Contacts of the helix formed by residues 145 - 151 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113D VAL* 3.6 29.0 + - + +
142D ASP* 3.0 21.3 + - - -
143D LEU 3.2 11.5 + - - -
144D THR* 1.3 79.4 + - - +
146D GLN* 1.3 63.7 + - - +
148D SER* 3.4 2.0 + - - -
149D LYS* 3.0 42.7 + - - +
154D TYR* 3.0 43.9 + + + -
159D GLY 4.0 1.8 + - - -
143J LEU 3.2 16.4 + - - -
144J THR 4.6 1.1 + - - -
145J HIS* 3.2 33.2 + + - -
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Residues in contact with GLN 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D LYS* 4.6 3.8 + - - -
142D ASP* 3.2 2.0 + - - +
144D THR* 3.1 21.7 + - - +
145D HIS* 1.3 78.6 - - - +
147D ILE* 1.3 65.7 + - + +
149D LYS* 3.4 9.8 + - - +
150D ASP* 3.0 57.2 + - - +
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Residues in contact with ILE 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D TRP* 3.8 28.3 - - + -
52D GLU 3.9 21.8 - - - +
53D GLY* 5.1 0.4 - - - -
76D PHE* 4.0 10.5 - - + -
78D PHE* 3.8 20.9 - - + -
111D CYS* 4.6 0.9 - - - -
140D LEU* 4.0 21.3 - - + -
141D SER 4.2 11.4 - - - +
142D ASP* 3.0 22.4 + - + +
146D GLN* 1.3 79.9 - - + +
148D SER* 1.3 63.8 - - - +
150D ASP* 3.2 7.6 + - - +
151D TYR* 3.0 29.4 + - + +
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Residues in contact with SER 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D PHE* 3.8 8.3 - - - -
113D VAL* 3.8 6.4 + - - +
142D ASP* 2.6 28.9 + - - +
145D HIS* 3.7 5.2 - - - -
147D ILE* 1.3 72.9 - - - +
149D LYS* 1.3 56.6 + - - +
151D TYR 3.3 1.7 + - - -
152D GLY 3.0 21.3 + - - -
153D VAL* 3.0 22.3 + - - +
154D TYR* 3.8 19.7 - - - -
161D THR* 3.0 32.3 - - - +
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Residues in contact with LYS 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LEU 4.6 1.7 - - - +
40D SER* 4.3 8.0 - - - -
144D THR 4.9 2.8 + - - +
145D HIS* 3.0 34.5 + - - +
146D GLN* 3.9 11.0 - - - +
148D SER* 1.3 72.4 - - - +
150D ASP* 1.3 68.4 + - - +
152D GLY* 3.0 14.3 + - - +
154D TYR* 3.7 41.5 - - + -
156D GLU* 3.8 15.8 + - - +
149J LYS* 5.4 8.1 - - - +
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Residues in contact with ASP 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D LYS* 2.8 71.2 + - + +
42D ALA 3.4 4.0 + - - -
49D PRO* 4.0 12.6 - - + +
50D TYR 4.4 11.9 - - - +
146D GLN* 3.0 40.8 + - - +
147D ILE* 3.6 7.4 - - - +
149D LYS* 1.3 76.4 - - - +
151D TYR* 1.3 66.0 + - + +
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Residues in contact with TYR 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D SER* 3.6 8.0 + - - -
42D ALA* 4.0 7.5 - - + +
48D ALA* 3.7 9.9 - - + +
49D PRO* 2.7 52.0 + - + -
50D TYR 5.1 0.7 - - - -
51D TRP* 3.4 23.8 + + + -
66D LEU* 4.1 0.7 - - - +
76D PHE* 3.8 17.0 - + - -
78D PHE* 3.6 29.4 - + + -
147D ILE* 3.0 20.8 + - + +
148D SER 4.0 1.8 - - - +
149D LYS 3.1 0.4 - - - -
150D ASP* 1.3 81.9 - - + +
152D GLY* 1.3 62.0 + - - +
153D VAL* 3.3 1.7 - - + +
166D PHE* 3.4 57.3 - + + -
168D ILE* 4.0 7.7 - - + +
174D LEU* 5.5 1.3 - - + -
179D LEU* 5.6 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