Contacts of the helix formed by residues 148 - 158 (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 ALA 148 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C SER* 3.5 32.7 + - - +
80C ILE* 5.1 0.2 - - + -
136C PHE* 4.4 3.8 - - + -
144C LEU* 3.6 23.6 - - + -
145C ASN 3.1 19.3 + - - +
146C ASP 3.2 1.2 - - - -
147C SER* 1.3 76.0 - - - +
149C GLY* 1.3 64.0 + - - +
151C TYR* 4.1 1.2 - - - +
152C LEU* 3.0 36.2 + - + +
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Residues in contact with GLY 149 (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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127C TRP* 3.9 10.8 - - - -
136C PHE* 3.7 27.4 - - - -
146C ASP 4.5 3.4 + - - -
147C SER 3.4 0.4 - - - -
148C ALA* 1.3 78.8 - - - +
150C TYR* 1.3 54.4 + - - +
153C SER* 2.7 39.9 + - - -
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Residues in contact with TYR 150 (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 5.3 0.6 + - - -
147C SER* 3.4 10.7 + - - +
148C ALA 3.3 0.2 - - - -
149C GLY* 1.3 75.9 - - - +
151C TYR* 1.3 90.2 + + - +
153C SER* 3.2 15.6 + - - -
154C ASP* 3.4 19.5 - - + +
157C ARG* 3.8 12.0 + - - -
166C THR* 4.3 0.9 + - - -
168C GLN* 3.2 36.3 - - + +
169C ASP* 2.7 29.5 + - - -
172C ARG* 3.6 49.8 - - + +
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Residues in contact with TYR 151 (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 19.9 - - + +
72C ASN* 3.8 29.6 - - + -
73C THR* 3.4 29.8 - - + +
76C SER* 5.6 0.4 - - - -
145C ASN* 6.5 0.2 - - + -
147C SER* 3.1 34.4 + - - +
148C ALA* 4.1 3.1 - - - +
150C TYR* 1.3 102.2 - + - +
152C LEU* 1.3 66.3 + - - +
154C ASP* 3.1 5.5 + - - -
155C LEU* 3.0 20.1 + - - +
158C LEU* 3.3 24.5 - - + +
169C ASP* 2.8 30.3 + - + -
172C ARG* 3.9 5.8 - - + -
173C SER* 2.9 21.1 + - - -
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Residues in contact with LEU 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C THR* 3.7 26.7 - - + +
76C SER* 4.1 14.1 - - - -
77C ILE* 4.1 8.5 - - + +
80C ILE* 3.9 17.0 - - + -
123C ILE* 3.6 31.0 - - + -
124C GLN* 4.5 3.3 + - - -
127C TRP* 3.5 52.6 - - + +
148C ALA 3.0 25.0 + - - +
151C TYR* 1.3 76.6 - - + +
153C SER* 1.3 61.7 + - - +
154C ASP 3.2 0.7 + - - -
155C LEU* 3.3 19.3 + - + +
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Residues in contact with SER 153 (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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124C GLN* 6.0 0.4 - - - -
127C TRP* 3.6 23.0 - - - +
149C GLY 2.7 24.6 + - - -
150C TYR* 3.2 9.9 + - - -
152C LEU* 1.3 76.3 - - - +
154C ASP* 1.3 58.1 + - - +
155C LEU 3.5 0.6 + - - -
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Residues in contact with ASP 154 (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* 3.4 21.8 + - + +
151C TYR* 3.1 5.9 + - - +
152C LEU 3.1 0.6 - - - -
153C SER* 1.3 81.9 + - - +
155C LEU* 1.3 61.7 + - - +
156C GLU* 3.2 4.6 + - - +
157C ARG* 3.0 58.3 + - - +
158C LEU* 3.3 15.4 + - + +
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Residues in contact with LEU 155 (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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70C TYR* 6.2 1.3 - - + -
73C THR* 3.9 24.9 - - + -
115C MET* 5.0 7.0 - - + -
120C SER* 3.9 16.6 - - - +
123C ILE* 3.5 37.7 - - + -
124C GLN* 3.5 23.0 - - - +
127C TRP* 6.2 0.7 - - + -
151C TYR 3.0 6.0 + - - +
152C LEU* 3.3 17.7 + - + +
153C SER 3.5 1.2 + - - -
154C ASP* 1.3 75.9 - - - +
156C GLU* 1.3 62.4 + - - +
158C LEU* 3.2 10.9 + - + -
159C VAL* 2.9 46.9 + - + +
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Residues in contact with GLU 156 (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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64A GLU* 5.2 5.7 - - - +
124C GLN* 3.6 24.8 + - - +
154C ASP* 3.2 1.5 + - - +
155C LEU* 1.3 77.0 - - - +
157C ARG* 1.3 57.1 + - - +
159C VAL* 3.3 9.8 + - - +
160C THR* 2.7 33.5 + - - -
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Residues in contact with ARG 157 (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* 3.8 9.3 + - - -
154C ASP* 3.0 43.9 + - - +
156C GLU* 1.3 79.0 - - - +
158C LEU* 1.3 73.7 + - - +
160C THR* 3.2 23.0 + - - -
163C TYR* 3.6 23.1 - - + +
164C VAL 5.2 0.2 + - - -
166C THR* 3.8 18.3 + - - +
169C ASP* 2.8 42.6 + - - -
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Residues in contact with LEU 158 (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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69C ILE* 4.3 8.1 - - + -
70C TYR* 2.7 35.1 + - + -
73C THR* 4.1 9.4 - - - +
151C TYR* 3.3 52.5 - - + +
154C ASP* 3.3 10.1 + - + +
155C LEU* 3.2 17.2 + - + +
157C ARG* 1.3 110.7 - - - +
159C VAL* 1.3 52.1 + - - +
163C TYR* 3.2 38.1 - - + +
169C ASP* 4.2 3.1 - - - +
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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