Contacts of the helix formed by residues 145 - 151 (chain E) in PDB entry 3TKR
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 HIS 145 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113E VAL* 3.5 28.1 + - + +
142E ASP* 3.0 20.7 + - - -
143E LEU 3.4 9.3 + - - -
144E THR* 1.3 78.7 + - - +
146E GLN* 1.3 64.4 + - - +
147E ILE 3.3 2.7 - - - -
148E SER* 3.4 1.6 + - - -
149E LYS* 3.0 43.7 + - - +
154E TYR* 3.1 41.4 + + + -
159E GLY 3.9 6.3 + - - -
143I LEU 3.3 16.7 + - - -
144I THR 4.7 0.8 + - - -
145I HIS* 3.2 34.4 + + - -
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Residues in contact with GLN 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E LYS* 4.4 7.1 - - - +
142E ASP* 3.2 2.3 + - - +
144E THR* 3.1 20.7 - - - +
145E HIS* 1.3 78.5 - - - +
147E ILE* 1.3 67.2 + - + +
149E LYS* 3.4 8.1 + - - +
150E ASP* 3.0 60.5 + - - +
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Residues in contact with ILE 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E TRP* 3.8 28.7 - - + -
52E GLU 3.7 23.1 - - - +
76E PHE* 4.1 10.1 - - + -
78E PHE* 3.9 20.2 - - + -
111E CYS* 4.7 1.3 - - - -
140E LEU* 3.9 25.8 - - + -
141E SER 4.5 5.2 - - - +
142E ASP* 2.9 23.8 + - + +
146E GLN* 1.3 80.8 - - + +
148E SER* 1.3 62.3 + - - +
150E ASP* 3.3 7.5 + - - +
151E TYR* 3.1 29.6 + - + -
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Residues in contact with SER 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E PHE* 3.7 16.0 - - - -
111E CYS* 5.2 0.2 - - - -
113E VAL* 4.0 5.1 + - - +
142E ASP* 2.7 25.2 + - - +
145E HIS* 3.7 5.6 - - - -
147E ILE* 1.3 79.1 - - - +
149E LYS* 1.3 60.6 + - - +
151E TYR 3.4 1.2 + - - -
152E GLY 3.1 3.6 + - - -
153E VAL* 3.0 28.6 + - - +
154E TYR* 3.5 17.8 + - - -
161E THR* 3.0 32.8 - - - +
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Residues in contact with LYS 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E LEU 4.7 1.4 - - - +
40E SER* 4.1 8.7 - - - -
144E THR 4.9 3.4 + - - +
145E HIS* 3.0 34.3 + - - +
146E GLN* 3.9 8.5 - - - +
148E SER* 1.3 74.6 - - - +
150E ASP* 1.3 66.3 + - - +
152E GLY* 3.0 15.4 + - - +
154E TYR* 3.7 33.5 - - + -
156E GLU* 3.7 23.4 + - - +
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Residues in contact with ASP 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E LYS* 2.8 64.0 + - + +
42E ALA 3.4 6.2 + - - -
49E PRO* 3.9 12.0 - - + +
50E TYR 4.3 11.8 - - - +
146E GLN* 3.0 44.0 + - - +
147E ILE* 3.5 8.5 - - + +
149E LYS* 1.3 76.2 - - - +
151E TYR* 1.3 65.3 + - + +
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Residues in contact with TYR 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E SER* 3.6 8.1 + - - -
42E ALA* 4.1 8.4 - - + +
48E ALA* 3.5 15.5 - - + +
49E PRO* 2.7 47.5 + - + -
50E TYR 5.1 0.7 - - - -
51E TRP* 3.4 24.2 + + + -
66E LEU* 4.0 1.0 - - - +
76E PHE* 3.8 17.9 - + - -
78E PHE* 3.6 28.9 - + + -
147E ILE* 3.1 21.3 + - + +
148E SER 3.4 2.0 + - - +
149E LYS 3.1 0.2 - - - -
150E ASP* 1.3 80.4 - - + +
152E GLY* 1.3 63.0 + - - +
153E VAL* 3.3 3.2 + - + +
166E PHE* 3.4 56.2 - + + -
168E ILE* 4.0 6.1 - - + +
174E LEU* 5.5 1.1 - - + -
179E LEU* 5.5 0.3 - - - +
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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