Contacts of the helix formed by residues 225 - 233 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220F ILE* 3.7 23.7 + - - +
222F ASP* 2.8 28.0 + - - -
224F ALA* 1.3 73.2 - - - +
226F LYS* 1.3 61.8 + - - +
227F LEU 3.0 1.6 + - - -
228F LYS* 3.1 32.7 + - - +
229F TYR 4.2 1.0 + - - -
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Residues in contact with LYS 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D PHE* 3.7 31.7 + - - +
84D THR 4.5 2.3 + - - +
85D PHE* 3.8 28.9 - - + -
129D GLN 3.8 23.9 + - - -
130D GLY* 4.7 4.2 + - - -
219F ILE* 3.8 12.3 - - + -
220F ILE 3.2 14.1 + - - +
222F ASP 2.9 14.6 + - - +
223F PRO* 3.4 25.4 - - - +
225F GLY* 1.3 75.3 - - - +
227F LEU* 1.3 71.9 + - + +
229F TYR* 3.1 14.1 + - - +
230F PHE* 3.1 32.5 + - + -
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Residues in contact with LEU 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D ARG 3.8 6.3 - - - +
129D GLN* 3.7 53.4 - - - +
223F PRO 4.0 11.0 - - - +
224F ALA* 3.1 18.9 + - + +
225F GLY 3.0 1.2 + - - -
226F LYS* 1.3 85.3 - - + +
228F LYS* 1.3 59.2 + - - +
230F PHE* 4.3 3.4 - - + +
231F ASP* 2.8 37.4 + - + +
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Residues in contact with LYS 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220F ILE* 3.9 27.4 - - + -
224F ALA 5.1 1.6 - - - +
225F GLY* 3.1 18.8 + - - +
227F LEU* 1.3 77.9 - - + +
229F TYR* 1.3 62.1 + - - +
231F ASP* 4.7 1.5 - - - +
232F LYS* 3.2 29.8 + - - +
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Residues in contact with TYR 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D THR* 3.6 22.7 - - + +
209F PRO* 3.7 27.3 - - + +
217F GLU* 3.9 25.1 - - + -
218F THR 3.6 25.4 - - - +
219F ILE* 3.6 22.7 - - + -
220F ILE 5.2 0.4 - - - +
225F GLY 4.2 0.6 + - - -
226F LYS* 3.1 9.1 + - - +
228F LYS* 1.3 78.5 - - - +
230F PHE* 1.3 97.5 + + - +
232F LYS* 3.2 15.1 + - + +
233F LEU* 3.1 47.0 + - + +
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Residues in contact with PHE 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D THR 4.4 3.8 - - - -
85D PHE* 3.6 11.7 - - - -
88D PRO* 3.5 34.1 - - + -
89D THR* 4.1 5.8 - - + -
92D ILE* 5.6 4.5 - - + -
127D ARG* 3.6 20.9 - - + +
128D ARG* 3.5 13.8 - - - +
130D GLY* 3.6 22.7 - - - +
131D GLY 5.4 1.6 - - - -
219F ILE* 4.4 3.6 - - + -
226F LYS* 3.1 48.3 + - + +
227F LEU* 4.4 2.9 - - - +
229F TYR* 1.3 107.3 - + - +
231F ASP* 1.3 62.9 + - - +
233F LEU* 3.3 4.1 - - + +
234F ASN* 2.9 35.5 + - - +
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Residues in contact with ASP 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D ARG* 3.8 37.3 + - - +
227F LEU* 2.8 25.3 + - + +
228F LYS* 4.7 1.3 - - - +
230F PHE* 1.3 71.5 - - - +
232F LYS* 1.3 59.2 + - - +
234F ASN 2.9 26.2 - - - +
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Residues in contact with LYS 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217F GLU* 3.3 43.9 + - + +
228F LYS* 3.2 24.5 + - - +
229F TYR* 3.2 7.7 + - + +
231F ASP* 1.3 82.2 + - - +
233F LEU* 1.3 61.6 + - + +
234F ASN 3.6 2.9 + - - +
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Residues in contact with LEU 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217F GLU* 6.1 4.7 - - + -
229F TYR* 3.1 51.1 - - + +
230F PHE* 3.3 9.0 - - + +
232F LYS* 1.3 79.6 - - + +
234F ASN* 1.3 96.5 + - - +
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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