Contacts of the helix formed by residues 167 - 172 (chain C) in PDB entry 1TAD
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 167 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A LYS* 6.2 0.3 - - - +
209A HIS* 4.6 15.2 + - - -
51C ILE* 3.8 43.1 - - + +
56C GLY* 5.4 1.7 - - - -
57C TYR* 5.1 13.4 + - + -
166C THR* 1.3 73.9 - - - +
168C GLN* 1.3 57.9 + - - +
170C VAL* 3.2 9.3 + - - +
171C LEU* 2.8 34.8 + - + +
325C THR* 4.9 4.2 + - - +
353C CAC 3.8 18.4 - - + +
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Residues in contact with GLN 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C TYR* 3.2 26.9 - - + +
166C THR* 3.2 6.0 + - - +
167C GLU* 1.3 78.9 - - - +
169C ASP* 1.3 57.8 + - - +
171C LEU* 3.3 8.7 + - - +
172C ARG* 2.8 66.7 + - - +
323C THR* 2.9 36.2 + - - -
325C THR* 5.6 0.2 + - - -
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Residues in contact with ASP 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ILE* 3.7 11.2 - - + +
150C TYR* 2.7 37.0 + - - -
151C TYR* 2.8 27.1 + - + -
157C ARG* 2.8 34.0 + - - -
158C LEU* 4.5 2.9 - - - +
163C TYR* 2.6 29.1 + - - +
165C PRO* 4.0 0.2 - - + -
166C THR* 3.1 29.1 + - - +
168C GLN* 1.3 76.1 - - - +
170C VAL* 1.3 62.6 + - - +
172C ARG 3.3 0.7 + - - -
173C SER* 3.2 5.7 + - - -
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Residues in contact with VAL 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LYS* 3.6 8.3 - - + -
57C TYR* 3.7 30.3 - - + +
62C CYS* 4.5 15.0 - - - -
65C PHE* 3.6 47.8 - - + -
69C ILE* 5.0 0.7 - - - -
165C PRO* 4.1 14.1 - - + -
166C THR 3.1 15.3 + - - +
167C GLU* 3.2 9.8 + - - +
169C ASP* 1.3 75.3 - - - +
171C LEU* 1.3 61.6 + - + +
173C SER* 2.7 26.9 + - - -
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Residues in contact with LEU 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C THR* 3.7 20.7 + - + +
47C LYS* 3.8 31.3 + - + +
48C GLN* 3.5 34.1 - - + +
51C ILE* 4.0 15.9 - - + -
167C GLU* 2.8 25.0 + - + +
168C GLN* 3.3 14.1 + - - +
170C VAL* 1.3 76.7 - - + +
172C ARG* 1.3 52.2 + - - +
173C SER 3.6 2.8 + - - +
323C THR* 3.5 31.8 - - + +
325C THR* 3.8 11.9 - - - +
351C GDP 2.7 22.5 + - - -
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Residues in contact with ARG 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C ASP 5.0 3.0 + - - -
147C SER* 2.6 41.0 + - - +
150C TYR* 3.6 50.2 - - + +
151C TYR* 3.1 19.0 + - + +
168C GLN* 2.8 48.4 + - - +
169C ASP 3.8 0.7 - - - +
170C VAL 3.2 0.2 - - - -
171C LEU* 1.3 73.9 - - - +
173C SER* 1.3 59.9 - - - +
174C ARG* 3.8 0.9 + - - +
268C ASP* 4.5 7.1 + - - -
323C THR* 4.0 15.5 + - - +
351C GDP 3.0 42.3 + - - -
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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