Contacts of the helix formed by residues 144 - 155 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141C ARG* 4.2 1.6 - - - +
142C ALA 4.2 1.2 + - - -
143C VAL* 1.3 75.0 - - - +
145C PHE* 1.3 67.1 + - - +
146C GLN* 3.0 22.7 + - - +
147C GLU* 3.2 28.3 + - + +
148C ALA* 2.9 22.5 + - - +
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Residues in contact with PHE 145 (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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141C ARG* 2.9 23.3 - - - +
143C VAL* 5.6 0.2 - - - -
144C ASP* 1.3 71.9 + - - +
146C GLN* 1.3 72.5 + - + +
148C ALA* 2.9 10.6 + - - +
149C GLN* 2.6 64.1 + - + +
159C PHE* 3.5 16.2 - + - -
160C MET* 5.6 1.3 - - - -
161C GLU* 3.1 40.2 - - + +
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Residues in contact with GLN 146 (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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144C ASP* 3.0 10.0 + - - +
145C PHE* 1.3 93.9 - - + +
147C GLU* 1.3 57.4 + - - +
149C GLN* 3.5 16.5 - - - +
150C SER* 2.6 48.1 + - - +
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Residues in contact with GLU 147 (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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108C PHE* 4.0 25.9 - - + -
112C LYS* 5.3 4.9 + - - +
143C VAL* 4.4 3.5 - - - +
144C ASP* 3.2 37.4 + - + +
146C GLN* 1.3 76.6 - - - +
148C ALA* 1.3 58.1 + - - +
150C SER* 3.4 4.1 + - - -
151C TYR* 2.9 30.3 + - + +
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Residues in contact with ALA 148 (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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100C TYR* 3.5 13.5 - - - +
108C PHE* 4.2 23.3 - - + -
130C LEU* 4.2 3.7 - - + +
143C VAL* 4.4 2.7 - - + -
144C ASP 2.9 11.1 + - - +
145C PHE* 2.9 9.2 + - - +
147C GLU* 1.3 76.4 - - - +
149C GLN* 1.3 57.6 + - - +
151C TYR* 3.6 2.5 - - - +
152C ALA* 2.9 28.9 + - - +
159C PHE* 3.4 28.8 - - + -
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Residues in contact with GLN 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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145C PHE* 2.6 41.0 + - + +
146C GLN* 3.5 22.9 - - - +
148C ALA* 1.3 72.0 - - - +
150C SER* 1.3 61.1 + - - +
152C ALA* 3.3 10.7 + - - +
153C ASP* 2.6 51.0 + - - +
159C PHE* 3.7 26.5 + - + +
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Residues in contact with SER 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 GLN* 2.6 31.5 + - - +
147C GLU* 3.8 5.2 - - - -
149C GLN* 1.3 71.3 - - - +
151C TYR* 1.3 56.9 + - - +
153C ASP* 3.0 11.0 + - - +
154C ASP* 2.4 46.4 + - - +
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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
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108C PHE* 4.4 4.3 - + + -
112C LYS* 3.3 71.3 + - + +
115C VAL* 3.6 19.6 - - + +
119C GLN* 5.5 0.3 + - - -
130C LEU* 4.0 20.9 - - + -
147C GLU* 2.9 22.6 + - + +
148C ALA* 3.6 4.5 - - - +
150C SER* 1.3 73.6 - - - +
152C ALA* 1.3 63.8 + - - +
154C ASP* 3.4 6.3 + - - -
155C ASN* 2.5 64.7 + - - +
157C LEU* 3.5 18.8 - - + -
812G ASP* 5.5 9.6 - - + -
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Residues in contact with ALA 152 (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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130C LEU* 4.6 1.1 - - + -
148C ALA 2.9 9.4 + - - +
149C GLN* 3.3 12.6 - - - +
150C SER 3.2 0.2 - - - -
151C TYR* 1.3 76.0 - - - +
153C ASP* 1.3 57.1 + - - +
155C ASN 3.0 2.1 + - - -
156C SER 2.9 9.0 + - - -
157C LEU* 2.7 53.9 + - + +
159C PHE* 3.3 36.6 - - + +
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Residues in contact with ASP 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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149C GLN* 2.6 44.9 + - - +
150C SER* 3.4 9.0 - - - +
152C ALA* 1.3 70.7 - - - +
154C ASP* 1.3 63.8 + - - +
155C ASN 2.9 10.4 + - - -
156C SER* 3.1 13.2 + - - +
157C LEU 5.4 1.7 - - - +
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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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81A ARG* 5.5 1.5 + - - +
150C SER* 2.4 42.0 + - - +
151C TYR* 3.4 8.1 + - - +
153C ASP* 1.3 78.4 - - - +
155C ASN* 1.3 62.8 + - - +
156C SER* 3.6 0.8 + - - -
813G VAL* 6.5 1.6 - - + -
816G GLN* 3.0 36.1 + - - +
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Residues in contact with ASN 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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115C VAL* 5.2 0.2 - - + -
119C GLN* 3.6 30.3 + - - +
151C TYR* 2.5 59.0 + - + +
152C ALA 3.0 1.0 + - - -
153C ASP 2.9 0.8 - - - -
154C ASP* 1.3 86.4 - - - +
156C SER* 1.3 74.1 + - - +
157C LEU* 3.4 22.0 + - + +
812G ASP* 5.5 4.2 - - - +
816G GLN* 3.8 15.2 + - - +
819G ARG* 4.9 4.3 + - - -
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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