Contacts of the helix formed by residues 225 - 237 (chain C) in PDB entry 2CNW
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 GLU 225 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222C THR* 5.0 0.2 - - - -
223C GLY 3.2 1.4 + - - -
224C GLN* 1.3 76.0 - - - +
226C ALA* 1.3 53.2 + - - +
227C LEU 3.2 0.7 - - - -
228C SER* 3.1 19.0 + - - +
229C VAL* 2.8 42.5 + - + +
41F ALA 4.1 14.4 - - - +
43F ASP* 4.7 5.3 + - - +
231F VAL* 4.1 18.8 - - + +
260F THR* 2.8 40.7 + - - +
261F ALA* 3.6 30.9 - - + +
262F LYS* 5.1 3.6 + - - +
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Residues in contact with ALA 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C LEU* 4.7 8.4 - - + +
222C THR* 4.1 13.0 - - + +
223C GLY 3.2 17.2 + - - +
224C GLN 3.1 1.0 - - - +
225C GLU* 1.3 77.7 - - - +
227C LEU* 1.3 63.9 + - - +
229C VAL* 3.9 4.6 - - - +
230C ALA* 2.9 29.2 + - - +
255C ALA* 3.4 39.0 - - + +
258C SER* 3.9 6.5 - - - +
259C ALA* 4.9 0.6 - - - +
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Residues in contact with LEU 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C ASN* 3.2 44.4 - - + +
46C GLU* 3.9 24.9 - - + +
47C VAL* 4.0 17.0 - - + -
224C GLN 3.7 1.8 + - - -
225C GLU 3.2 0.6 - - - -
226C ALA* 1.3 82.7 - - - +
228C SER* 1.3 63.0 + - - +
231C ARG* 3.1 27.3 + - + +
258C SER* 3.8 13.6 - - - +
261C HIS* 5.0 2.5 - - + +
262C VAL* 3.4 39.5 - - + +
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Residues in contact with SER 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C GLN* 3.4 16.4 + - - +
224C GLN 4.7 0.6 + - - -
225C GLU* 3.1 23.6 + - - -
227C LEU* 1.3 83.4 - - - +
229C VAL* 1.3 59.8 + - - +
231C ARG* 3.9 8.1 - - - +
232C ALA* 3.3 23.7 + - - +
260F THR* 4.5 2.6 + - - +
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Residues in contact with VAL 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C LEU* 3.9 33.0 - - + -
193C GLN* 3.8 28.5 - - + +
216C LEU* 4.9 8.3 - - + -
218C LEU* 5.2 8.3 - - + -
222C THR* 5.9 0.2 - - + -
225C GLU* 2.8 32.9 + - + +
226C ALA* 3.9 5.2 - - - +
228C SER* 1.3 69.8 - - - +
230C ALA* 1.3 67.2 + - - +
232C ALA* 3.4 1.4 + - - +
233C PHE* 3.0 49.3 + - + -
231F VAL* 5.4 0.2 - - + -
260F THR* 5.1 0.2 - - - +
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Residues in contact with ALA 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C LEU* 3.7 26.8 - - + +
218C LEU* 6.0 0.9 - - + -
226C ALA 2.9 18.7 + - - +
227C LEU 3.9 2.0 - - - +
229C VAL* 1.3 76.7 - - - +
231C ARG* 1.3 56.4 + - - +
233C PHE* 3.6 2.1 + - - +
234C ASP* 3.0 31.9 + - - +
239C VAL* 4.9 0.2 - - - +
259C ALA* 3.7 29.2 - - + +
262C VAL* 3.9 5.8 - - + -
263C THR* 3.8 7.6 - - + +
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Residues in contact with ARG 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C LEU* 3.1 21.9 + - - +
228C SER* 3.9 8.3 - - - +
230C ALA* 1.3 74.3 - - - +
232C ALA* 1.3 52.4 + - - +
234C ASP* 3.1 7.0 + - - +
235C GLU* 2.7 68.6 + - + +
262C VAL* 3.8 29.1 - - + +
263C THR* 5.1 0.2 - - - -
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Residues in contact with ALA 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C GLN* 3.6 27.1 - - + +
199C MET* 4.3 1.6 - - - -
228C SER 3.3 16.4 + - - +
231C ARG* 1.3 75.6 - - - +
233C PHE* 1.3 61.2 + - - +
235C GLU* 4.5 3.8 - - - +
236C LYS* 2.8 57.5 + - - +
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Residues in contact with PHE 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C VAL* 3.9 17.7 - - + -
105C GLY* 3.5 40.4 - - - -
106C LEU* 4.5 0.9 - - + -
191C ARG* 3.7 23.6 - - + -
193C GLN* 3.9 18.8 - - + -
199C MET* 3.9 16.2 - - + -
202C LEU* 3.8 23.1 - - + -
216C LEU* 4.0 10.5 - - + -
229C VAL* 3.0 45.8 + - + +
230C ALA 3.9 3.6 - - - +
232C ALA* 1.3 75.4 - - - +
234C ASP* 1.3 57.1 + - - +
237C VAL* 3.0 29.0 + - + +
238C GLY 3.2 5.7 + - - -
239C VAL* 3.9 15.7 - - + +
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Residues in contact with ASP 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C ALA 3.0 18.1 + - - +
231C ARG* 3.4 4.9 - - - +
233C PHE* 1.3 75.4 - - - +
235C GLU* 1.3 63.1 + - + +
237C VAL 4.0 0.2 - - - -
238C GLY* 3.0 23.8 + - - +
239C VAL* 3.1 29.7 + - + +
262C VAL 4.5 2.9 - - - +
263C THR* 3.7 36.9 - - + +
265C LYS* 4.6 5.2 - - - -
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Residues in contact with GLU 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C ARG* 2.7 59.0 + - + +
232C ALA* 4.2 3.4 - - - +
234C ASP* 1.3 75.9 - - + +
236C LYS* 1.3 67.2 + - + +
237C VAL 3.6 0.6 - - - -
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Residues in contact with LYS 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C GLN 2.8 27.7 + - - -
194C ILE* 5.0 0.2 - - - +
196C GLU* 4.0 19.7 + - - -
199C MET* 3.6 33.3 - - + +
203C ALA* 3.4 22.6 - - + +
232C ALA* 2.8 41.0 + - - +
235C GLU* 1.3 85.8 - - + +
237C VAL* 1.3 58.6 + - + +
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Residues in contact with VAL 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C PHE* 5.2 2.5 - - + -
199C MET* 4.1 15.9 - - + +
202C LEU* 3.7 43.5 - - + +
203C ALA* 4.3 6.1 - - - +
206C LYS* 3.1 55.1 + - + +
214C VAL* 4.0 24.5 - - + -
233C PHE* 3.0 14.1 + - + +
234C ASP 4.0 0.4 - - - -
235C GLU 5.2 0.4 - - - -
236C LYS* 1.3 84.2 - - + +
238C GLY* 1.3 59.2 + - - +
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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