Contacts of the helix formed by residues 171 - 188 (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 VAL 171 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ASN* 3.6 5.6 - - - +
170A ASP* 1.3 88.8 + - + +
172A VAL* 1.3 68.3 + - - +
173A ALA* 3.9 19.7 - - + +
174A ASN* 3.0 36.6 + - - +
175A ALA* 3.1 9.9 + - - +
207A SO4 3.3 21.5 - - - +
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Residues in contact with VAL 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A THR* 3.8 32.8 - - + +
21A VAL* 4.3 9.6 - - + -
24A ALA* 3.7 29.2 - - + -
169A ASN* 3.5 24.0 + - - +
171A VAL* 1.3 70.8 - - - +
173A ALA* 1.4 62.9 + - - +
175A ALA* 3.1 6.5 + - - +
176A VAL* 3.0 21.5 + - - +
207A SO4 2.8 35.4 + - - +
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Residues in contact with ALA 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA* 6.2 0.2 - - - -
171A VAL* 3.3 14.1 - - + +
172A VAL* 1.4 77.4 - - - +
174A ASN* 1.4 60.1 + - - +
176A VAL* 3.5 9.1 + - - +
177A GLN* 3.1 25.6 + - - +
207A SO4 4.6 0.8 + - - -
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Residues in contact with ASN 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ASP* 3.3 34.5 + - - +
171A VAL* 3.0 25.0 + - - +
173A ALA* 1.4 78.0 - - - +
175A ALA* 1.3 65.5 + - - +
177A GLN* 3.3 7.3 + - - +
178A LYS* 3.1 42.3 + - - +
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Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 4.1 22.9 - - + -
123A LEU* 4.1 8.5 - - + -
167A VAL* 3.8 23.7 - - + +
168A VAL 4.0 10.5 + - - +
169A ASN* 4.1 3.4 - - - +
170A ASP* 4.6 1.0 + - - -
171A VAL 3.1 9.3 + - - +
172A VAL 3.1 10.5 + - - +
174A ASN* 1.3 72.3 - - - +
176A VAL* 1.3 60.0 + - - +
178A LYS* 3.4 2.1 + - - +
179A ILE* 2.9 36.3 + - - +
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Residues in contact with VAL 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 4.1 5.2 - - + +
24A ALA* 3.5 31.6 - - + +
25A VAL* 4.0 34.7 - - + +
28A ASP* 3.8 25.8 - - + +
172A VAL* 3.0 20.2 + - + +
173A ALA* 3.6 10.5 - - - +
174A ASN 3.3 0.2 - - - -
175A ALA* 1.3 76.2 - - - +
177A GLN* 1.3 56.9 + - - +
179A ILE* 3.3 2.9 + - - +
180A LYS* 2.9 35.8 + - + +
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Residues in contact with GLN 177 (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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30A GLU* 5.2 1.2 + - - -
173A ALA 3.1 17.4 + - - +
174A ASN* 3.3 8.7 + - - +
176A VAL* 1.3 76.2 - - - +
178A LYS* 1.3 59.0 + - + +
180A LYS* 3.5 19.1 + - - +
181A GLY* 3.0 24.2 + - - +
208A NA 2.2 32.0 - - - -
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Residues in contact with LYS 178 (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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167A VAL* 4.0 23.3 - - + -
168A VAL* 5.2 7.9 - - - +
170A ASP* 5.3 4.5 + - - -
174A ASN* 3.1 32.9 + - - +
175A ALA* 3.8 4.0 - - - +
177A GLN* 1.3 75.0 - - + +
179A ILE* 1.3 60.5 + - - +
181A GLY* 3.3 2.3 + - - +
182A ILE* 2.9 34.2 + - - +
184B GLU* 3.4 33.5 + - + +
185B THR* 5.0 0.3 + - - -
187B HIS* 6.4 0.2 - - - -
188B LEU* 3.9 30.1 - - + +
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Residues in contact with ILE 179 (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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10A LEU* 4.0 21.3 - - + -
21A VAL* 3.6 28.3 - - + -
25A VAL* 4.3 13.2 - - + -
33A PHE* 5.1 2.5 - - + -
100A PHE* 3.8 26.7 - - + -
121A ILE* 4.3 26.2 - - + -
123A LEU* 4.9 1.3 - - + -
167A VAL* 4.5 8.5 - - + -
175A ALA* 2.9 25.7 + - + +
176A VAL* 3.3 4.7 + - - +
178A LYS* 1.3 73.1 - - - +
180A LYS* 1.4 66.1 + - + +
182A ILE* 3.2 8.4 + - - +
183A VAL* 3.1 28.0 + - + +
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Residues in contact with LYS 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL* 6.0 1.1 - - + -
28A ASP* 2.7 40.2 + - - +
30A GLU* 2.7 33.6 + - + +
31A THR* 3.8 23.8 - - + -
33A PHE* 5.8 2.5 - - + -
176A VAL* 2.9 21.0 + - + +
177A GLN* 3.8 24.2 - - - +
179A ILE* 1.4 76.8 - - + +
181A GLY* 1.3 57.2 + - - +
183A VAL* 3.4 5.7 + - - +
184A GLU* 3.0 30.1 + - - +
208A NA 3.1 22.8 - - - -
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Residues in contact with GLY 181 (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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177A GLN* 3.0 15.2 + - - +
178A LYS* 3.3 4.5 + - - -
180A LYS* 1.3 73.8 - - - +
182A ILE* 1.3 55.4 + - - +
184A GLU* 3.5 5.1 + - - +
185A THR* 2.7 36.8 + - - -
181B GLY* 5.0 11.4 - - - -
184B GLU* 6.5 0.9 - - - -
185B THR* 3.4 8.3 - - - -
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Residues in contact with ILE 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ILE* 3.9 14.8 - - + -
121A ILE* 4.0 17.9 - - + -
165A TYR* 3.6 48.5 - - + -
167A VAL* 3.7 28.3 - - + -
178A LYS 2.9 20.9 + - - +
179A ILE* 3.2 6.9 + - - +
181A GLY* 1.3 74.9 - - - +
183A VAL* 1.4 59.1 + - + +
185A THR* 3.3 3.5 + - - -
186A GLU* 2.9 29.2 + - + +
185B THR* 3.6 21.9 - - + +
188B LEU* 4.1 9.9 - - + -
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Residues in contact with VAL 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 4.8 0.9 - - + -
8A ILE* 3.8 34.8 - - + -
33A PHE* 3.7 31.6 - - + -
98A ASP* 3.3 25.8 - - - +
179A ILE* 3.1 18.8 + - + +
180A LYS* 4.0 4.7 - - - +
182A ILE* 1.4 79.3 - - + +
184A GLU* 1.3 63.4 + - - +
186A GLU* 3.4 8.1 + - - +
187A HIS* 3.2 32.9 + - + +
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Residues in contact with GLU 184 (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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180A LYS 3.0 18.4 + - - +
181A GLY* 3.9 5.6 - - - +
183A VAL* 1.3 75.4 - - - +
185A THR* 1.3 63.6 + - - +
187A HIS* 3.1 21.0 + - - +
188A LEU* 3.2 25.3 + - + +
178B LYS* 2.8 52.1 + - + +
181B GLY* 6.3 2.7 - - - -
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Residues in contact with THR 185 (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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165A TYR* 5.4 1.3 - - - +
181A GLY 2.7 22.0 + - - -
182A ILE 3.6 3.8 - - - -
184A GLU* 1.3 77.2 - - - +
186A GLU* 1.3 64.2 + - - +
188A LEU* 2.9 22.6 + - - +
189A LYS* 3.4 8.4 + - - -
165B TYR* 3.4 32.6 - - + +
178B LYS 4.9 0.5 + - - -
181B GLY* 3.2 15.6 + - - -
182B ILE* 3.5 15.1 + - + +
185B THR* 3.1 31.4 + - + -
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Residues in contact with GLU 186 (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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6A LEU* 3.6 20.0 - - + -
119A ILE* 3.7 34.8 - - + +
164A ASP* 5.6 0.5 - - - +
165A TYR* 2.5 35.2 + - + +
182A ILE 2.9 20.5 + - - +
183A VAL* 3.7 3.6 - - - +
185A THR* 1.3 76.5 - - - +
187A HIS* 1.4 59.5 + - - +
188A LEU 3.4 0.5 + - - -
189A LYS* 3.0 36.0 + - - +
192A ARG* 2.8 53.1 + - - +
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Residues in contact with HIS 187 (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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3A GLU* 3.9 22.3 + - - +
4A ARG 4.5 9.5 + - - -
5A GLY* 5.1 0.2 - - - -
6A LEU* 3.6 20.9 - - + +
98A ASP* 2.6 41.7 + - - -
183A VAL* 3.2 25.6 + - + -
184A GLU* 3.1 14.4 + - - +
186A GLU* 1.4 75.9 - - - +
188A LEU* 1.3 62.9 + - + +
189A LYS 3.4 0.8 + - - -
192A ARG* 4.1 16.4 - - - +
193A VAL* 3.7 12.5 - - - +
196A ARG* 3.9 10.4 + - - +
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Residues in contact with LEU 188 (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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184A GLU* 3.3 43.5 - - + +
185A THR* 2.9 10.7 + - - +
187A HIS* 1.3 79.5 - - + +
189A LYS* 1.3 65.4 + - - +
193A VAL* 3.5 6.1 - - - +
196A ARG* 5.0 8.7 - - - +
165B TYR* 3.3 13.4 - - + -
166B ALA 3.0 42.3 + - - +
167B VAL* 4.2 3.4 - - + -
168B VAL 5.9 0.4 - - - +
178B LYS* 3.7 36.6 - - + +
182B ILE* 4.1 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
------------------------------------------------------------
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