Contacts of the helix formed by residues 143 - 160 (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 MSE 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A ARG 6.1 1.3 - - - +
142A SER* 1.3 75.4 - - - +
144A GLU* 1.3 60.3 + - - +
145A VAL* 3.7 27.8 - - + -
146A VAL* 3.3 29.0 + - + +
147A GLU* 3.0 27.6 + - - +
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Residues in contact with GLU 144 (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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142A SER 3.9 1.3 + - - +
143A MSE 1.3 73.6 - - - +
145A VAL* 1.4 55.8 + - - +
147A GLU* 3.6 17.1 - - - +
148A GLU* 2.9 42.9 + - - +
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Residues in contact with VAL 145 (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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143A MSE 3.7 29.8 - - + -
144A GLU* 1.4 75.7 - - - +
146A VAL* 1.4 58.4 + - + +
148A GLU* 3.2 14.4 + - + +
149A ARG* 2.8 66.6 + - + +
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Residues in contact with VAL 146 (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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134A ARG* 5.8 9.6 - - + +
142A SER* 5.0 10.1 - - - +
143A MSE 3.3 47.8 + - + +
145A VAL* 1.4 75.1 - - + +
147A GLU* 1.4 57.7 + - - +
149A ARG* 3.3 13.2 + - + +
150A MSE 3.0 45.6 + - + +
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Residues in contact with GLU 147 (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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142A SER* 4.0 25.7 - - - +
143A MSE 3.0 19.0 + - - +
144A GLU* 3.6 19.8 - - - +
146A VAL* 1.4 76.7 - - - +
148A GLU* 1.4 55.9 + - + +
150A MSE 3.7 10.9 + - - +
151A GLU* 3.1 27.8 + - - +
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Residues in contact with GLU 148 (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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144A GLU* 2.9 33.8 + - + +
145A VAL* 3.2 13.5 + - + +
147A GLU* 1.4 74.6 - - + +
149A ARG* 1.4 55.0 + - + +
151A GLU* 3.3 6.8 + - - +
152A THR* 2.8 40.1 + - - +
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Residues in contact with ARG 149 (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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131A LEU* 3.6 16.4 - - + +
134A ARG* 3.1 48.5 - - - +
145A VAL* 2.8 50.0 + - + +
146A VAL* 3.3 12.9 + - + +
148A GLU* 1.4 70.4 - - + +
150A MSE 1.3 57.6 + - + +
152A THR* 3.5 8.1 + - - -
153A ALA* 3.1 27.5 + - - +
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Residues in contact with MSE 150 (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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131A LEU* 3.9 25.4 - - + -
132A LYS* 5.2 16.2 - - - +
142A SER* 5.7 3.8 - - - -
146A VAL* 3.0 34.9 + - + +
147A GLU* 3.9 10.5 - - - +
149A ARG* 1.3 72.6 - - - +
151A GLU* 1.4 60.2 + - - +
153A ALA* 3.4 3.1 + - - +
154A LYS* 3.0 27.5 + - - +
201B LEU* 5.0 8.6 - - + +
202B GLU* 5.8 4.9 - - - +
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Residues in contact with GLU 151 (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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147A GLU 3.1 19.0 + - - +
148A GLU* 3.3 8.7 + - - +
150A MSE 1.4 74.3 - - - +
152A THR* 1.4 62.8 + - - +
154A LYS* 3.4 16.3 + - - +
155A LYS* 3.1 56.3 + - - +
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Residues in contact with THR 152 (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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148A GLU* 2.8 25.6 + - - +
149A ARG* 3.6 8.9 - - - +
151A GLU* 1.4 73.6 - - - +
153A ALA* 1.3 58.0 + - - +
155A LYS* 3.2 14.0 + - - +
156A GLU* 2.9 54.4 + - + +
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Residues in contact with ALA 153 (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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128A LEU* 3.5 26.5 - - + -
131A LEU* 3.8 23.6 - - + -
149A ARG 3.1 16.9 + - - +
150A MSE 3.5 5.8 - - - +
152A THR* 1.3 75.4 - - - +
154A LYS* 1.3 62.3 + - - +
156A GLU* 3.3 7.9 + - - +
157A ILE* 3.1 30.4 + - - +
201B LEU* 4.6 6.3 - - + -
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Residues in contact with LYS 154 (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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150A MSE 3.0 16.9 + - - +
151A GLU* 3.7 21.3 - - - +
153A ALA* 1.3 74.1 - - - +
155A LYS* 1.3 58.9 + - + +
157A ILE* 3.4 4.3 + - + +
158A GLU* 3.0 31.7 + - - +
198B LYS* 6.3 0.8 - - - +
201B LEU* 4.3 26.8 - - + +
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Residues in contact with LYS 155 (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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151A GLU* 3.1 47.8 + - - +
152A THR* 3.7 9.6 - - - +
154A LYS* 1.3 73.7 - - + +
156A GLU* 1.3 61.2 + - - +
158A GLU* 3.4 11.0 + - - +
159A MSE 2.9 30.0 + - - +
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Residues in contact with GLU 156 (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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13A PRO* 3.6 23.5 - - + +
122A PHE* 4.1 16.6 - - + -
125A PRO* 3.6 21.8 - - - +
127A ASP* 5.1 2.1 - - - +
128A LEU* 3.5 27.7 - - + +
152A THR* 2.9 38.0 + - + +
153A ALA* 3.3 12.9 + - - +
155A LYS* 1.3 76.5 - - + +
157A ILE* 1.3 57.8 + - - +
159A MSE 3.4 7.8 + - - +
160A MSE 3.1 35.3 + - + +
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Residues in contact with ILE 157 (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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128A LEU* 4.1 12.6 - - + -
153A ALA 3.1 20.6 + - - +
154A LYS* 3.7 4.9 - - - +
155A LYS 3.3 0.2 - - - -
156A GLU* 1.3 72.8 - - - +
158A GLU* 1.3 65.5 + - - +
160A MSE 3.2 30.4 + - + +
161A ALA* 3.7 2.1 + - - +
194B ILE* 3.7 39.7 - - + +
197B TYR* 3.7 28.0 - - + +
198B LYS* 4.1 19.7 - - + -
200B MSE 4.6 0.9 - - + -
201B LEU* 3.5 32.5 - - + -
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Residues in contact with GLU 158 (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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154A LYS* 3.0 20.6 + - + +
155A LYS* 3.7 11.9 - - - +
157A ILE* 1.3 73.9 - - - +
159A MSE 1.4 63.6 + - - +
160A MSE 3.2 0.9 + - - -
161A ALA* 3.3 20.6 + - - +
162A SER* 4.5 1.6 + - - -
198B LYS* 6.5 0.4 - - - +
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Residues in contact with MSE 159 (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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105A VAL* 3.5 44.6 - - + +
106A GLN* 5.1 5.4 - - - +
109A MSE 3.9 29.4 - - + -
112A ARG* 6.1 0.7 - - - +
122A PHE* 3.7 17.7 - - + -
155A LYS 2.9 18.8 + - - +
156A GLU* 3.7 6.5 - - - +
158A GLU* 1.4 74.2 - - - +
160A MSE 1.3 62.4 + - - +
161A ALA 3.0 1.4 + - - -
162A SER* 3.1 23.5 + - - -
163A TYR* 3.5 14.3 - - + -
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Residues in contact with MSE 160 (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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122A PHE* 3.9 24.5 - - + -
124A THR* 4.7 2.2 - - + -
128A LEU* 3.8 24.5 - - + -
156A GLU 3.1 38.9 + - - +
157A ILE* 3.2 22.0 - - + +
158A GLU 3.1 0.4 - - - -
159A MSE 1.3 76.6 - - - +
161A ALA* 1.3 56.3 + - - +
162A SER 3.1 1.3 - - - -
163A TYR* 3.0 23.0 + - - +
166A ALA* 3.9 22.9 - - + -
190B THR* 3.2 34.6 - - + +
193B VAL* 4.1 5.2 - - - -
194B ILE* 3.8 13.9 - - + -
197B TYR* 4.0 20.0 - - + -
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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