Contacts of the helix formed by residues 237 - 247 (chain C) in PDB entry 1C7G
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 ILE 237 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219C VAL* 4.2 20.0 - - + -
222C ALA* 4.1 7.6 - - + +
223C TYR* 3.9 28.5 - - - +
226C LYS* 3.9 20.3 - - + +
235C VAL 3.8 0.6 + - - -
236C SER* 1.3 72.7 - - - +
238C LYS* 1.3 64.2 + - - +
240C ILE* 3.2 5.3 + - - +
241C VAL* 3.0 28.0 + - + +
309C ALA 4.5 0.2 - - - +
310C MET* 3.5 33.6 + - - +
312C TYR* 4.0 28.4 - - + +
315C ILE* 4.0 16.8 - - + -
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Residues in contact with LYS 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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86C GLU* 4.5 13.7 + - + +
87C LEU* 3.8 31.2 - - + +
236C SER* 3.9 9.6 - - - +
237C ILE* 1.3 80.8 - - - +
239C ASP* 1.3 67.6 + - - +
241C VAL* 3.6 3.3 + - - +
242C HIS* 3.2 22.2 + - + +
307C ARG* 5.8 1.6 - - - +
310C MET* 4.1 24.9 + - + +
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Residues in contact with ASP 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 VAL* 3.6 16.4 - - + +
236C SER* 2.9 26.5 + - - +
238C LYS* 1.3 85.2 - - - +
240C ILE* 1.3 65.5 + - - +
242C HIS* 3.4 7.8 + - - +
243C GLU* 3.1 22.5 + - - +
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Residues in contact with ILE 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C MET* 3.4 23.3 - - + +
222C ALA* 3.7 25.6 - - + +
225C ILE* 3.9 17.3 - - + -
226C LYS* 3.5 39.7 - - + +
232C TYR* 3.9 12.6 - - + -
235C VAL* 3.6 23.8 - - + +
236C SER 2.9 17.5 + - - +
237C ILE* 3.7 8.1 - - - +
239C ASP* 1.3 73.0 - - - +
241C VAL* 1.3 62.1 + - - +
243C GLU* 3.3 1.2 + - - -
244C MET* 3.0 29.1 + - - +
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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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87C LEU 4.0 12.8 - - - +
88C PHE* 4.1 12.1 - - + -
218C CYS* 4.6 9.0 - - - +
219C VAL* 4.8 5.2 - - + -
222C ALA* 3.8 19.7 - - + -
237C ILE* 3.0 23.5 + - + +
238C LYS 3.8 4.0 - - - +
240C ILE* 1.3 76.6 - - - +
242C HIS* 1.3 62.6 + - - +
244C MET* 3.4 8.8 + - - +
245C PHE* 3.2 46.6 + - + -
310C MET* 4.1 25.6 - - + -
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Residues in contact with HIS 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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85C LYS 5.0 0.2 - - - -
86C GLU 3.7 17.9 + - - -
87C LEU* 3.5 20.7 + - - +
88C PHE 4.6 3.1 - - - +
89C GLY* 3.9 21.6 + - - -
238C LYS 3.2 14.4 + - - +
239C ASP* 3.7 9.6 - - - +
240C ILE 3.3 0.2 - - - -
241C VAL* 1.3 81.1 - - - +
243C GLU* 1.3 63.2 + - - +
245C PHE* 3.6 2.9 + - - +
246C SER* 3.2 21.3 + - - -
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Residues in contact with GLU 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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194C MET* 3.5 8.6 - - + +
198C ARG* 3.0 18.8 + - - -
232C TYR* 2.7 31.6 + - - -
239C ASP 3.1 17.2 + - - +
240C ILE 3.8 3.8 - - - +
241C VAL 3.3 0.2 - - - -
242C HIS* 1.3 76.9 - - - +
244C MET* 1.3 67.5 + - - +
246C SER* 2.7 28.9 + - - +
247C TYR* 2.6 37.4 + - + +
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Residues in contact with MET 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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182C VAL* 3.9 24.2 - - + -
194C MET* 3.8 20.6 - - + -
197C MET* 3.9 19.7 - - + -
213C TYR* 3.1 28.6 + - + -
218C CYS* 3.8 41.3 - - + +
221C ASN* 4.3 12.1 - - - +
222C ALA* 4.3 11.4 - - - -
225C ILE* 4.3 2.0 - - + -
240C ILE* 3.0 19.7 + - - +
241C VAL* 3.5 16.8 - - - +
243C GLU* 1.3 79.0 - - - +
245C PHE* 1.3 67.7 + - + +
247C TYR* 3.2 7.6 + - - -
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Residues in contact with PHE 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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88C PHE* 3.4 57.2 - + - +
90C PHE* 3.5 29.7 - + + -
213C TYR* 3.9 22.4 - + - -
215C ALA* 3.5 33.9 - - + -
218C CYS* 3.8 17.3 - - + -
241C VAL* 3.2 34.1 + - + +
242C HIS 4.1 0.7 - - - +
243C GLU 3.2 0.4 - - - -
244C MET* 1.3 79.3 - - + +
246C SER* 1.3 60.7 + - - +
247C TYR 2.9 7.4 + - - -
248C ALA* 3.1 19.3 + - - +
251C CYS* 4.1 13.5 - - + -
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Residues in contact with SER 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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201C HIS* 4.7 7.4 + - - -
242C HIS* 3.2 20.1 + - - -
243C GLU* 2.7 26.6 + - - +
245C PHE* 1.3 76.2 - - - +
247C TYR* 1.3 73.6 + - - +
248C ALA 3.4 4.6 + - - +
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Residues in contact with TYR 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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194C MET* 3.9 10.8 - - + -
197C MET* 3.6 26.1 - - + +
198C ARG* 3.0 43.5 + - + -
201C HIS* 3.6 46.1 + + + +
211C ILE* 3.9 12.6 - - - +
213C TYR* 3.5 16.3 + - - +
243C GLU* 2.6 52.1 + - + +
244C MET* 3.2 6.9 + - - -
245C PHE 2.9 1.4 - - - -
246C SER* 1.3 91.4 - - - +
248C ALA* 1.3 57.4 + - - +
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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