Contacts of the helix formed by residues 117 - 128 (chain B) 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 LYS 117 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115B MET 3.9 0.6 + - - -
116B PRO* 1.3 70.6 - - - +
118B GLU* 1.3 59.8 + - + +
120B SER* 2.8 23.6 + - - +
121B ASP* 2.8 49.8 + - - +
159B VAL* 5.9 3.6 + - - +
161B PRO* 6.0 5.5 - - - +
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Residues in contact with GLU 118 (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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102B LYS* 2.9 34.7 + - - +
106B MET* 3.5 22.0 - - + +
116B PRO* 3.4 4.4 - - + +
117B LYS* 1.3 79.5 - - + +
119B MET* 1.3 58.2 + - - +
121B ASP* 3.9 11.2 - - - +
122B ILE* 3.1 31.1 + - + +
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Residues in contact with MET 119 (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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74B LEU* 3.8 25.1 - - + -
103B LEU* 3.9 9.6 - - + -
106B MET* 3.7 50.0 - - + -
107B ALA 3.9 1.6 - - - +
110B ILE* 3.7 36.3 - - + -
115B MET* 3.7 23.8 - - - +
116B PRO* 2.9 17.5 + - + +
118B GLU* 1.3 77.2 - - - +
120B SER* 1.3 67.5 + - - +
122B ILE* 3.2 6.5 + - - +
123B ILE* 3.0 33.2 + - + +
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Residues in contact with SER 120 (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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115B MET* 4.0 10.0 + - - -
116B PRO 2.9 7.9 + - - -
117B LYS* 2.8 31.2 + - - +
119B MET* 1.3 78.6 - - - +
121B ASP* 1.3 63.7 + - - +
123B ILE* 3.4 1.2 + - - -
124B GLN* 3.0 33.2 + - - +
155B LEU* 3.6 12.9 - - - +
159B VAL* 3.7 38.5 - - - +
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Residues in contact with ASP 121 (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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117B LYS* 2.8 49.5 + - - +
118B GLU* 3.9 10.0 - - - +
119B MET 3.2 0.2 - - - -
120B SER* 1.3 74.3 + - - +
122B ILE* 1.3 63.0 + - - +
124B GLN* 3.2 13.6 + - - +
125B ARG* 3.1 42.2 + - - +
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Residues in contact with ILE 122 (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 ASP* 3.4 29.2 - - + +
102B LYS* 3.5 38.6 - - + +
103B LEU* 4.1 11.9 - - + +
106B MET* 4.0 12.3 - - - -
118B GLU* 3.1 17.2 + - + +
119B MET* 3.2 7.9 + - - +
121B ASP* 1.3 77.1 - - + +
123B ILE* 1.3 63.7 + - - +
125B ARG* 3.1 29.4 + - - +
126B LEU* 2.9 40.4 + - + +
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Residues in contact with ILE 123 (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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73B THR* 5.0 1.6 - - + -
74B LEU* 4.6 2.2 - - + -
77B ILE* 4.0 34.5 - - + +
103B LEU* 3.9 17.3 - - + -
115B MET* 3.8 33.2 - - + -
119B MET* 3.0 27.2 + - + +
120B SER* 3.8 4.0 - - - +
122B ILE* 1.3 73.9 - - - +
124B GLN* 1.3 57.7 + - - +
126B LEU* 3.3 9.0 + - - +
127B TRP* 2.8 28.1 + - + +
152B LEU* 4.1 20.6 - - + +
155B LEU* 3.7 16.6 - - + -
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Residues in contact with GLN 124 (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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120B SER* 3.0 27.9 + - - +
121B ASP* 3.7 12.0 + - - +
122B ILE 3.2 0.2 - - - -
123B ILE* 1.3 76.4 - - - +
125B ARG* 1.3 63.0 + - + +
127B TRP* 3.2 8.2 + - - +
128B LYS* 3.1 36.9 + - + +
152B LEU 5.8 0.4 - - - +
155B LEU* 3.5 21.9 - - + +
156B GLU* 4.0 38.6 + - - +
159B VAL* 4.4 9.7 - - - +
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Residues in contact with ARG 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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96B ARG* 3.5 34.3 + - - +
99B ASP* 2.9 36.3 + - - +
121B ASP* 3.1 27.0 + - - +
122B ILE* 3.1 28.0 + - - +
124B GLN* 1.3 75.2 - - + +
126B LEU* 1.3 62.8 + - - +
128B LYS* 3.4 29.5 + - - +
129B ASP 3.4 8.8 + - - -
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Residues in contact with LEU 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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77B ILE* 4.1 17.9 - - + -
81B VAL* 4.3 6.7 - - + -
91B TYR* 4.1 15.5 - - + +
96B ARG* 3.8 38.8 - - + +
99B ASP* 4.0 7.9 - - + -
100B ALA* 4.2 6.7 - - - +
103B LEU* 3.7 23.1 - - + -
122B ILE* 2.9 38.2 + - + +
123B ILE* 3.5 7.0 - - - +
125B ARG* 1.3 77.2 - - - +
127B TRP* 1.3 62.0 + - - +
129B ASP* 3.0 11.8 + - - +
132B ILE* 3.1 25.9 - - + +
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Residues in contact with TRP 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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77B ILE* 4.8 3.8 - - + +
80B ILE* 4.0 6.1 - - + -
123B ILE* 2.8 21.4 + - + +
124B GLN* 3.2 8.3 + - - +
126B LEU* 1.3 73.1 - - - +
128B LYS* 1.3 63.7 + - + +
129B ASP 3.5 0.7 + - - +
132B ILE* 4.1 9.2 - - + -
133B GLN* 2.7 58.4 + - - +
136B PHE* 3.8 42.4 - + + -
149B GLY* 4.0 17.7 - - - -
152B LEU* 3.8 51.1 - - + +
153B SER* 3.4 28.5 - - - +
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Residues in contact with LYS 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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124B GLN* 3.1 27.0 + - + +
125B ARG* 3.6 26.1 - - - +
126B LEU 3.1 0.4 - - - -
127B TRP* 1.3 82.6 - - + +
129B ASP* 1.3 63.3 + - - +
130B SER* 3.4 2.6 + - - -
133B GLN* 5.0 3.4 - - - +
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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