Contacts of the helix formed by residues 147 - 161 (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 147 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148B GLU* 1.4 64.2 + - + +
149B ARG* 3.5 5.8 - - - +
150B MSE 3.6 15.7 + - - +
151B GLU* 3.1 34.5 + - + +
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Residues in contact with GLU 148 (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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147B GLU* 1.4 77.3 - - + +
149B ARG* 1.4 54.5 + - + +
151B GLU* 3.3 8.5 + - - +
152B THR* 2.8 41.8 + - - +
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Residues in contact with ARG 149 (chain B).
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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147B GLU 3.5 3.7 - - - +
148B GLU* 1.4 76.9 - - + +
150B MSE 1.3 58.5 + - + +
152B THR* 3.5 7.9 + - - -
153B ALA* 3.1 27.9 + - - +
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Residues in contact with MSE 150 (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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201A LEU* 4.1 29.8 - - + -
147B GLU* 3.6 17.5 + - - +
148B GLU 3.3 0.4 - - - -
149B ARG* 1.3 75.6 - - + +
151B GLU* 1.4 60.3 + - - +
153B ALA* 3.4 10.2 + - - +
154B LYS* 3.1 29.2 + - - +
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Residues in contact with GLU 151 (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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147B GLU* 3.1 25.8 + - + +
148B GLU* 3.5 7.9 - - - +
150B MSE 1.4 73.3 - - + +
152B THR* 1.4 64.6 + - - +
154B LYS* 3.4 14.0 + - - +
155B LYS* 3.1 44.2 + - - +
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Residues in contact with THR 152 (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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148B GLU* 2.8 24.7 + - - +
149B ARG* 3.6 8.4 - - - -
150B MSE 3.4 0.2 - - - -
151B GLU* 1.4 74.6 - - - +
153B ALA* 1.3 56.7 + - - +
155B LYS* 3.2 13.9 + - - +
156B GLU* 2.9 61.2 + - + +
159B MSE 5.1 0.2 - - - +
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Residues in contact with ALA 153 (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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200A MSE 6.5 0.4 - - + -
201A LEU* 5.5 5.2 - - + -
128B LEU* 3.6 26.9 - - + +
149B ARG 3.1 15.0 + - - +
150B MSE 3.5 17.0 - - - +
152B THR* 1.3 74.3 - - - +
154B LYS* 1.3 61.7 + - - +
156B GLU* 3.2 9.0 + - - +
157B ILE* 3.0 33.0 + - + +
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Residues in contact with LYS 154 (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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201A LEU* 5.5 7.4 - - + +
150B MSE 3.1 17.4 + - - +
151B GLU* 3.7 15.9 - - - +
153B ALA* 1.3 74.6 - - - +
155B LYS* 1.3 60.3 + - + +
157B ILE* 3.4 11.7 + - - +
158B GLU* 3.0 27.2 + - + +
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Residues in contact with LYS 155 (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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151B GLU* 3.1 35.5 + - - +
152B THR* 3.7 10.1 - - - +
154B LYS* 1.3 74.8 - - + +
156B GLU* 1.3 60.0 + - - +
158B GLU* 3.7 7.8 - - - +
159B MSE 2.9 45.5 + - + +
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Residues in contact with GLU 156 (chain B).
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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13B PRO* 3.3 35.9 - - + +
122B PHE* 3.9 13.4 - - + -
125B PRO* 3.6 20.2 - - + +
128B LEU* 4.5 14.2 - - + +
152B THR* 2.9 43.5 + - + +
153B ALA* 3.2 9.4 + - - +
155B LYS* 1.3 73.5 - - - +
157B ILE* 1.3 57.8 + - - +
159B MSE 3.5 22.2 + - + +
160B MSE 3.1 31.6 + - - +
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Residues in contact with ILE 157 (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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194A ILE* 4.0 31.0 - - + +
197A TYR* 4.2 26.0 - - + +
198A LYS* 4.2 23.6 - - + +
200A MSE 5.9 0.7 - - + -
201A LEU* 3.7 29.8 - - + -
128B LEU* 4.0 22.7 - - + -
153B ALA* 3.0 24.7 + - + +
154B LYS* 3.7 6.3 - - - +
156B GLU* 1.3 73.7 - - - +
158B GLU* 1.4 64.6 + - - +
160B MSE 3.3 21.8 - - - +
161B ALA* 3.7 3.8 + - - +
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Residues in contact with GLU 158 (chain B).
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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198A LYS* 5.0 10.1 + - - +
154B LYS 3.0 17.0 + - - +
155B LYS* 3.7 8.7 - - - +
156B GLU 3.4 0.2 - - - -
157B ILE* 1.4 76.5 - - - +
159B MSE 1.4 61.6 + - - +
161B ALA* 3.3 24.6 + - - +
162B SER* 4.6 1.6 + - - -
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Residues in contact with MSE 159 (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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13B PRO* 5.5 5.8 - - + -
105B VAL* 4.2 26.7 - - + -
122B PHE* 4.1 22.4 - - + -
155B LYS* 2.9 42.1 + - + +
156B GLU* 3.5 24.0 - - + +
157B ILE 3.4 0.2 - - - -
158B GLU* 1.4 75.2 - - - +
160B MSE 1.3 63.3 + - - +
162B SER* 3.0 21.3 + - - -
163B TYR* 3.3 15.4 - - + -
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Residues in contact with MSE 160 (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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190A THR* 3.3 23.1 - - + +
193A VAL* 4.0 4.0 - - - -
194A ILE* 3.9 22.0 - - + -
197A TYR* 3.7 34.5 - - + -
122B PHE* 3.9 22.7 - - + -
124B THR* 4.0 12.1 - - + +
128B LEU* 3.8 20.4 - - + -
156B GLU 3.1 18.2 + - - +
157B ILE* 3.3 16.8 - - - +
159B MSE 1.3 77.5 - - - +
161B ALA* 1.4 56.8 + - - +
163B TYR* 3.0 26.4 + - - +
166B ALA* 3.9 23.6 - - + -
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Residues in contact with ALA 161 (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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190A THR* 4.5 3.0 + - - -
191A GLU* 5.7 0.5 - - - +
194A ILE* 3.6 20.7 - - + +
157B ILE 3.7 1.5 + - - +
158B GLU* 3.3 20.5 + - - +
159B MSE 3.0 0.6 + - - -
160B MSE 1.4 76.9 - - - +
162B SER* 1.3 59.1 + - - +
163B TYR 3.3 6.4 + - - +
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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