Contacts of the strand formed by residues 71 - 77 (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 MSE 71 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B MSE 4.5 10.1 - - + +
62B PHE* 3.6 18.6 - - + -
65B ALA* 3.9 14.6 + - - -
66B ILE* 4.0 36.1 - - + +
69B GLY* 3.5 6.1 - - - +
70B LYS* 1.3 85.5 - - - +
72B LEU* 1.3 63.9 + - - +
73B GLU* 3.4 7.1 - - - +
74B TYR* 4.1 18.7 - - + -
83B GLY* 3.3 14.6 - - - +
84B THR 3.3 37.5 - - - +
85B PRO* 3.9 8.1 - - + -
86B LEU* 4.3 4.6 - - - +
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Residues in contact with LEU 72 (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* 4.6 3.4 - - + -
71B MSE 1.3 73.9 - - - +
73B GLU* 1.3 60.6 + - - +
84B THR* 2.8 24.8 + - + +
86B LEU* 3.8 27.0 - - + +
89B VAL* 4.0 35.4 - - + -
101B LEU* 4.8 2.7 - - + -
110B GLN* 4.4 12.5 - - - +
111B VAL* 4.2 25.8 - - + -
114B ALA* 3.8 28.4 - - + +
115B MSE 3.9 23.6 - - + -
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Residues in contact with GLU 73 (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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38B SER* 4.9 0.9 + - - -
71B MSE 3.4 4.3 - - - +
72B LEU* 1.3 80.5 - - - +
74B TYR* 1.3 75.0 + - - +
82B TYR 4.6 1.0 - - - +
83B GLY* 3.2 8.1 - - - -
84B THR* 2.7 61.8 + - - +
103B ILE* 3.8 19.8 - - + +
104B GLU* 4.2 5.7 - - - +
107B GLY* 3.9 15.6 - - - +
110B GLN* 3.4 26.5 - - + +
111B VAL* 3.5 25.4 - - + -
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Residues in contact with TYR 74 (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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62B PHE* 3.8 15.7 - - + -
66B ILE* 3.6 52.2 - - + +
71B MSE 4.1 15.7 - - + -
73B GLU* 1.3 83.4 + - - +
75B ALA* 1.3 69.4 + - - +
76B GLU* 5.6 0.7 - - + -
81B TYR* 4.3 12.8 - + - -
82B TYR 3.3 14.4 - - - +
110B GLN* 3.1 33.2 + - - +
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Residues in contact with ALA 75 (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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73B GLU* 5.5 0.2 - - - +
74B TYR* 1.3 81.9 - - - +
76B GLU* 1.3 60.9 + - - +
77B TYR* 3.6 33.5 - - + +
80B ASN 3.9 0.3 - - - +
81B TYR* 3.4 8.1 - - - -
82B TYR* 3.0 31.9 + - - +
104B GLU* 4.2 8.1 - - - +
106B GLN* 6.6 0.2 - - + -
110B GLN* 5.2 2.2 - - - +
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Residues in contact with GLU 76 (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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59B ARG* 2.8 37.1 + - - -
74B TYR* 5.1 0.8 - - + -
75B ALA* 1.3 74.5 - - - +
77B TYR* 1.3 68.1 + - - +
78B VAL 4.0 1.2 + - - -
79B GLY* 3.4 16.4 - - - +
80B ASN 3.4 16.2 - - - +
81B TYR* 3.4 30.6 + - + -
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Residues in contact with TYR 77 (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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75B ALA* 3.6 25.6 - - + +
76B GLU* 1.3 75.4 - - - +
78B VAL* 1.3 77.4 + - + +
79B GLY 3.2 0.2 - - - -
80B ASN* 2.7 31.0 + - - +
82B TYR* 3.7 36.1 - + + -
104B GLU* 3.0 41.3 + - + +
106B GLN* 5.6 1.0 - - - +
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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