Contacts of the helix formed by residues 104 - 115 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B SER* 3.3 1.7 + - - -
18B LYS* 4.4 12.9 - - - +
73B GLU* 4.2 7.0 - - - +
75B ALA* 4.2 11.3 - - - +
77B TYR* 3.0 30.8 + - + +
103B ILE* 1.4 85.8 - - - +
105B VAL* 1.3 63.7 + - + +
106B GLN* 3.9 9.4 - - + +
107B GLY* 3.1 32.1 + - - +
108B ALA 3.0 17.0 + - - -
110B GLN* 5.3 0.7 + - - -
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Residues in contact with VAL 105 (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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11B SER* 3.3 11.2 + - - +
12B GLY* 3.5 32.8 + - - +
13B PRO* 4.2 4.5 - - + -
104B GLU* 1.3 72.8 - - + +
106B GLN* 1.3 71.7 + - + +
108B ALA* 3.4 3.1 + - - +
109B MSE 3.3 27.1 + - + +
122B PHE* 4.3 1.8 - - + -
159B MSE 4.2 27.6 - - + -
163B TYR* 3.8 14.0 + - + +
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Residues in contact with GLN 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TYR* 5.6 0.7 - - - +
104B GLU* 3.3 10.5 - - + +
105B VAL* 1.3 84.6 - - + +
107B GLY* 1.3 61.5 + - - +
109B MSE 3.6 8.0 + - - +
110B GLN* 3.5 26.4 + - - +
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Residues in contact with GLY 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLU* 3.9 13.3 - - - +
103B ILE* 3.6 9.2 - - - -
104B GLU* 3.1 30.8 + - - -
106B GLN* 1.3 75.1 - - - +
108B ALA* 1.3 62.3 + - - +
110B GLN* 3.1 22.0 + - - +
111B VAL* 3.2 16.3 + - - +
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Residues in contact with ALA 108 (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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9B VAL* 4.2 9.2 - - + -
11B SER* 3.7 22.0 - - - +
103B ILE* 3.5 15.8 - - + +
104B GLU 3.0 5.4 + - - +
105B VAL 3.4 9.2 + - - +
107B GLY* 1.3 76.2 - - - +
109B MSE 1.3 62.0 + - + +
111B VAL* 3.3 2.3 + - - +
112B ARG* 2.9 28.8 + - - +
120B PHE* 3.6 5.6 - - + -
163B TYR* 3.7 19.7 - - + +
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Residues in contact with MSE 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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105B VAL* 3.3 16.3 + - + +
106B GLN* 3.6 7.2 + - - +
107B GLY 3.3 0.4 - - - -
108B ALA* 1.3 81.9 - - + +
110B GLN* 1.3 63.7 + - - +
112B ARG* 3.7 32.5 + - + +
113B LYS* 3.1 23.7 + - - +
120B PHE* 4.6 3.1 - - + -
162B SER* 3.7 25.8 - - - +
163B TYR* 3.4 43.1 - - + +
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Residues in contact with GLN 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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72B LEU 4.4 5.8 - - - +
73B GLU* 3.4 12.1 - - + -
74B TYR* 3.1 49.9 + - - +
75B ALA* 5.2 2.6 - - - +
104B GLU* 5.3 0.2 + - - -
106B GLN* 3.5 17.7 + - - +
107B GLY* 3.1 14.4 + - - +
109B MSE 1.3 77.3 - - - +
111B VAL* 1.3 56.9 + - - +
113B LYS* 3.4 8.3 + - - +
114B ALA* 3.0 28.2 + - - +
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Residues in contact with VAL 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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7B LEU* 3.8 28.5 - - + -
9B VAL* 3.8 16.4 - - + -
72B LEU* 4.2 20.6 - - + -
73B GLU* 3.5 25.6 - - + -
101B LEU* 3.9 8.3 - - + -
103B ILE* 3.6 14.1 - - + -
107B GLY 3.2 13.6 + - - +
108B ALA 3.3 7.4 + - - +
110B GLN* 1.3 76.0 - - - +
112B ARG* 1.4 51.1 + - - +
115B MSE 2.6 35.7 + - + +
120B PHE* 3.9 6.3 - - + -
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Residues in contact with ARG 112 (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 2.9 18.6 + - - +
109B MSE 3.7 34.4 + - + +
110B GLN 3.3 0.2 - - - -
111B VAL* 1.4 73.7 - - - +
113B LYS* 1.3 63.0 + - - +
116B PRO* 3.2 29.8 - - + +
120B PHE* 3.4 30.4 - - + -
162B SER* 3.2 40.1 + - - +
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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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109B MSE 3.1 17.4 + - - +
110B GLN* 3.6 6.3 - - - +
112B ARG* 1.3 78.8 - - - +
114B ALA* 1.3 60.9 + - - +
116B PRO* 4.1 5.7 - - - +
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Residues in contact with ALA 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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72B LEU* 3.8 28.9 - - + +
110B GLN 3.0 17.0 + - - +
111B VAL 3.8 0.2 - - - +
113B LYS* 1.3 79.5 - - - +
115B MSE 1.3 63.8 + - + +
116B PRO* 3.6 5.6 - - - +
117B GLU* 4.8 0.7 - - - +
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Residues in contact with MSE 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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4B ARG* 4.1 2.0 - - - +
7B LEU* 3.9 24.5 - - + -
72B LEU* 3.9 31.2 - - + -
86B LEU* 4.7 7.6 - - + -
89B VAL* 4.3 6.3 - - - -
90B GLU* 3.7 19.5 - - - +
93B LEU* 3.7 26.7 - - + -
111B VAL* 2.6 18.2 + - + +
112B ARG 3.5 3.4 - - - -
114B ALA* 1.3 80.2 - - + +
116B PRO* 1.3 67.9 - - - +
117B GLU* 3.2 34.3 - - + +
118B GLY* 3.2 9.2 + - - +
120B PHE* 3.6 10.0 - - - -
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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