Contacts of the helix formed by residues 225 - 234 (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 GLY 225 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220J ILE* 3.8 30.4 + - - +
222J ASP* 2.5 18.5 + - - -
224J ALA* 1.3 73.2 - - - +
226J LYS* 1.3 61.3 + - - +
227J LEU 3.0 2.0 + - - -
228J LYS* 3.2 35.0 + - - +
229J TYR 4.4 0.7 + - - -
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Residues in contact with LYS 226 (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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83E PHE* 3.8 29.1 + - - +
84E THR 4.6 2.6 + - - +
85E PHE* 3.8 23.8 - - + -
129E GLN 3.6 26.1 + - - -
130E GLY* 4.6 4.9 + - - -
219J ILE* 4.0 12.3 - - + -
220J ILE 3.3 13.8 + - - +
222J ASP 2.8 22.1 + - - +
223J PRO* 3.5 25.7 + - + +
224J ALA 3.1 0.4 + - - -
225J GLY* 1.3 72.0 - - - +
227J LEU* 1.3 71.3 + - - +
228J LYS 3.3 0.2 - - - -
229J TYR* 3.2 6.1 + - - +
230J PHE* 3.1 36.9 + - + -
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Residues in contact with LEU 227 (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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128E ARG 3.7 20.6 - - - +
129E GLN* 3.8 27.1 - - + +
223J PRO 4.0 10.8 - - - +
224J ALA* 3.0 20.1 + - + +
225J GLY 3.0 1.0 - - - -
226J LYS* 1.3 85.6 - - + +
228J LYS* 1.3 59.2 + - - +
230J PHE* 3.8 2.7 - - + +
231J ASP* 2.8 38.9 + - + +
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Residues in contact with LYS 228 (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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220J ILE* 4.0 25.1 - - + +
224J ALA 4.9 2.8 + - - -
225J GLY* 3.2 23.3 + - - +
227J LEU* 1.3 78.6 - - - +
229J TYR* 1.3 61.6 + - - +
231J ASP* 4.5 1.7 - - - +
232J LYS* 3.3 22.5 + - - +
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Residues in contact with TYR 229 (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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89E THR* 3.5 25.2 - - + +
209J PRO* 3.9 23.1 - - + +
217J GLU* 4.1 16.8 - - + -
218J THR 3.7 25.8 - - - +
219J ILE* 3.7 19.1 - - + -
220J ILE 5.4 0.2 - - - +
225J GLY 4.4 0.4 + - - -
226J LYS* 3.2 8.5 + - - +
227J LEU 3.1 0.2 - - - -
228J LYS* 1.3 79.5 - - - +
230J PHE* 1.3 102.3 + + - +
232J LYS* 3.3 3.9 + - - -
233J LEU* 3.1 65.9 + - + +
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Residues in contact with PHE 230 (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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84E THR 4.4 3.1 - - - -
85E PHE* 3.6 12.3 - - - -
88E PRO* 3.5 35.4 - - + -
89E THR* 4.3 6.1 - - + -
92E ILE* 5.7 4.9 - - + -
127E ARG* 3.5 21.5 - - + +
128E ARG* 3.4 12.9 - - - +
129E GLN 4.6 0.2 - - - -
130E GLY* 3.6 20.9 - - - +
131E GLY 5.4 1.1 - - - -
219J ILE* 4.4 5.2 - - + -
226J LYS* 3.1 48.5 + - + +
227J LEU* 4.5 2.5 - - - +
229J TYR* 1.3 106.4 - + - +
231J ASP* 1.3 60.3 + - - +
233J LEU* 5.1 0.2 - - - -
234J ASN* 2.7 36.3 + - - +
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Residues in contact with ASP 231 (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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128E ARG* 3.8 34.8 + - - +
227J LEU* 2.8 22.1 + - + +
228J LYS* 4.5 1.6 - - - +
230J PHE* 1.3 74.0 - - - +
232J LYS* 1.3 65.8 + - - +
234J ASN 3.0 21.0 - - - +
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Residues in contact with LYS 232 (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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217J GLU* 3.9 30.5 + - + +
228J LYS 3.3 17.7 + - - +
229J TYR* 3.3 5.8 + - - +
231J ASP* 1.3 82.4 - - - +
233J LEU* 1.3 74.7 + - + +
234J ASN 3.3 4.7 + - - +
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Residues in contact with LEU 233 (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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217J GLU* 4.4 11.2 - - + -
229J TYR* 3.1 63.9 + - + +
232J LYS* 1.3 97.4 - - + +
234J ASN* 1.3 74.1 + - - +
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Residues in contact with ASN 234 (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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127E ARG* 3.5 46.3 - - + +
128E ARG* 3.9 28.1 - - + +
230J PHE* 2.7 30.5 + - - +
231J ASP 3.0 17.3 + - - +
232J LYS 3.2 5.0 - - - +
233J LEU* 1.3 93.2 + - - +
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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