Contacts of the helix formed by residues 145 - 151 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143D LEU 3.3 15.9 + - - -
144D THR* 4.7 1.5 + - - -
145D HIS* 3.2 34.0 + + - -
113J VAL* 3.6 27.5 + - + +
142J ASP* 3.0 22.3 + - - -
143J LEU 3.4 8.6 + - - -
144J THR* 1.3 78.5 + - - +
146J GLN* 1.3 63.1 + - - +
148J SER* 3.5 1.5 + - - -
149J LYS* 3.0 44.2 + - - +
154J TYR* 3.2 41.9 + + + -
159J GLY 3.9 7.0 + - - -
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Residues in contact with GLN 146 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41J LYS* 5.6 3.2 - - - +
142J ASP* 3.1 3.0 + - - +
144J THR* 3.2 19.1 + - - +
145J HIS* 1.3 78.8 - - - +
147J ILE* 1.3 65.5 + - + +
149J LYS* 3.9 6.0 - - - +
150J ASP* 3.0 41.7 + - - +
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Residues in contact with ILE 147 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50J TYR 6.2 0.2 - - - -
51J TRP* 3.8 27.4 - - + -
52J GLU 4.0 20.2 - - - +
53J GLY* 5.1 0.4 - - - -
76J PHE* 4.0 10.3 - - + -
78J PHE* 3.8 20.9 - - + -
111J CYS* 4.6 1.1 - - - -
140J LEU* 3.7 25.4 - - + -
141J SER 4.3 7.2 - - - +
142J ASP* 3.0 25.2 + - + +
146J GLN* 1.3 81.1 - - + +
148J SER* 1.3 64.6 + - - +
150J ASP* 3.1 7.8 + - - +
151J TYR* 3.0 29.1 + - + -
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Residues in contact with SER 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78J PHE* 3.8 16.5 - - - -
111J CYS* 5.1 0.2 - - - -
113J VAL* 3.9 6.1 + - - +
142J ASP* 2.6 28.8 + - - +
145J HIS* 3.8 5.6 - - - -
147J ILE* 1.3 74.3 - - - +
149J LYS* 1.3 58.1 + - - +
151J TYR 3.2 2.3 + - - -
152J GLY 3.0 21.8 + - - -
153J VAL* 3.1 12.9 + - - +
154J TYR* 3.9 17.5 - - - -
161J THR* 3.1 33.0 - - - +
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Residues in contact with LYS 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39J LEU 4.6 2.1 - - - +
40J SER* 4.2 8.1 - - - -
144J THR 4.8 3.8 + - - +
145J HIS* 3.0 34.4 + - + +
146J GLN* 4.0 5.6 - - - +
148J SER* 1.3 75.5 - - - +
150J ASP* 1.3 66.2 + - - +
152J GLY* 3.1 13.9 + - - +
154J TYR* 3.8 41.2 - - + -
156J GLU* 3.9 16.1 + - - +
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Residues in contact with ASP 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41J LYS* 2.9 73.6 + - + +
42J ALA 3.4 3.5 + - - -
49J PRO* 3.9 9.4 - - + +
50J TYR 4.4 11.5 - - - +
146J GLN* 3.0 40.6 + - - +
147J ILE* 3.1 7.5 + - - +
149J LYS* 1.3 77.2 - - - +
151J TYR* 1.3 65.7 + - + +
152J GLY 3.3 0.2 - - - -
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Residues in contact with TYR 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40J SER* 3.6 7.3 + - - -
42J ALA* 4.0 7.1 - - + +
48J ALA* 3.6 10.3 - - + +
49J PRO* 2.7 53.7 + - + +
50J TYR 5.0 0.2 - - - -
51J TRP* 3.4 25.3 + + + -
66J LEU* 3.9 1.6 - - - +
76J PHE* 3.8 17.5 - + - -
78J PHE* 3.6 30.7 - + + -
147J ILE* 3.0 19.4 + - + +
148J SER 3.2 2.2 + - - +
149J LYS 3.1 0.2 - - - -
150J ASP* 1.3 81.5 - - + +
152J GLY* 1.3 61.8 + - - +
153J VAL* 3.3 2.4 + - + +
166J PHE* 3.3 58.2 - + + -
168J ILE* 4.0 5.8 - - + +
174J LEU* 5.5 0.9 - - + -
179J LEU* 5.5 0.5 - - - +
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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