Contacts of the helix formed by residues 233 - 244 (chain C) in PDB entry 4PKO
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 MET 233 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221C LEU* 4.4 14.8 - - + -
227C ILE* 5.3 15.3 - - + -
231C ARG* 4.4 18.6 - - + +
232C GLU* 1.3 79.3 - - - +
234C LEU* 1.3 67.4 + - + +
235C PRO* 3.1 3.8 - - - -
236C VAL* 2.8 25.8 + - + +
237C LEU* 3.1 36.5 + - + -
247C LEU* 5.9 2.7 - - + -
249C ILE* 4.2 33.0 - - + -
258C ALA* 6.3 1.3 - - + -
262C LEU* 5.1 13.0 - - + -
309C LEU 4.2 16.4 - - - +
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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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231C ARG* 2.9 42.4 - - + +
232C GLU* 2.6 11.6 + - - +
233C MET* 1.3 74.2 - - + +
235C PRO* 1.3 55.0 - - + +
237C LEU* 2.7 28.3 + - + +
238C GLU* 2.5 38.4 + - + +
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Residues in contact with PRO 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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232C GLU 3.0 11.7 - - - +
233C MET 3.1 2.2 - - - +
234C LEU* 1.3 97.5 - - + +
236C VAL* 1.3 61.9 + - + +
238C GLU* 3.9 10.7 - - + +
239C ALA* 3.3 20.4 + - - +
310C GLU* 3.6 24.0 - - + +
312C ALA 5.1 3.4 - - - +
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Residues in contact with VAL 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C LEU* 5.2 14.4 - - + -
233C MET* 2.8 23.8 + - + +
235C PRO* 1.3 77.5 - - + +
237C LEU* 1.3 62.6 + - - +
239C ALA* 3.3 7.9 + - - +
240C VAL* 3.1 34.4 + - + +
247C LEU* 6.3 1.6 - - + -
309C LEU 5.2 1.8 - - - +
310C GLU 4.8 1.3 - - - +
312C ALA* 3.0 53.8 - - + +
313C THR 4.2 16.2 - - - +
314C LEU* 4.8 0.9 - - - +
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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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231C ARG* 6.5 0.7 - - + -
233C MET* 3.1 37.6 + - + +
234C LEU* 2.7 35.6 + - + +
236C VAL* 1.3 71.2 - - - +
238C GLU* 1.3 55.3 + - - +
240C VAL* 3.0 8.3 + - - +
241C ALA* 2.6 46.2 + - + -
247C LEU* 5.4 9.9 - - + -
262C LEU* 5.2 9.9 - - + -
265C ASN* 5.3 12.8 - - - +
271C VAL* 5.1 10.1 - - + -
273C VAL* 5.9 4.5 - - + -
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Residues in contact with GLU 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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234C LEU* 2.5 18.3 + - + +
235C PRO* 3.9 11.1 - - + +
237C LEU* 1.3 74.9 - - + +
239C ALA* 1.3 62.7 + - - +
241C ALA* 3.9 7.6 - - + +
242C LYS* 3.0 35.7 + - - +
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Residues in contact with ALA 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 PRO 3.3 11.8 + - - +
236C VAL* 3.3 12.9 + - - +
237C LEU 3.1 0.4 - - - -
238C GLU* 1.3 85.6 + - - +
240C VAL* 1.3 57.3 + - - +
242C LYS* 3.5 8.3 + - - +
243C ALA* 3.1 23.2 + - - +
314C LEU* 4.5 21.3 - - - +
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Residues in contact with VAL 240 (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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219C PHE* 3.6 34.5 - - + -
236C VAL* 3.2 22.9 - - + +
237C LEU* 3.0 6.1 + - + +
239C ALA* 1.3 75.5 - - + +
241C ALA* 1.3 61.5 + - - +
242C LYS 3.2 0.2 - - - -
243C ALA* 3.1 6.3 + - - +
244C GLY 2.8 23.0 + - - -
245C LYS 3.5 23.8 + - - +
247C LEU* 3.7 27.8 - - + -
271C VAL* 4.9 0.4 - - + -
314C LEU* 5.1 8.1 - - - -
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Residues in contact with ALA 241 (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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237C LEU* 2.6 29.9 + - + +
238C GLU* 3.9 7.9 - - + +
240C VAL* 1.3 72.3 - - - +
242C LYS* 1.3 61.5 + - - +
244C GLY* 3.2 12.8 + - - -
270C ILE* 4.8 12.0 - - + +
271C VAL* 3.4 34.9 - - + +
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Residues in contact with LYS 242 (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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238C GLU* 3.0 29.7 + - - +
239C ALA* 3.5 8.7 - - - +
241C ALA* 1.3 77.8 - - - +
243C ALA* 1.3 60.6 + - - +
244C GLY 3.7 0.2 + - - -
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Residues in contact with ALA 243 (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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219C PHE* 4.9 7.2 - - + -
239C ALA 3.1 15.1 + - - +
240C VAL* 3.1 15.2 + - + +
242C LYS* 1.3 81.8 - - - +
244C GLY* 1.3 60.1 + - - +
245C LYS* 4.3 15.8 - - + +
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Residues in contact with GLY 244 (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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240C VAL 2.8 9.2 + - - -
241C ALA 3.2 13.3 + - - -
243C ALA* 1.3 78.6 - - - +
245C LYS* 1.3 66.7 + - - -
246C PRO* 4.4 1.7 - - - +
270C ILE 5.5 0.7 - - - -
271C VAL* 4.2 11.4 - - - -
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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