Contacts of the helix formed by residues 144 - 155 (chain A) in PDB entry 1TU3
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 ASP 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A ARG* 4.3 5.3 - - - +
142A ALA 4.1 2.0 + - - -
143A VAL* 1.3 74.4 - - - +
145A PHE* 1.3 70.4 + - - +
146A GLN* 3.1 17.6 + - - +
147A GLU* 2.7 40.5 + - + +
148A ALA* 3.2 20.3 + - - +
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Residues in contact with PHE 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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141A ARG* 3.7 19.1 - - - +
143A VAL 3.2 4.4 + - - -
144A ASP* 1.3 75.9 + - - +
146A GLN* 1.3 68.2 + - + +
148A ALA* 3.5 3.4 + - - +
149A GLN* 2.9 49.9 + - + +
159A PHE* 3.6 18.0 - + - -
160A MET* 5.8 0.9 - - - -
161A GLU* 3.2 44.0 - - + -
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Residues in contact with GLN 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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144A ASP* 3.1 14.5 + - - +
145A PHE* 1.3 85.9 - - + +
147A GLU* 1.3 54.4 + - - +
148A ALA 3.0 4.3 - - - -
149A GLN* 3.3 25.6 - - - +
150A SER* 2.8 52.4 + - - +
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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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105A GLU* 4.2 16.4 - - - +
108A PHE* 4.3 21.3 - - + -
112A LYS* 5.2 4.8 + - - +
143A VAL* 4.1 7.3 - - - +
144A ASP* 2.7 44.3 + - + +
146A GLN* 1.3 70.9 - - - +
148A ALA* 1.3 57.3 + - - +
150A SER* 4.1 4.9 - - - -
151A TYR* 3.7 19.2 + - - +
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Residues in contact with ALA 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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100A TYR* 3.3 25.6 - - + +
108A PHE* 3.8 23.8 - - + -
130A LEU* 4.2 4.7 - - - +
143A VAL* 4.3 3.4 - - + -
144A ASP 3.2 13.8 + - - +
145A PHE* 3.8 0.9 - - - +
146A GLN 3.0 0.6 - - - -
147A GLU* 1.3 75.8 - - - +
149A GLN* 1.3 65.9 + - - +
150A SER 3.1 1.1 - - - -
151A TYR* 3.8 2.2 - - - +
152A ALA* 3.1 23.9 + - - +
159A PHE* 3.7 13.0 - - + -
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Residues in contact with GLN 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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145A PHE* 2.9 37.3 + - + +
146A GLN* 3.2 22.9 + - - +
148A ALA* 1.3 77.4 - - - +
150A SER* 1.3 61.0 + - - +
152A ALA* 3.8 0.8 - - - +
153A ASP* 3.1 51.3 + - - +
157A LEU 5.9 0.2 + - - -
159A PHE* 3.5 37.7 + - + +
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Residues in contact with SER 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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146A GLN* 2.8 36.6 + - - +
147A GLU* 4.3 5.7 - - - -
148A ALA 3.1 0.2 - - - -
149A GLN* 1.3 74.7 - - - +
151A TYR* 1.3 65.5 + - - +
153A ASP* 3.2 7.7 + - - +
154A ASP* 2.9 36.2 + - - +
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Residues in contact with TYR 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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108A PHE* 4.3 13.2 - + + -
111A ALA* 6.3 0.4 - - + -
112A LYS* 3.4 50.6 + - + +
115A VAL* 3.2 35.3 - - + +
130A LEU* 4.1 20.6 - - + -
147A GLU 3.7 16.3 + - - +
148A ALA* 3.6 4.2 + - - +
150A SER* 1.3 78.7 - - - +
152A ALA* 1.3 64.9 + - - +
154A ASP* 3.5 6.5 + - - +
155A ASN* 3.0 55.2 + - - +
157A LEU* 3.6 18.4 - - + -
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Residues in contact with ALA 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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130A LEU* 4.1 6.3 - - + -
148A ALA 3.1 14.4 + - - +
149A GLN* 3.8 4.9 - - - +
151A TYR* 1.3 78.3 - - - +
153A ASP* 1.3 57.3 + - - +
155A ASN 3.0 2.1 + - - -
156A SER 2.9 24.6 + - - -
157A LEU* 2.9 35.6 + - + +
159A PHE* 3.4 33.0 - - + -
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Residues in contact with ASP 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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146A GLN* 5.7 0.3 + - - -
149A GLN* 3.1 42.4 + - - +
150A SER* 3.2 6.3 + - - +
152A ALA* 1.3 75.9 - - - +
154A ASP* 1.3 66.3 + - - +
155A ASN 3.2 1.0 + - - -
156A SER* 3.2 15.3 + - - +
157A LEU 5.0 4.8 - - - +
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Residues in contact with ASP 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 SER* 2.9 25.2 + - - +
151A TYR* 3.9 7.1 + - - +
153A ASP* 1.3 77.8 - - - +
155A ASN* 1.3 66.6 + - - +
156A SER* 3.6 0.7 - - - -
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Residues in contact with ASN 155 (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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115A VAL* 4.8 0.2 - - + -
119A GLN* 3.4 32.3 + - - +
151A TYR* 3.0 50.2 + - - +
152A ALA 3.0 2.4 + - - -
154A ASP* 1.3 84.5 + - - +
156A SER* 1.3 71.1 + - - +
157A LEU* 3.2 33.8 + - + +
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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
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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