Contacts of the helix formed by residues 235 - 244 (chain A) in PDB entry 2CUK
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 ASP 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A ARG* 4.3 28.8 + - + +
211A LEU 3.1 17.5 + - - +
212A ASN* 4.0 12.2 - - + +
213A ARG* 4.6 13.2 + - - -
216A LEU* 4.2 0.5 - - - +
234A VAL* 1.3 70.0 - - - +
236A THR* 1.3 63.4 + - - +
237A GLU* 3.2 12.0 + - - +
238A ALA* 3.0 29.0 + - + +
239A LEU* 3.0 19.2 + - - +
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Residues in contact with THR 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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231A GLY 5.0 0.5 + - - -
234A VAL* 3.1 9.7 + - - +
235A ASP* 1.3 70.9 + - - +
237A GLU* 1.3 63.2 + - - +
239A LEU* 3.1 18.9 + - - +
240A VAL* 3.1 12.6 + - - +
252A LEU* 6.2 0.4 - - + -
255A THR* 5.2 1.7 - - - -
256A ASP* 2.5 43.7 + - - +
260A LEU* 4.4 5.2 - - + -
264A HIS* 3.5 32.3 - - + +
266A LEU* 3.9 15.7 - - + -
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Residues in contact with GLU 237 (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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213A ARG* 4.6 3.1 - - - +
235A ASP* 3.2 8.1 + - - +
236A THR* 1.3 78.8 - - - +
238A ALA* 1.3 62.4 + - - +
240A VAL* 3.3 18.9 + - + +
241A GLU* 3.3 26.5 + - + +
264A HIS* 5.6 2.5 - - - -
34B LYS* 4.0 14.8 - - - +
35B ALA* 3.5 33.8 + - + +
38B LEU* 6.0 0.7 - - - +
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Residues in contact with ALA 238 (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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213A ARG* 3.7 32.0 - - + +
216A LEU* 3.6 15.7 - - + +
217A PHE* 4.5 2.5 - - + -
235A ASP* 3.0 29.6 + - + +
237A GLU* 1.3 73.8 - - - +
239A LEU* 1.3 65.7 + - - +
241A GLU* 3.1 15.7 + - - +
242A ALA* 3.0 21.8 + - - +
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Residues in contact with LEU 239 (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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216A LEU* 3.5 12.3 - - + +
225A LEU* 3.8 21.5 - - + -
234A VAL* 4.2 14.1 - - + -
235A ASP 3.0 12.0 + - - +
236A THR* 3.1 11.4 + - - +
238A ALA* 1.3 76.6 - - - +
240A VAL* 1.3 62.9 + - - +
242A ALA* 3.2 1.8 + - - -
243A LEU* 2.9 43.8 + - + +
247A LEU* 3.9 22.2 - - + -
250A ALA* 4.2 10.1 - - + -
252A LEU* 3.7 38.8 - - + -
266A LEU* 4.5 7.9 - - + -
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Residues in contact with VAL 240 (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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236A THR 3.1 13.6 + - - +
237A GLU* 3.4 11.9 - - + +
238A ALA 3.2 0.4 - - - -
239A LEU* 1.3 77.3 - - - +
241A GLU* 1.3 64.5 + - + +
243A LEU* 3.3 10.7 + - - +
244A ARG* 3.5 42.6 + - - +
264A HIS* 3.9 15.0 - - + -
265A PRO* 4.1 18.4 - - + -
266A LEU* 3.8 27.4 - - + +
269A LEU* 4.2 12.9 - - + +
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Residues in contact with GLU 241 (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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213A ARG* 2.7 51.7 + - - +
217A PHE* 3.9 16.7 - - + -
237A GLU* 3.5 20.7 - - + +
238A ALA* 3.1 8.1 + - - +
240A VAL* 1.3 81.6 - - + +
242A ALA* 1.3 61.0 + - - +
243A LEU 3.3 0.3 + - - -
244A ARG* 3.3 22.9 + - - +
245A GLY 4.6 1.2 + - - -
33B PRO* 3.5 43.2 - - + +
35B ALA* 4.1 4.3 - - - +
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Residues in contact with ALA 242 (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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216A LEU* 4.3 13.9 - - + -
217A PHE* 3.6 27.8 - - + -
238A ALA 3.0 15.1 + - - +
239A LEU* 3.2 5.6 + - - +
241A GLU* 1.3 75.6 - - - +
243A LEU* 1.3 58.1 + - - +
244A ARG 3.3 0.2 - - - -
246A HIS* 3.2 11.0 + - + -
247A LEU* 2.8 50.6 + - + -
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Residues in contact with LEU 243 (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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239A LEU* 2.9 30.7 + - + +
240A VAL 3.7 0.7 - - - +
241A GLU 3.2 0.8 - - - -
242A ALA* 1.3 75.3 - - - +
244A ARG* 1.3 64.6 + - - +
245A GLY* 3.2 1.6 + - - -
247A LEU* 4.1 15.1 - - + +
249A GLY* 3.6 39.7 - - - +
250A ALA* 3.8 7.6 - - + +
266A LEU* 3.4 32.5 - - + -
269A LEU* 3.7 22.7 - - + +
271A ASN* 3.1 29.6 + - - +
272A ALA* 4.1 11.7 - - + -
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Residues in contact with ARG 244 (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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240A VAL* 3.5 37.8 + - - +
241A GLU* 3.7 13.0 - - - +
242A ALA 3.3 1.4 - - - -
243A LEU* 1.3 79.5 - - - +
245A GLY* 1.3 57.0 + - - +
265A PRO* 4.6 10.7 - - - +
269A LEU* 4.0 23.7 - - + +
31B PHE* 3.7 59.4 - - + -
33B PRO* 6.1 4.9 - - - +
130D LYS* 5.1 7.6 - - - +
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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