Contacts of the helix formed by residues 232 - 244 (chain B) in PDB entry 2CUY
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 232 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216B ARG* 3.9 13.3 + - - +
230B GLU* 5.0 1.2 + - - +
231B GLU* 1.3 77.3 - - - +
233B PRO* 1.3 70.5 - - - +
234B GLU* 3.2 19.3 + - - +
235B ARG* 3.0 19.8 + - + +
236B ILE* 2.8 29.1 + - - +
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Residues in contact with PRO 233 (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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214B LEU* 3.7 41.1 - - + +
215B ARG* 4.2 4.7 - - - +
216B ARG* 4.2 23.8 - - + +
231B GLU 3.3 11.2 - - - +
232B ASP* 1.3 89.3 - - - +
234B GLU* 1.3 61.5 + - - +
236B ILE* 3.6 11.5 - - + +
237B ARG* 3.0 28.7 + - - +
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Residues in contact with GLU 234 (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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232B ASP* 3.2 15.5 + - - +
233B PRO* 1.3 80.7 - - - +
235B ARG* 1.3 60.8 + - - +
237B ARG* 3.6 12.4 + - - +
238B ALA* 3.4 18.4 + - - +
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Residues in contact with ARG 235 (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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226B THR* 3.7 23.2 - - - +
230B GLU* 3.3 29.4 + - + +
232B ASP* 3.0 24.6 + - + +
234B GLU* 1.3 78.4 - - - +
236B ILE* 1.3 54.4 + - + +
238B ALA* 3.1 10.2 + - - +
239B LEU* 2.7 58.9 + - + +
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Residues in contact with ILE 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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92B GLU* 6.0 0.2 - - - +
96B HIS* 3.6 41.3 - - + +
101B THR* 4.2 12.6 - - + -
214B LEU* 4.6 3.1 - - + -
217B PRO* 4.0 14.4 - - + -
230B GLU* 4.1 17.7 - - + +
231B GLU* 3.9 15.5 - - - -
232B ASP 2.8 28.9 + - - +
233B PRO* 3.6 10.3 - - + +
235B ARG* 1.3 76.9 - - - +
237B ARG* 1.3 57.1 + - - +
239B LEU* 3.1 8.1 + - - +
240B LEU* 2.8 46.6 + - + +
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Residues in contact with ARG 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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209B LEU* 2.9 45.7 + - + +
210B ALA* 4.3 11.9 + - - +
212B VAL 2.7 27.1 + - - -
213B PRO* 4.7 1.0 - - - +
214B LEU* 3.5 42.4 + - + +
233B PRO* 3.0 20.5 + - - +
234B GLU* 3.7 11.0 - - - +
236B ILE* 1.3 77.0 - - - +
238B ALA* 1.3 66.2 + - - +
240B LEU* 3.4 6.8 + - - -
241B LEU* 3.4 23.1 + - + +
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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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234B GLU 3.4 9.7 + - - +
235B ARG* 3.1 15.1 + - - +
237B ARG* 1.3 80.3 - - - +
239B LEU* 1.3 64.6 + - + +
241B LEU* 3.2 13.2 + - - +
242B GLU* 3.0 24.0 + - - +
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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
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92B GLU* 4.9 3.3 - - - +
223B SER* 3.6 18.7 + - - +
225B VAL* 3.7 14.3 - - + +
226B THR* 4.0 13.7 - - + -
230B GLU* 3.3 44.6 - - + +
235B ARG* 2.7 51.8 + - + +
236B ILE* 3.7 5.6 - - - +
238B ALA* 1.3 75.6 - - + +
240B LEU* 1.3 56.8 + - - +
242B GLU* 4.0 20.6 - - - +
243B GLN* 3.0 29.6 + - - +
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Residues in contact with LEU 240 (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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92B GLU* 3.6 32.3 - - + +
93B TRP* 3.9 57.2 + - + +
96B HIS* 4.4 13.5 - - + -
101B THR* 6.3 0.2 - - + -
102B LEU* 5.9 3.6 - - + -
209B LEU* 4.2 11.9 - - + -
214B LEU* 5.1 5.4 - - + -
236B ILE* 2.8 40.9 + - + +
237B ARG* 3.7 6.7 - - - +
238B ALA 3.3 0.4 - - - -
239B LEU* 1.3 73.6 - - - +
241B LEU* 1.3 63.6 + - - +
243B GLN* 3.5 17.9 - - - +
244B ILE* 4.0 10.7 + - - +
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Residues in contact with LEU 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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202B ARG* 3.4 28.0 - - + +
205B LEU* 3.9 16.6 - - + -
206B ALA* 3.6 46.9 - - + +
209B LEU* 3.8 20.9 - - + -
237B ARG* 3.5 19.7 - - + +
238B ALA* 3.2 9.3 + - - +
240B LEU* 1.3 74.5 - - - +
242B GLU* 1.3 64.7 + - - +
243B GLN 3.1 1.6 - - - -
244B ILE* 3.1 23.6 + - + +
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Residues in contact with GLU 242 (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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202B ARG* 4.5 11.4 - - - +
225B VAL* 3.4 26.6 - - + +
238B ALA* 3.0 16.5 + - - +
239B LEU* 3.4 20.0 + - - +
241B LEU* 1.3 75.9 - - - +
243B GLN* 1.3 64.1 + - - +
244B ILE 3.2 0.5 + - - -
245B THR* 3.3 9.6 + - - +
246B ALA* 3.1 24.9 + - + +
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Residues in contact with GLN 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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89B SER* 3.1 26.9 + - - +
92B GLU* 3.0 32.6 + - - +
93B TRP* 4.4 4.6 + - - -
114B ARG* 2.9 32.6 + - - -
194B HIS* 3.0 25.3 + - + -
224B ASN* 3.2 25.0 + - + -
225B VAL* 3.5 13.9 - - + +
239B LEU 3.0 18.4 + - - +
240B LEU* 3.5 12.7 - - - +
241B LEU 3.1 0.4 - - - -
242B GLU* 1.3 76.5 - - - +
244B ILE* 1.3 63.0 + - - +
245B THR 3.2 0.2 + - - -
246B ALA* 3.2 10.9 - - - +
248B VAL* 5.5 0.2 - - + -
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Residues in contact with ILE 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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114B ARG* 4.3 11.0 - - + +
118B MET* 3.8 28.9 - - + +
194B HIS* 3.4 30.2 + - - -
198B MET* 3.7 30.7 - - + +
201B ALA* 4.3 5.8 - - + +
202B ARG* 3.7 28.0 - - + +
205B LEU* 3.9 28.9 - - + -
240B LEU 4.0 5.8 - - - +
241B LEU* 3.1 25.3 + - - +
243B GLN* 1.3 79.2 - - - +
245B THR* 1.3 57.6 + - - +
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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