Contacts of the helix formed by residues 225 - 236 (chain A) in PDB entry 1CK4
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 MET 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A TYR* 3.3 16.6 - - + +
191A GLY 5.4 0.2 - - - +
192A GLU* 3.6 34.4 - - - +
193A ASN 5.4 0.4 - - - +
223A GLN* 3.9 10.5 + - + +
224A THR* 1.3 70.4 - - - +
226A THR* 1.3 58.9 + - - +
227A ALA 3.3 3.1 - - - -
228A LEU* 3.2 27.4 + - + +
229A GLY 2.9 22.5 + - - -
261A HIS* 3.7 23.6 - - - -
262A ASP* 2.6 36.1 - - + +
264A TYR* 5.4 0.7 - - - +
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Residues in contact with THR 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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190A TYR* 2.9 34.7 + - + +
224A THR* 3.3 10.3 + - - +
225A MET* 1.3 71.3 - - - +
227A ALA* 1.3 65.5 + - - +
230A ILE* 2.9 46.1 + - + +
254A ILE* 4.0 12.1 - - + -
256A THR* 4.3 7.8 + - + +
258A GLY 5.0 1.0 + - - -
260A SER* 3.5 21.6 + - - -
266A LEU* 4.6 3.8 - - + -
302A GLU* 4.9 3.0 + - - -
303A ILE* 5.9 1.4 - - + +
306A ILE* 4.8 11.4 - - + -
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Residues in contact with ALA 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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225A MET 3.3 0.6 - - - -
226A THR* 1.3 77.6 - - - +
228A LEU* 1.3 58.4 + - - +
231A ASP* 3.0 33.1 + - - +
260A SER* 4.7 0.8 - - - -
262A ASP* 3.4 35.2 - - + +
265A ARG* 3.5 20.4 - - + +
266A LEU* 3.8 21.7 - - + +
269A VAL* 3.8 12.2 - - + +
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Residues in contact with LEU 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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192A GLU 4.1 20.2 - - - +
193A ASN* 4.2 6.1 - - - -
194A VAL* 3.8 20.4 - - + +
225A MET* 3.2 33.7 + - + +
227A ALA* 1.3 81.2 - - - +
229A GLY* 1.3 58.0 + - - +
231A ASP* 4.0 1.0 - - + +
232A THR* 2.7 40.1 + - - +
262A ASP* 4.3 3.1 + - - -
265A ARG* 3.3 26.0 - - - +
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Residues in contact with GLY 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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152A VAL* 4.0 10.2 - - - +
188A VAL* 4.6 3.0 - - - +
190A TYR* 4.1 14.8 - - - -
194A VAL* 3.9 17.4 - - - +
225A MET 2.9 14.4 + - - -
226A THR 3.2 1.8 + - - -
228A LEU* 1.3 76.6 - - - +
230A ILE* 1.3 61.8 + - - +
232A THR* 3.2 4.0 + - - -
233A ALA* 2.9 23.9 + - - +
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Residues in contact with ILE 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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152A VAL* 4.0 6.4 - - + +
226A THR* 2.9 36.8 + - + +
229A GLY* 1.3 74.1 - - - +
231A ASP* 1.3 57.3 + - - +
233A ALA* 3.3 6.8 + - - +
234A ARG* 2.9 26.5 + - - +
252A MET* 3.8 10.7 - - - +
254A ILE* 3.9 23.6 - - + -
266A LEU* 4.7 5.2 - - + -
269A VAL* 3.4 22.4 - - + -
270A ILE* 4.4 9.0 - - + -
273A CYS* 3.7 19.5 - - - -
280A ARG* 5.5 0.7 - - - -
306A ILE* 3.8 32.1 - - + -
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Residues in contact with ASP 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 ALA 3.0 19.7 + - - +
228A LEU* 4.0 3.4 - - + +
230A ILE* 1.3 74.8 - - - +
232A THR* 1.3 56.3 + - - +
234A ARG* 3.4 11.2 + - - +
235A LYS* 2.8 57.6 + - - +
265A ARG* 2.4 31.8 + - - +
269A VAL* 3.8 20.1 - - + +
272A ASP* 6.0 0.7 - - - +
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Residues in contact with THR 232 (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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188A VAL* 5.1 0.7 - - + -
194A VAL* 3.8 32.2 - - + +
196A HIS* 4.4 7.6 - - + +
228A LEU* 2.7 32.2 + - - +
229A GLY 3.5 4.7 - - - -
231A ASP* 1.3 78.3 - - - +
233A ALA* 1.3 54.2 + - - +
235A LYS* 4.2 5.8 - - - -
236A GLU* 2.4 70.9 + - + +
237A ALA 3.5 0.2 + - - -
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Residues in contact with ALA 233 (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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150A VAL* 3.9 25.1 - - + -
152A VAL* 4.2 9.9 - - + -
188A VAL* 4.9 8.5 - - + +
229A GLY 2.9 15.9 + - - +
230A ILE 3.6 5.6 - - - +
232A THR* 1.3 77.3 - - - +
234A ARG* 1.3 57.8 + - - +
237A ALA* 3.5 11.3 - - + +
238A PHE* 3.0 35.8 + - - -
252A MET* 4.0 9.9 - - + -
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Residues in contact with ARG 234 (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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230A ILE 2.9 15.7 + - - +
231A ASP* 3.8 13.7 + - - +
233A ALA* 1.3 78.3 - - - +
235A LYS* 1.3 62.3 - - + +
238A PHE* 3.8 21.8 - - - +
252A MET* 4.0 3.1 - - + +
269A VAL* 3.3 5.1 + - - +
272A ASP* 2.2 76.0 + - - +
273A CYS* 2.4 27.0 - - - +
275A ASP* 4.1 3.4 - - - +
276A GLU* 2.7 54.8 + - - +
278A ILE* 3.8 12.6 - - + -
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Residues in contact with LYS 235 (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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231A ASP* 2.8 41.9 + - - +
232A THR* 3.9 4.5 - - - +
234A ARG* 1.3 82.4 - - + +
236A GLU* 1.3 65.9 + - + +
239A THR* 3.2 17.8 - - - +
265A ARG* 5.9 0.4 - - - +
276A GLU* 6.2 0.2 - - - +
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Residues in contact with GLU 236 (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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196A HIS* 2.8 35.6 + - + +
232A THR* 2.4 41.8 + - - +
234A ARG 3.6 0.2 - - - -
235A LYS* 1.3 81.9 - - + +
237A ALA* 1.3 67.3 + - - +
238A PHE 3.1 1.3 - - - -
239A THR* 2.9 17.8 - - - +
242A ARG* 3.0 27.1 + - - +
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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