Contacts of the helix formed by residues 227 - 239 (chain C) in PDB entry 2W93
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 VAL 227 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222C CYS* 3.1 28.6 + - - +
225C HIS 3.5 9.0 - - - +
226C ASP* 1.3 81.4 - - - +
228C LYS* 1.3 56.6 + - - +
229C ALA 3.4 2.7 - - - -
230C GLU* 3.4 12.0 + - - +
231C THR* 2.7 36.5 + - - -
285C VAL* 3.8 18.6 - - + -
326C MET* 4.0 15.7 - - + -
327C LYS* 3.8 26.5 - - + -
330C LEU* 3.7 23.8 - - + -
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Residues in contact with LYS 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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222C CYS* 3.6 19.1 - - - +
223C SER* 4.1 21.5 + - - +
226C ASP* 3.7 2.7 - - - -
227C VAL* 1.3 76.6 - - - +
229C ALA* 1.3 62.6 + - - +
231C THR* 3.4 1.8 + - - -
232C LYS* 3.0 24.3 + - - +
250C GLY 3.9 12.6 + - - -
251C SER* 3.7 41.2 - - - +
404C THR 5.1 1.8 + - - -
405C TYR* 3.6 32.3 - - + +
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Residues in contact with ALA 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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226C ASP 5.7 0.2 - - - -
227C VAL 3.4 1.0 - - - -
228C LYS* 1.3 78.0 - - - +
230C GLU* 1.3 65.8 + - - +
232C LYS* 3.2 10.8 + - - +
233C LYS* 3.0 32.4 + - + +
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Residues in contact with GLU 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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226C ASP 3.9 0.2 - - - +
227C VAL* 3.4 23.9 - - - +
229C ALA* 1.3 81.4 + - - +
231C THR* 1.3 57.6 + - - +
233C LYS* 3.3 4.3 + - - +
234C LEU* 2.8 28.6 + - - +
327C LYS* 2.9 31.5 + - - +
330C LEU* 4.0 30.0 - - + +
331C GLN* 2.9 35.8 + - + -
334C LEU* 3.9 21.5 - - + +
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Residues in contact with THR 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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216C ILE* 4.5 15.7 - - + -
218C ALA* 4.6 3.4 - - + -
222C CYS* 3.4 19.8 - - - -
227C VAL* 2.7 23.6 + - - +
228C LYS* 3.7 4.3 - - - -
229C ALA 3.3 0.2 - - - -
230C GLU* 1.3 74.3 - - - +
232C LYS* 1.3 64.5 + - - +
234C LEU* 3.2 9.7 + - + +
235C ILE* 3.0 28.1 + - + +
252C ILE* 3.8 27.1 - - + -
285C VAL* 3.7 19.1 - - + +
330C LEU* 4.8 3.2 - - - +
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Residues in contact with LYS 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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228C LYS 3.0 13.8 + - - +
229C ALA* 3.2 11.2 + - - +
231C THR* 1.3 75.5 - - - +
233C LYS* 1.3 58.6 + - + +
235C ILE* 3.3 12.7 + - + +
236C ASP* 3.0 42.6 + - - +
252C ILE* 5.7 1.0 - - - +
253C ASP* 3.5 25.6 + - - +
256C HIS* 4.9 15.1 - - + -
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Residues in contact with LYS 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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229C ALA* 3.0 19.6 + - + +
230C GLU* 3.6 7.2 - - - +
231C THR 3.3 0.2 - - - -
232C LYS* 1.3 78.6 - - + +
234C LEU* 1.3 55.7 + - - +
236C ASP* 3.1 13.2 + - - +
237C LEU* 2.8 55.1 + - + +
334C LEU* 3.9 23.3 - - + -
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Residues in contact with LEU 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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216C ILE* 3.9 33.0 - - + -
230C GLU 2.8 17.8 + - - +
231C THR* 3.4 9.4 - - - +
233C LYS* 1.3 75.8 - - - +
235C ILE* 1.3 53.7 + - - +
237C LEU* 4.4 1.5 - - - +
238C THR* 2.7 43.4 + - - +
283C LEU* 4.3 15.7 - - + -
285C VAL* 4.6 11.7 - - + -
309C PHE* 5.3 2.0 - - + -
330C LEU* 4.5 17.5 - - + -
333C LEU* 4.5 10.5 - - + -
334C LEU* 3.6 15.8 - - + +
337C ILE* 4.1 31.0 - - + -
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Residues in contact with ILE 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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216C ILE* 3.7 19.3 - - + -
231C THR* 3.0 21.9 + - + +
232C LYS* 3.6 11.0 - - + +
234C LEU* 1.3 75.0 - - - +
236C ASP* 1.3 57.8 + - - +
238C THR* 3.9 6.1 - - - -
239C GLN* 2.8 33.1 + - - -
240C PHE 4.4 11.7 - - - +
242C ALA* 3.6 23.1 - - + -
252C ILE* 3.9 28.7 - - + -
256C HIS* 3.7 35.7 - - + +
258C ARG* 4.4 4.3 - - + -
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Residues in contact with ASP 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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232C LYS* 3.0 36.2 + - - +
233C LYS* 3.4 19.6 - - - +
235C ILE* 1.3 77.9 - - - +
237C LEU* 1.3 67.6 + - + +
239C GLN* 3.1 27.2 + - - +
256C HIS* 3.4 24.1 + - - -
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Residues in contact with LEU 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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233C LYS* 2.8 43.8 + - + +
236C ASP* 1.3 77.0 - - + +
238C THR* 1.3 60.0 + - - +
239C GLN* 5.2 0.8 - - - +
334C LEU* 3.4 38.8 - - + +
337C ILE* 3.8 20.4 - - + -
338C ALA* 3.9 33.2 - - + +
341C ALA* 4.5 2.8 - - - +
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Residues in contact with THR 238 (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 ILE* 3.8 8.1 - - + -
234C LEU* 2.7 29.6 + - - +
235C ILE 3.6 2.7 - - - +
237C LEU* 1.3 80.4 - - - +
239C GLN* 1.3 72.5 + - - +
240C PHE* 3.1 62.3 + - + +
337C ILE* 3.8 22.0 - - - +
341C ALA* 4.2 10.2 - - - +
344C TYR* 3.9 5.2 - - - -
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Residues in contact with GLN 239 (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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235C ILE 2.8 21.3 + - - -
236C ASP* 3.1 27.1 + - - +
237C LEU 5.2 0.9 - - - +
238C THR* 1.3 74.8 - - - +
240C PHE* 1.3 60.6 + - - +
256C HIS* 4.7 6.7 + - - -
258C ARG* 2.6 61.4 + - - +
344C TYR* 3.5 9.3 - - + -
346C PRO* 5.3 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