Contacts of the helix formed by residues 124 - 132 (chain B) in PDB entry 1T6S
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 TYR 124 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123B ASP* 1.3 85.1 - - + +
125B SER* 1.3 63.8 + - - +
126B ILE 3.3 2.5 - - - -
127B ASP* 3.2 22.4 + - + -
128B ARG* 3.0 40.3 + - + +
409B NO3 3.2 10.8 - - - +
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Residues in contact with SER 125 (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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95B SER 3.6 11.7 + - - -
96B MET* 4.7 3.8 - - - -
99B VAL* 3.5 27.1 - - - +
123B ASP* 2.9 25.0 + - - -
124B TYR* 1.3 77.6 - - - +
126B ILE* 1.3 58.7 + - - +
128B ARG* 2.7 31.9 + - - +
129B LEU* 2.9 36.4 + - - +
409B NO3 3.3 0.8 + - - -
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Residues in contact with ILE 126 (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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99B VAL* 3.9 22.4 - - + -
111B LYS* 3.7 37.5 - - + +
114B ILE* 4.2 23.1 - - + -
123B ASP* 5.2 1.8 - - - +
125B SER* 1.3 73.3 - - - +
127B ASP* 1.3 55.9 + - - +
129B LEU* 3.2 1.8 + - - -
130B LEU* 2.9 48.0 + - + +
135B ILE* 3.7 15.4 - - + +
150B TYR* 3.8 16.8 - - + -
409B NO3 2.7 28.8 + - - +
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Residues in contact with ASP 127 (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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111B LYS* 4.4 10.3 + - - -
124B TYR* 3.2 22.5 + - + +
126B ILE* 1.3 76.4 - - - +
128B ARG* 1.3 58.5 + - + +
130B LEU* 3.3 14.7 + - - +
131B ALA* 2.9 30.8 + - - +
409B NO3 3.0 26.1 + - - +
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Residues in contact with ARG 128 (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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92B LEU* 4.0 24.7 + - - +
95B SER* 2.7 29.9 + - - -
96B MET* 3.3 28.6 - - - +
123B ASP* 4.2 4.2 + - - +
124B TYR* 3.0 48.3 + - + +
125B SER* 2.7 28.9 + - - +
127B ASP* 1.3 78.1 - - + +
129B LEU* 1.3 60.4 + - - +
131B ALA* 3.4 3.4 + - - +
132B ARG* 3.0 51.7 + - - +
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Residues in contact with LEU 129 (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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96B MET* 3.4 39.0 - - + +
99B VAL* 3.8 16.2 - - + -
100B LEU* 3.8 50.0 - - + +
103B VAL* 5.3 0.4 - - + -
125B SER 2.9 20.4 + - - +
128B ARG* 1.3 73.4 - - - +
130B LEU* 1.3 66.1 + - - +
132B ARG* 3.3 3.6 + - - +
133B GLY 3.2 2.8 + - - -
134B LEU* 3.1 38.6 + - + -
135B ILE* 3.5 29.9 + - + -
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Residues in contact with LEU 130 (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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126B ILE* 2.9 38.7 + - + +
127B ASP* 3.7 14.1 - - - +
129B LEU* 1.3 76.9 - - - +
131B ALA* 1.3 57.6 + - - +
133B GLY* 3.0 18.0 + - - -
135B ILE* 3.6 32.3 - - + +
136B GLU* 4.0 13.5 - - - -
137B VAL* 4.7 4.5 - - + +
150B TYR* 3.8 20.0 - - + +
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Residues in contact with ALA 131 (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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161A HIS* 5.4 2.9 - - - -
127B ASP 2.9 17.8 + - - +
128B ARG* 3.4 6.7 + - - +
130B LEU* 1.3 76.6 - - - +
132B ARG* 1.3 66.2 + - - +
133B GLY 3.4 0.7 + - - -
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Residues in contact with ARG 132 (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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159A LEU 5.6 1.1 - - - +
160A PHE* 2.7 24.7 + - - +
161A HIS* 3.3 52.6 + - + +
162A LEU* 5.2 1.0 - - - +
96B MET* 3.5 35.1 - - - -
128B ARG* 3.0 43.7 + - - +
129B LEU 3.3 4.9 + - - +
130B LEU 3.1 0.8 - - - -
131B ALA* 1.3 84.5 - - - +
133B GLY* 1.3 63.3 + - - +
134B LEU* 3.2 21.6 + - + +
155B VAL* 4.9 5.0 - - - +
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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