Contacts of the helix formed by residues 224 - 231 (chain A) in PDB entry 5UKM
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 LYS 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A ASP* 1.3 73.7 + - - +
225A LYS* 1.3 65.2 + - - +
227A ILE* 3.1 9.6 + - - +
228A LYS* 3.1 24.6 + - - +
262A HIS* 4.3 11.7 - - - +
263A THR 3.3 14.6 + - - -
265A ASP* 3.3 17.9 + - - +
266A LYS* 3.6 24.4 + - - +
267A LEU* 3.7 25.8 - - + +
498A LEU* 3.9 20.4 - - + -
503A GLN* 3.1 36.4 - - + +
506A TYR* 4.0 32.9 + - + +
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Residues in contact with LYS 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ASP* 3.2 20.6 + - - +
224A LYS* 1.3 77.4 - - + +
226A ARG* 1.3 60.3 + - - +
228A LYS* 3.8 5.4 + - - +
229A MET* 3.3 27.4 + - + +
265A ASP* 4.6 21.0 + - + +
496A ILE* 4.8 18.9 + - - +
497A LYS* 5.8 8.7 - - - +
498A LEU* 4.4 19.7 - - + -
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Residues in contact with ARG 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A GLY 5.2 2.2 + - - -
201A GLY 3.9 15.2 + - - +
202A PHE* 3.6 32.5 + - + +
203A GLY* 3.8 5.1 + - - -
204A GLU* 3.1 34.5 + - - -
223A ASP* 3.3 26.6 + - - +
224A LYS 3.2 0.4 - - - -
225A LYS* 1.3 78.0 - - - +
227A ILE* 1.3 56.6 + - - +
229A MET* 2.9 10.8 + - - +
230A LYS* 2.8 39.3 + - + +
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Residues in contact with ILE 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A PHE* 3.8 27.8 - - + -
222A LEU* 4.3 13.0 - - + -
223A ASP 3.4 16.5 + - - +
224A LYS* 3.1 8.8 + - - +
226A ARG* 1.3 76.7 - - - +
228A LYS* 1.3 59.6 + - - +
230A LYS 3.7 0.3 - - - -
231A GLN* 2.9 25.6 + - - -
232A GLY 3.1 13.6 + - - +
233A GLU* 3.6 28.9 - - + +
236A ALA* 3.7 26.0 - - + -
267A LEU* 3.8 19.7 - - + -
506A TYR* 3.5 20.2 - - - +
701A T0E 6.3 0.2 - - + -
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Residues in contact with LYS 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A LYS 3.1 12.7 + - - +
225A LYS* 4.0 5.8 - - - +
227A ILE* 1.3 79.1 - - - +
229A MET* 1.3 63.4 + - - +
231A GLN* 3.3 17.3 + - - +
233A GLU* 3.4 21.6 - - - +
496A ILE* 4.8 14.7 - - + +
497A LYS 2.7 28.8 + - - +
498A LEU* 3.8 7.7 - - + +
499A LEU 4.6 0.8 - - - +
502A ASP* 3.1 37.7 + - - +
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Residues in contact with MET 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A LYS* 3.3 17.5 + - + +
226A ARG* 2.9 14.3 + - - +
228A LYS* 1.3 79.5 - - - +
230A LYS* 1.3 62.5 + - + +
231A GLN* 3.9 3.6 + - - +
496A ILE* 3.6 49.4 - - + +
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Residues in contact with LYS 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A GLY* 3.8 21.9 + - - +
202A PHE* 3.9 30.9 - - + -
226A ARG* 2.8 19.5 + - + +
229A MET* 1.3 78.2 - - + +
231A GLN* 1.3 70.5 + - - +
232A GLY* 3.5 1.4 + - - -
484A ASP* 3.9 18.6 + - - -
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Residues in contact with GLN 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ILE 2.9 9.1 + - - -
228A LYS 3.3 11.3 + - - +
229A MET 4.8 2.9 + - - +
230A LYS* 1.3 82.6 - - - +
232A GLY* 1.3 56.3 + - - +
233A GLU* 3.6 14.4 - - - +
234A THR* 5.4 2.8 + - - -
235A LEU* 4.8 5.0 - - - +
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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