Contacts of the helix formed by residues 238 - 249 (chain C) in PDB entry 4CFE
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 ASN 238 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113C GLU* 3.3 28.5 + - - -
235C GLU 5.4 0.2 - - - -
236C TYR 3.6 5.4 + - - +
237C LEU* 1.3 78.2 - - - +
239C ARG* 1.3 72.5 + - - +
240C SER* 3.1 15.3 + - - +
241C VAL* 3.0 36.8 + - - +
242C ALA* 3.2 19.9 + - - +
267C TRP* 4.3 4.5 - - - +
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Residues in contact with ARG 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 GLU* 5.1 6.5 + - - +
237C LEU 4.6 8.9 + - - -
238C ASN* 1.3 78.5 - - - +
240C SER* 1.3 63.4 + - - +
242C ALA* 3.5 6.2 + - - +
243C THR* 3.3 29.8 + - + +
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Residues in contact with SER 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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238C ASN* 3.1 9.9 + - - +
239C ARG* 1.3 79.6 - - - +
241C VAL* 1.3 60.6 + - - +
243C THR* 2.6 25.3 + - - -
244C LEU 3.5 0.2 + - - -
265C HIS* 3.1 26.3 + - - -
266C GLU* 4.7 6.6 - - - +
267C TRP* 3.7 16.0 + - - +
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Residues in contact with VAL 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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113C GLU* 5.2 0.7 - - - +
204C LEU* 4.7 6.7 - - + -
208C LEU* 3.6 24.0 - - + -
237C LEU* 4.2 16.4 - - + -
238C ASN* 3.0 38.8 + - - +
240C SER* 1.3 76.9 + - - +
242C ALA* 1.3 64.2 + - - +
244C LEU* 3.3 7.3 + - + +
245C LEU* 3.2 23.5 + - + +
267C TRP* 3.5 47.7 - - + +
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Residues in contact with ALA 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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233C ILE* 4.2 28.1 - - + +
237C LEU* 4.6 3.8 - - + +
238C ASN 3.2 20.3 + - - +
239C ARG* 3.7 8.5 - - - +
240C SER 3.1 0.2 - - - -
241C VAL* 1.3 80.6 - - + +
243C THR* 1.3 61.3 - - + +
245C LEU* 3.4 9.6 + - - +
246C MET* 3.2 31.6 + - - +
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Residues in contact with THR 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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239C ARG* 3.3 14.1 + - + +
240C SER* 2.6 23.1 + - - -
242C ALA* 1.3 78.7 - - + +
244C LEU* 1.3 60.7 + - - +
245C LEU 3.4 0.2 - - - -
246C MET* 3.7 12.3 + - - +
247C HIS* 3.3 22.3 + - - +
265C HIS* 3.2 11.7 + - - -
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Residues in contact with LEU 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C PHE* 4.8 1.6 - - + -
204C LEU* 4.5 9.6 - - + -
240C SER 3.5 0.6 + - - +
241C VAL* 3.3 9.8 + - + +
242C ALA 3.2 0.6 - - - -
243C THR* 1.3 78.8 + - - +
245C LEU* 1.3 64.9 + - - +
247C HIS* 3.3 9.3 + - + +
248C MET* 3.1 50.1 + - + +
257C ALA* 5.7 1.1 - - + -
261C ASP 5.6 0.4 - - - +
262C ILE* 4.2 28.3 - - + -
265C HIS* 3.5 42.0 - - + +
267C TRP* 3.7 32.5 - - + -
268C PHE* 4.7 3.1 - - + -
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Residues in contact with LEU 245 (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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201C GLY* 3.4 29.2 - - - +
204C LEU* 3.7 27.1 - - + -
205C TYR* 4.0 28.0 - - + +
208C LEU* 4.9 7.4 - - + -
231C PHE* 4.4 13.7 - - + -
233C ILE* 5.6 2.9 - - + -
237C LEU* 3.8 29.4 - - + -
241C VAL* 3.2 14.1 + - + +
242C ALA* 3.4 9.2 + - - +
244C LEU* 1.3 79.9 - - - +
246C MET* 1.3 57.0 + - + +
248C MET* 3.3 3.6 + - - -
249C LEU* 3.0 36.8 + - + +
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Residues in contact with MET 246 (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 PHE* 4.4 12.3 - - + -
233C ILE* 3.7 26.7 - - + -
242C ALA* 3.2 21.4 + - - +
243C THR* 4.0 11.7 - - - +
245C LEU* 1.3 75.9 - - - +
247C HIS* 1.3 60.7 + - - +
249C LEU 4.1 0.9 - - - -
250C GLN* 3.6 27.0 + - - +
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Residues in contact with HIS 247 (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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243C THR 3.3 16.1 + - - +
244C LEU* 3.6 11.7 - - + +
245C LEU 3.1 0.4 - - - -
246C MET* 1.3 80.0 - - - +
248C MET* 1.3 62.5 + - + +
249C LEU 3.6 0.2 + - - -
250C GLN* 3.6 7.5 - - - +
255C LYS 3.2 23.5 + - - -
256C ARG* 3.6 6.9 - - - -
257C ALA* 3.1 41.4 + - + +
261C ASP* 3.9 20.4 + - + -
265C HIS* 6.2 3.4 - + - -
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Residues in contact with MET 248 (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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120C PHE* 3.7 27.4 - - + -
197C ILE* 3.4 27.5 - - + +
198C TRP* 3.9 11.3 - - - -
200C CYS* 3.6 12.3 - - + -
201C GLY* 3.4 24.9 - - - +
204C LEU* 4.7 5.4 - - - -
244C LEU* 3.1 37.0 + - + +
245C LEU* 4.0 4.3 - - - +
247C HIS* 1.3 78.3 - - - +
249C LEU* 1.3 58.3 + - - +
250C GLN 3.3 1.1 - - - -
256C ARG* 3.3 24.8 - - - +
257C ALA* 4.4 6.3 - - + -
262C ILE* 3.8 27.1 - - + -
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Residues in contact with LEU 249 (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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198C TRP* 3.4 57.9 + - + +
201C GLY* 3.9 19.3 - - - +
202C VAL* 3.7 11.7 - - + +
205C TYR* 5.1 1.8 - - + -
213C PRO* 4.5 10.1 - - + -
214C PHE* 4.4 10.0 - - + -
229C GLY* 5.1 6.2 - - - +
231C PHE* 3.8 43.1 - - + -
245C LEU* 3.0 20.8 + - + +
246C MET 4.1 3.1 - - - -
247C HIS 3.3 0.2 - - - -
248C MET* 1.3 77.5 - - - +
250C GLN* 1.3 63.7 + - - +
251C VAL* 3.4 7.3 + - - +
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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