
142A ASP* 3.8 6.3 - - - +
144A ASP* 5.7 3.5 - - + +
145A LEU* 4.3 12.6 - - + +
247A LYS 4.8 9.6 - - - +
248A VAL* 4.7 4.8 - - + -
900A ZN 2.6 34.3 - - - -
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Residues in contact with ASP 120 (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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116A TYR* 5.4 2.9 - - + -
117A GLU* 3.0 28.6 + - - +
119A ASP* 1.3 73.9 - - - +
121A VAL* 1.3 69.7 + - + +
123A ALA 3.4 0.9 + - - -
124A SER* 2.9 26.2 + - - -
247A LYS* 2.8 43.1 + - - +
248A VAL* 4.5 1.8 - - - +
249A ARG* 2.8 44.7 + - - +
252A LEU* 3.8 15.7 - - + -
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Residues in contact with VAL 121 (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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65A VAL* 3.9 17.3 - - + -
66A PHE 5.8 0.9 - - - +
111A LEU* 4.0 18.6 - - + +
113A VAL* 3.8 21.1 - - + +
116A TYR* 3.7 28.0 - - + +
117A GLU 3.2 13.6 + - - +
118A ALA* 3.7 7.6 - - - +
120A ASP* 1.3 77.4 - - - +
122A LEU* 1.3 58.9 + - - +
124A SER* 3.1 9.0 + - - -
125A LEU* 2.9 29.3 + - + +
252A LEU* 4.6 2.4 - - - +
254A LEU* 3.8 21.7 - - + +
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Residues in contact with LEU 122 (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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16A LEU* 3.3 32.7 - - + +
17A VAL 3.6 22.2 - - - +
18A ASP* 3.6 38.8 - - + +
65A VAL* 3.7 19.1 - - + -
118A ALA 3.0 26.8 + - - +
119A ASP* 3.5 12.6 - - - +
121A VAL* 1.3 76.5 - - - +
123A ALA* 1.3 63.2 + - - +
125A LEU* 3.1 4.0 + - - +
126A ALA* 2.9 22.3 + - - +
138A ILE* 4.8 5.6 - - + -
145A LEU* 4.5 16.4 - - + -
148A LEU* 4.9 0.7 - - - -
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Residues in contact with ALA 123 (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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119A ASP 3.0 19.7 + - - +
120A ASP 3.7 4.7 - - - +
122A LEU* 1.3 72.6 - - - +
124A SER* 1.3 57.6 + - - +
126A ALA* 3.4 2.3 - - - +
127A LYS* 3.0 34.8 + - - +
145A LEU* 4.7 0.2 - - + -
148A LEU* 3.5 38.2 - - + +
248A VAL* 3.9 17.3 - - + +
249A ARG 3.7 10.3 - - - +
250A THR* 4.3 1.1 - - + -
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Residues in contact with SER 124 (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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120A ASP 2.9 5.8 + - - -
121A VAL* 3.1 9.0 + - - -
123A ALA* 1.3 75.7 - - - +
125A LEU* 1.3 57.8 + - - +
127A LYS* 3.1 2.1 + - - +
128A LYS* 2.7 36.9 + - - +
249A ARG 2.8 19.4 + - - -
250A THR 3.3 25.1 - - - +
252A LEU* 3.3 30.0 + - - +
254A LEU* 5.1 6.3 - - - -
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Residues in contact with LEU 125 (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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16A LEU* 3.7 19.1 - - + -
63A ILE* 3.7 15.9 - - + -
65A VAL* 3.4 33.7 - - + -
111A LEU* 3.4 14.6 - - + -
121A VAL* 2.9 22.7 + - + +
122A LEU* 3.7 6.3 - - - +
124A SER* 1.3 70.2 - - - +
126A ALA* 1.3 63.9 + - - +
128A LYS* 4.6 3.1 - - - -
129A ALA* 2.9 26.9 + - - +
254A LEU* 3.6 17.7 - - + +
256A VAL* 3.4 33.0 - - + -
258A PHE* 3.7 11.7 - - + -
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Residues in contact with ALA 126 (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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16A LEU* 3.2 18.5 - - + +
122A LEU 2.9 16.9 + - - +
123A ALA* 3.4 7.2 - - - +
125A LEU* 1.3 78.6 - - - +
127A LYS* 1.3 64.5 + - + +
130A GLU* 2.9 23.0 + - - +
136A VAL* 3.6 15.5 - - + +
138A ILE* 3.7 18.8 - - + -
148A LEU* 4.4 2.7 - - + -
153A ILE* 4.1 14.6 - - + -
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Residues in contact with LYS 127 (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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123A ALA 3.0 18.0 + - - +
124A SER 3.7 2.7 - - - +
126A ALA* 1.3 75.4 - - - +
128A LYS* 1.3 56.9 + - - +
130A GLU* 3.0 23.4 + - - +
131A LYS* 2.8 31.9 + - - +
148A LEU* 4.4 14.0 + - + +
150A SER* 5.9 1.8 + - - -
153A ILE* 3.7 19.4 - - + +
250A THR* 3.4 38.1 - - + +
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Residues in contact with LYS 128 (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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124A SER 2.7 20.4 + - - +
125A LEU* 3.9 3.1 - - - +
127A LYS* 1.3 73.0 - - - +
129A ALA* 1.3 57.5 + - - +
131A LYS* 3.3 7.6 + - + +
132A GLU* 2.8 62.0 + - + +
250A THR 5.4 0.8 + - - +
252A LEU 6.0 0.7 - - - +
254A LEU* 3.9 35.7 - - + +
255A GLU* 4.2 11.4 + - - -
256A VAL 3.6 13.3 + - - -
257A ASP* 5.2 4.9 + - - +
258A PHE* 3.6 21.7 - - + -
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Residues in contact with ALA 129 (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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14A VAL* 4.0 4.9 - - + -
125A LEU 2.9 18.5 + - - +
126A ALA 3.6 2.9 - - - +
128A LYS* 1.3 74.7 - - - +
130A GLU* 1.3 65.1 + - - +
132A GLU 2.9 10.6 + - - -
133A GLY 3.2 0.3 + - - -
134A TYR* 2.9 36.9 + - + -
136A VAL* 3.7 14.1 - - + -
258A PHE* 3.5 30.4 - - + -
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Residues in contact with GLU 130 (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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126A ALA 2.9 14.5 + - - +
127A LYS* 3.0 36.6 + - - +
129A ALA* 1.3 74.5 - - - +
131A LYS* 1.3 64.1 + - - +
133A GLY* 3.0 14.6 + - - -
134A TYR 3.6 12.2 + - - +
136A VAL* 3.8 3.9 - - + +
150A SER* 3.9 8.0 + - - -
151A ASP* 3.1 26.2 - - - +
152A ARG* 3.9 19.5 + - + +
153A ILE* 3.2 27.3 - - + +
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Residues in contact with LYS 131 (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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127A LYS 2.8 21.7 + - - +
128A LYS* 3.5 9.2 - - + +
130A GLU* 1.3 73.6 + - - +
132A GLU* 1.3 59.7 + - + +
133A GLY* 2.8 12.5 + - - -
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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