Contacts of the helix formed by residues 225 - 234 (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 GLY 225 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220D ILE* 3.7 27.2 + - - +
222D ASP* 3.0 23.7 + - - -
224D ALA* 1.3 76.7 - - - +
226D LYS* 1.3 61.7 + - - +
227D LEU 3.2 0.9 + - - -
228D LYS* 3.3 28.3 + - - +
229D TYR 4.4 0.5 + - - -
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Residues in contact with LYS 226 (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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219D ILE* 4.0 11.0 - - + -
220D ILE 3.4 14.3 + - - +
222D ASP 2.9 11.9 + - - +
223D PRO* 3.3 28.8 - - + +
224D ALA 3.1 0.4 + - - -
225D GLY* 1.3 76.6 - - - +
227D LEU* 1.3 69.4 + - + +
228D LYS 3.2 0.2 - - - -
229D TYR* 3.1 14.1 + - - +
230D PHE* 3.1 30.1 + - + -
83F PHE* 3.7 30.5 + - - +
84F THR 4.5 2.7 + - - +
85F PHE* 3.9 28.0 - - + -
129F GLN 3.7 24.4 + - - -
130F GLY* 4.7 5.1 + - - -
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Residues in contact with LEU 227 (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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223D PRO 4.0 10.3 - - - +
224D ALA* 3.1 20.3 + - + +
226D LYS* 1.3 86.3 - - + +
228D LYS* 1.3 67.8 + - + +
230D PHE* 3.8 3.1 - - + +
231D ASP* 2.8 38.3 + - - +
128F ARG 3.9 4.7 - - - +
129F GLN* 3.9 38.1 - - + +
130F GLY 4.8 0.2 - - - +
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Residues in contact with LYS 228 (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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220D ILE* 4.7 18.6 - - + +
224D ALA 4.9 2.7 - - - +
225D GLY* 3.6 22.0 - - - +
226D LYS 3.2 0.2 - - - -
227D LEU* 1.3 79.2 - - + +
229D TYR* 1.3 61.5 + - - +
231D ASP* 4.6 0.8 - - - +
232D LYS* 3.1 24.8 + - - +
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Residues in contact with TYR 229 (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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209D PRO* 3.8 28.0 - - + +
217D GLU* 4.0 22.2 - - + -
218D THR 3.6 25.8 - - - +
219D ILE* 3.5 20.6 - - + -
220D ILE 5.4 0.4 - - - +
225D GLY 4.4 0.2 + - - -
226D LYS* 3.1 10.0 + - - +
228D LYS* 1.3 80.4 - - - +
230D PHE* 1.3 94.1 + + - +
232D LYS* 3.4 4.5 + - - +
233D LEU* 3.0 63.1 + - + +
89F THR* 3.6 20.3 - - + +
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Residues in contact with PHE 230 (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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219D ILE* 4.2 4.5 - - + -
226D LYS* 3.1 49.4 + - + +
227D LEU* 4.5 2.0 - - - +
229D TYR* 1.3 102.9 - + - +
231D ASP* 1.3 62.9 + - - +
233D LEU* 5.7 0.4 - - + -
234D ASN* 3.0 37.3 + - - +
84F THR 4.5 3.8 - - - -
85F PHE* 3.7 13.2 - - - -
88F PRO* 3.6 31.4 - - + -
89F THR* 4.1 6.1 - - + -
92F ILE* 5.7 5.6 - - + -
127F ARG 3.5 16.2 - - - +
128F ARG* 3.5 18.2 - - - +
129F GLN 4.6 0.4 - - - -
130F GLY* 3.6 23.1 - - - +
131F GLY 5.6 0.9 - - - -
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Residues in contact with ASP 231 (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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227D LEU* 2.8 28.7 + - - +
228D LYS* 4.6 1.1 - - - +
230D PHE* 1.3 74.8 - - - +
232D LYS* 1.3 58.1 + - - +
234D ASN* 2.8 23.2 - - - +
128F ARG* 2.7 58.3 + - - +
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Residues in contact with LYS 232 (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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217D GLU* 3.0 38.7 + - + +
228D LYS 3.1 20.6 + - - +
229D TYR* 3.4 4.7 + - - +
230D PHE 3.2 0.4 - - - -
231D ASP* 1.3 82.1 - - - +
233D LEU* 1.3 63.1 + - - +
234D ASN* 3.4 4.2 + - - +
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Residues in contact with LEU 233 (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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217D GLU* 6.3 3.1 - - + -
229D TYR* 3.0 54.6 + - + +
230D PHE* 5.7 0.2 - - + -
232D LYS* 1.3 79.8 - - + +
234D ASN* 1.3 76.5 + - - +
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Residues in contact with ASN 234 (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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230D PHE* 3.0 26.3 + - - +
231D ASP 2.8 18.2 - - - +
232D LYS 3.8 3.6 - - - +
233D LEU* 1.3 104.4 - - - +
92F ILE* 6.1 1.0 - - - +
127F ARG* 3.5 45.3 + - + +
128F ARG* 3.0 50.7 + - + +
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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