Contacts of the helix formed by residues 235 - 246 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B ARG* 3.8 42.8 + - + +
211B LEU 3.1 17.5 + - - +
212B ASN* 3.9 13.9 - - - +
213B ARG* 4.4 6.6 + - - +
216B LEU* 4.0 0.9 - - - +
234B VAL* 1.3 70.6 - - - +
236B THR* 1.3 63.2 + - - +
237B GLU* 3.2 20.4 + - - +
238B ALA* 3.2 20.5 + - + +
239B LEU* 3.0 20.8 + - - +
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Residues in contact with THR 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B ARG* 5.3 2.6 - - - +
231B GLY 5.1 0.3 + - - -
234B VAL* 3.1 12.9 + - - +
235B ASP* 1.3 71.8 + - - +
237B GLU* 1.3 62.0 + - - +
239B LEU* 3.3 9.4 + - + +
240B VAL* 3.3 21.7 + - - +
252B LEU* 6.0 0.4 - - + -
255B THR* 5.3 1.1 - - - -
256B ASP* 2.5 38.7 + - - +
260B LEU* 4.2 7.0 - - + -
264B HIS* 3.4 31.0 - - + +
266B LEU* 3.7 16.8 - - + -
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Residues in contact with GLU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ASP* 2.8 51.3 - - + +
128A LEU* 4.2 23.9 - - + +
130A LYS* 5.7 0.5 + - - -
209B ARG* 4.8 11.6 + - - +
235B ASP* 3.2 9.9 + - - +
236B THR* 1.3 77.8 - - - +
238B ALA* 1.3 64.0 + - - +
240B VAL* 3.2 15.5 + - - +
241B GLU* 3.4 10.7 + - - +
264B HIS* 5.7 1.1 - - - +
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Residues in contact with ALA 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B ARG* 3.8 31.0 - - + +
216B LEU* 3.6 17.0 - - + +
217B PHE* 4.6 2.9 - - + -
235B ASP* 3.2 25.3 + - - +
237B GLU* 1.3 79.8 - - - +
239B LEU* 1.3 57.2 + - - +
241B GLU* 3.1 11.2 + - - +
242B ALA* 2.9 27.7 + - - +
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Residues in contact with LEU 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B LEU* 3.6 8.7 - - + +
225B LEU* 4.1 15.3 - - + -
234B VAL* 4.3 17.5 - - + -
235B ASP 3.0 12.5 + - - +
236B THR* 3.5 11.2 - - + +
237B GLU 3.2 0.2 - - - -
238B ALA* 1.3 76.8 - - - +
240B VAL* 1.3 63.9 + - - +
242B ALA* 3.0 1.9 + - - -
243B LEU* 2.9 47.1 + - + +
247B LEU* 4.0 20.6 - - + -
250B ALA* 4.3 11.0 - - + -
252B LEU* 3.7 37.9 - - + -
266B LEU* 4.3 10.8 - - + -
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Residues in contact with VAL 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 4.5 5.8 - - + -
130A LYS* 3.6 30.7 - - + +
236B THR 3.5 13.9 - - - +
237B GLU* 3.2 9.5 + - - +
239B LEU* 1.3 76.8 - - - +
241B GLU* 1.3 60.9 + - - +
243B LEU* 3.3 10.1 + - - +
244B ARG* 3.5 14.9 + - + +
264B HIS* 3.6 25.8 - - + -
265B PRO* 4.0 16.2 - - + -
266B LEU* 3.7 19.5 - - + +
269B LEU* 4.2 19.9 - - + +
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Residues in contact with GLU 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LYS* 4.7 11.8 + - - +
213B ARG* 2.5 49.3 + - - +
217B PHE* 4.1 13.3 - - + -
237B GLU 3.4 5.3 + - - +
238B ALA* 3.1 13.9 + - - +
240B VAL* 1.3 81.5 - - - +
242B ALA* 1.3 62.2 + - - +
244B ARG* 3.2 24.1 + - + +
245B GLY 4.3 1.9 + - - -
246B HIS 5.1 0.2 + - - -
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Residues in contact with ALA 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B LEU* 4.4 11.9 - - + -
217B PHE* 3.6 25.7 - - + -
238B ALA 2.9 12.9 + - - +
239B LEU* 3.0 11.4 + - - +
241B GLU* 1.3 76.2 - - - +
243B LEU* 1.3 57.9 + - - +
246B HIS* 3.1 13.1 + - + +
247B LEU* 2.8 50.4 + - + -
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Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B LEU* 2.9 31.7 + - + +
240B VAL 3.7 6.3 - - - +
241B GLU 3.1 0.6 - - - -
242B ALA* 1.3 76.4 - - - +
244B ARG* 1.3 65.8 + - - +
245B GLY 3.4 0.2 - - - -
247B LEU* 4.0 12.8 - - + +
249B GLY* 3.5 40.8 - - - +
250B ALA* 3.8 8.1 - - + +
266B LEU* 3.5 31.9 - - + -
269B LEU* 3.9 16.8 - - + +
271B ASN* 3.0 32.6 + - - +
272B ALA* 4.2 11.2 - - + -
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Residues in contact with ARG 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LYS* 3.7 27.6 - - - +
240B VAL* 3.5 14.8 + - - +
241B GLU* 3.2 15.1 + - + +
243B LEU* 1.3 80.6 - - - +
245B GLY* 1.3 59.0 + - - +
269B LEU* 4.8 9.0 - - - -
31C PHE* 3.4 50.9 - - - -
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Residues in contact with GLY 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B ARG* 5.8 0.2 - - - +
241B GLU 4.3 1.4 + - - -
242B ALA 3.9 0.4 + - - -
243B LEU 3.4 0.4 - - - -
244B ARG* 1.3 82.2 - - - +
246B HIS* 1.3 66.5 + - - +
247B LEU 3.8 3.3 - - - +
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Residues in contact with HIS 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B LEU 3.5 18.3 + - - -
217B PHE* 3.5 48.8 + + + -
219B MET 2.8 28.8 + - - -
220B LYS 4.0 1.0 + - - -
221B ARG* 3.4 30.7 - - + +
222B GLY* 2.8 23.7 + - - -
241B GLU 5.1 0.2 + - - -
242B ALA* 3.1 11.0 + - + +
245B GLY* 1.3 79.0 - - - +
247B LEU* 1.3 74.7 + - + +
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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