Contacts of the helix formed by residues 171 - 188 (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 VAL 171 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B ASN* 4.2 2.7 - - - -
170B ASP* 1.3 86.5 + - + +
172B VAL* 1.3 68.2 + - - +
173B ALA* 4.0 16.2 - - + +
174B ASN* 2.9 41.7 + - - +
175B ALA* 3.2 10.7 + - - +
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Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B THR* 4.0 30.5 - - + +
21B VAL* 4.3 9.2 - - + -
24B ALA* 3.6 30.7 - - + -
169B ASN* 3.7 23.7 + - - +
171B VAL* 1.3 70.4 - - - +
173B ALA* 1.4 64.0 + - - +
175B ALA* 3.1 6.6 + - - +
176B VAL* 3.0 22.8 + - + +
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Residues in contact with ALA 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ALA* 6.1 0.2 - - - -
171B VAL* 3.3 11.9 - - + +
172B VAL* 1.4 77.0 - - - +
174B ASN* 1.4 62.6 + - - +
176B VAL* 3.5 9.6 + - - +
177B GLN* 3.1 37.3 + - - +
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Residues in contact with ASN 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ASP* 3.2 27.8 + - - +
171B VAL* 2.9 31.7 + - - +
173B ALA* 1.4 75.7 - - - +
175B ALA* 1.4 66.1 + - - +
177B GLN* 3.4 14.6 + - - +
178B LYS* 3.1 42.0 + - - +
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Residues in contact with ALA 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B VAL* 4.1 23.1 - - + -
123B LEU* 4.2 7.4 - - + -
167B VAL* 3.7 23.8 - - + -
168B VAL 3.9 11.0 - - - +
169B ASN* 4.3 3.8 - - - +
170B ASP* 4.5 1.2 + - - -
171B VAL 3.2 8.0 + - - +
172B VAL 3.1 9.4 + - - +
174B ASN* 1.4 71.8 - - - +
176B VAL* 1.3 59.9 + - - +
178B LYS* 3.4 2.5 + - - +
179B ILE* 3.0 36.8 + - - +
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Residues in contact with VAL 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B VAL* 4.0 5.4 - - + +
24B ALA* 3.6 31.0 - - + +
25B VAL* 3.9 36.5 - - + +
28B ASP* 3.8 24.9 - - + +
172B VAL* 3.0 20.4 + - + +
173B ALA* 3.6 10.5 - - - +
174B ASN 3.3 0.2 - - - -
175B ALA* 1.3 76.6 - - - +
177B GLN* 1.3 57.7 + - + +
179B ILE* 3.3 3.0 + - - +
180B LYS* 2.9 34.6 + - + +
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Residues in contact with GLN 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ASP* 5.5 0.7 - - - +
173B ALA* 3.1 32.7 + - - +
174B ASN* 3.4 13.3 + - - +
176B VAL* 1.3 76.9 - - + +
178B LYS* 1.3 57.6 + - + +
180B LYS* 3.4 25.4 + - - +
181B GLY* 2.9 26.0 + - - -
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Residues in contact with LYS 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A GLU* 2.8 35.8 + - + +
185A THR* 4.9 0.3 + - - -
188A LEU* 3.7 28.4 - - + +
167B VAL* 4.0 23.3 - - + -
168B VAL* 5.3 5.4 - - - +
170B ASP* 5.3 4.0 + - - +
174B ASN* 3.1 37.2 + - - +
175B ALA 3.7 4.0 - - - +
177B GLN* 1.3 75.0 - - + +
179B ILE* 1.3 58.4 + - - +
181B GLY* 3.3 2.2 + - - -
182B ILE* 2.9 34.2 + - - +
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Residues in contact with ILE 179 (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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10B LEU* 4.0 21.1 - - + -
21B VAL* 3.6 28.9 - - + -
25B VAL* 4.4 11.0 - - + -
33B PHE* 4.7 4.7 - - + -
100B PHE* 3.7 26.7 - - + -
121B ILE* 4.3 26.0 - - + -
123B LEU* 4.9 4.0 - - + -
167B VAL* 4.5 6.1 - - + -
175B ALA* 3.0 25.0 + - + +
176B VAL* 3.7 4.5 - - - +
178B LYS* 1.3 76.0 - - - +
180B LYS* 1.4 62.9 + - - +
182B ILE* 3.2 9.8 + - - +
183B VAL* 3.1 28.4 + - + +
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Residues in contact with LYS 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL* 5.8 1.8 - - + -
28B ASP* 2.8 45.0 + - - +
30B GLU* 3.3 27.2 + - + +
31B THR* 4.5 9.4 - - - +
33B PHE* 4.4 24.1 - - + -
176B VAL* 2.9 21.1 + - + +
177B GLN* 3.8 28.1 - - - +
179B ILE* 1.4 75.3 - - + +
181B GLY* 1.3 57.6 + - - +
183B VAL* 3.4 2.9 + - - +
184B GLU* 3.0 29.3 + - - +
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Residues in contact with GLY 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A GLY* 5.0 11.8 - - - -
184A GLU* 6.3 1.8 - - - -
185A THR* 3.4 8.3 - - - -
177B GLN 2.9 15.2 + - - -
178B LYS* 3.6 4.7 - - - -
180B LYS* 1.3 74.7 - - - +
182B ILE* 1.4 55.7 + - - +
184B GLU* 3.5 5.4 + - - +
185B THR* 2.7 37.8 + - - -
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Residues in contact with ILE 182 (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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185A THR* 3.6 23.2 - - + +
188A LEU* 4.1 9.9 - - + -
119B ILE* 3.9 15.5 - - + -
121B ILE* 4.0 17.5 - - + -
165B TYR* 3.7 48.2 - - + -
167B VAL* 3.7 28.3 - - + -
178B LYS 2.9 20.3 + - - +
179B ILE* 3.2 6.7 + - - +
181B GLY* 1.4 75.6 - - - +
183B VAL* 1.3 60.4 + - + +
185B THR* 3.3 2.6 + - - -
186B GLU* 2.9 29.5 + - + +
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Residues in contact with VAL 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 4.0 3.2 - - + +
8B ILE* 3.8 42.4 - - + -
33B PHE* 3.2 45.1 - - + -
98B ASP* 3.3 20.4 - - - +
179B ILE* 3.1 16.1 + - + +
180B LYS 3.9 2.7 - - - +
181B GLY 3.4 0.2 - - - -
182B ILE* 1.3 77.5 - - + +
184B GLU* 1.3 62.8 + - - +
186B GLU* 3.4 7.7 + - - +
187B HIS* 3.2 21.4 + - + +
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Residues in contact with GLU 184 (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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178A LYS* 3.4 40.5 + - + +
181A GLY* 6.5 0.9 - - - -
180B LYS 3.0 17.5 + - - +
181B GLY* 3.9 5.6 - - - +
183B VAL* 1.3 77.0 - - - +
185B THR* 1.3 62.7 + - - +
187B HIS* 3.1 35.2 + - - +
188B LEU* 3.2 25.5 + - + +
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Residues in contact with THR 185 (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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165A TYR* 3.4 34.8 - - + +
178A LYS 5.0 0.5 + - - -
181A GLY* 3.2 15.8 + - - -
182A ILE* 3.5 14.0 + - + +
185A THR* 3.1 31.7 + - + -
165B TYR* 5.4 1.1 - - - +
181B GLY 2.7 22.0 + - - -
182B ILE 3.6 4.0 - - - -
184B GLU* 1.3 77.4 - - - +
186B GLU* 1.3 62.5 + - - +
188B LEU* 2.9 22.6 + - - +
189B LYS* 3.4 8.6 + - - -
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Residues in contact with GLU 186 (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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6B LEU* 4.0 12.3 - - + -
119B ILE* 3.8 30.6 - - + +
164B ASP* 5.6 1.0 - - - +
165B TYR* 2.5 34.3 + - - +
182B ILE 2.9 20.8 + - - +
183B VAL* 3.7 6.5 - - - +
185B THR* 1.3 74.4 - - - +
187B HIS* 1.3 61.3 + - - +
188B LEU 3.4 0.9 + - - -
189B LYS* 3.0 35.9 + - - +
192B ARG* 2.8 59.4 + - - +
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Residues in contact with HIS 187 (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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178A LYS* 6.4 0.2 - - - -
6B LEU* 4.1 12.2 - - + +
98B ASP* 6.0 0.7 - - - +
183B VAL* 3.2 12.0 + - + +
184B GLU* 3.1 31.0 + - - +
186B GLU* 1.3 74.5 - - - +
188B LEU* 1.3 71.7 + - + +
189B LYS 3.4 0.8 + - - -
192B ARG* 4.1 14.3 - - - +
193B VAL* 3.7 12.9 + - - +
196B ARG* 3.7 36.4 + - - -
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Residues in contact with LEU 188 (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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165A TYR* 3.3 13.3 - - + -
166A ALA 3.0 39.8 + - - +
167A VAL* 4.2 4.3 - - + -
168A VAL 5.9 0.2 - - - +
178A LYS* 3.9 45.5 - - + +
182A ILE* 4.1 19.1 - - + -
184B GLU* 3.3 27.1 - - + +
185B THR* 2.9 10.0 + - - +
187B HIS* 1.3 92.1 - - + +
189B LYS* 1.4 65.6 + - - +
193B VAL* 3.5 8.8 - - + +
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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