Contacts of the helix formed by residues 145 - 151 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B VAL* 3.5 27.2 + - + +
142B ASP* 3.0 21.6 + - - -
143B LEU 3.4 9.5 + - - -
144B THR* 1.3 76.5 + - - +
146B GLN* 1.3 64.5 + - - +
147B ILE 3.3 2.2 - - - -
148B SER* 3.4 1.3 + - - -
149B LYS* 3.0 42.4 + - - +
154B TYR* 3.2 43.4 + + + -
159B GLY 3.9 6.7 + - - -
143G LEU 3.3 16.4 + - - -
144G THR 4.5 1.5 + - - -
145G HIS* 3.2 34.3 + + - -
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Residues in contact with GLN 146 (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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38B HIS* 2.7 32.9 + - - -
41B LYS* 4.6 2.3 + - - -
142B ASP* 3.3 2.0 + - - +
144B THR* 3.1 19.2 + - - +
145B HIS* 1.3 77.5 - - - +
147B ILE* 1.3 62.1 + - + +
149B LYS* 3.9 4.2 - - - +
150B ASP* 3.0 51.7 + - - +
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Residues in contact with ILE 147 (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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51B TRP* 3.8 29.2 - - + -
52B GLU 3.9 22.0 - - - +
53B GLY* 5.1 0.4 - - - -
76B PHE* 4.1 10.3 - - + -
78B PHE* 3.8 20.4 - - + -
111B CYS* 4.7 1.6 - - - -
140B LEU* 4.1 21.1 - - + -
141B SER 4.3 7.4 - - - +
142B ASP* 3.0 24.3 + - + +
146B GLN* 1.3 78.2 - - + +
148B SER* 1.3 66.0 + - - +
150B ASP* 3.2 6.9 + - - +
151B TYR* 3.0 29.3 + - + -
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Residues in contact with SER 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B PHE* 3.7 16.1 - - - -
111B CYS* 5.2 0.2 - - - -
113B VAL* 4.0 5.7 + - - +
142B ASP* 2.6 26.6 + - - +
145B HIS* 3.4 4.5 + - - -
147B ILE* 1.3 72.8 - - - +
149B LYS* 1.3 56.8 + - - +
151B TYR 3.2 1.6 + - - -
152B GLY 3.0 8.1 + - - -
153B VAL* 3.0 28.2 + - - +
154B TYR* 3.9 17.9 - - - -
161B THR* 3.1 33.3 - - - +
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Residues in contact with LYS 149 (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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38B HIS* 3.7 46.3 + - + +
39B LEU 3.8 12.3 - - - +
40B SER* 3.8 2.3 + - - -
144B THR 4.9 3.6 + - - +
145B HIS* 3.0 35.9 + - + +
146B GLN* 3.9 2.2 - - - +
148B SER* 1.3 74.1 - - - +
150B ASP* 1.3 65.8 + - - +
152B GLY* 3.1 14.2 + - - +
154B TYR* 3.7 40.7 - - + -
156B GLU* 3.8 16.4 + - - +
149G LYS* 5.3 9.1 - - - +
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Residues in contact with ASP 150 (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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38B HIS* 2.8 26.3 + - - -
41B LYS* 2.8 53.8 + - + +
42B ALA 3.4 5.9 + - - -
49B PRO* 3.8 12.5 - - + +
50B TYR 4.3 11.8 - - - +
146B GLN* 3.0 33.3 + - - +
147B ILE* 3.2 8.5 + - - +
149B LYS* 1.3 75.8 - - - +
151B TYR* 1.3 66.0 + - + +
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Residues in contact with TYR 151 (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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40B SER* 3.7 7.3 + - - -
42B ALA* 4.0 9.0 - - + +
48B ALA* 3.6 14.2 - - + +
49B PRO* 2.7 54.9 + - + +
50B TYR 5.1 0.2 - - - -
51B TRP* 3.5 23.5 + + + -
66B LEU* 3.9 1.2 - - - +
76B PHE* 3.8 16.6 - + - -
78B PHE* 3.6 28.3 - + + -
147B ILE* 3.0 21.0 + - + +
148B SER 4.0 2.0 - - - +
149B LYS 3.1 0.2 - - - -
150B ASP* 1.3 81.3 - - + +
152B GLY* 1.3 62.7 + - - +
153B VAL* 3.3 1.9 - - + +
166B PHE* 3.4 58.3 - + + -
168B ILE* 4.1 3.4 - - + +
174B LEU* 5.5 0.9 - - + -
179B 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