Contacts of the helix formed by residues 237 - 247 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219B VAL* 4.2 14.8 - - + +
222B ALA* 3.9 10.8 - - + +
223B TYR* 3.9 30.5 - - - +
226B LYS* 4.1 15.1 - - + +
235B VAL 3.8 1.6 + - - -
236B SER* 1.3 71.5 - - - +
238B LYS* 1.3 58.2 + - - +
240B ILE* 3.1 5.8 + - + +
241B VAL* 2.9 42.7 + - + +
309B ALA 4.5 0.2 - - - +
310B MET* 3.6 29.8 + - - +
312B TYR* 4.2 23.4 - - + +
315B ILE* 4.0 20.6 - - + -
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Residues in contact with LYS 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B GLU* 4.6 12.7 + - + -
87B LEU* 3.9 31.3 - - + +
236B SER* 3.8 8.7 - - - +
237B ILE* 1.3 80.7 - - - +
239B ASP* 1.3 69.1 + - - +
241B VAL* 3.3 4.2 + - - +
242B HIS* 3.1 22.9 + - + +
307B ARG* 5.9 0.4 - - - +
310B MET* 3.9 27.0 + - + +
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Residues in contact with ASP 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B VAL* 3.6 16.8 - - + +
236B SER* 2.9 27.6 + - - +
238B LYS* 1.3 86.0 - - - +
240B ILE* 1.3 62.9 + - - +
242B HIS* 3.6 7.8 + - - +
243B GLU* 3.3 21.7 + - - +
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Residues in contact with ILE 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B MET* 3.5 21.1 - - + +
222B ALA* 3.9 24.0 - - + +
225B ILE* 4.0 14.6 - - + -
226B LYS* 3.4 40.4 - - + +
232B TYR* 3.8 14.4 - - + -
235B VAL* 3.5 24.9 - - + +
236B SER 2.8 18.9 + - - +
237B ILE* 3.5 8.7 - - - +
239B ASP* 1.3 75.1 - - - +
241B VAL* 1.3 66.3 + - - +
243B GLU* 3.5 0.6 + - - -
244B MET* 3.0 23.7 + - - +
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Residues in contact with VAL 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 4.0 9.0 - - + +
88B PHE* 4.0 15.7 - - + -
218B CYS* 4.5 10.1 - - - +
219B VAL* 4.8 5.4 - - + -
222B ALA* 3.8 20.6 - - + -
237B ILE* 2.9 28.2 + - + +
238B LYS 3.7 4.7 - - - +
240B ILE* 1.3 78.7 - - - +
242B HIS* 1.3 62.6 + - - +
244B MET* 3.3 8.6 + - - +
245B PHE* 3.1 53.4 + - + -
310B MET* 4.3 19.5 - - + -
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Residues in contact with HIS 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B LYS 5.2 0.2 - - - -
86B GLU 3.6 23.2 + - - -
87B LEU 3.8 13.1 + - - +
88B PHE 4.5 3.8 - - - +
89B GLY* 4.1 19.3 + - - -
238B LYS* 3.1 17.0 + - + +
239B ASP* 3.8 11.0 - - - +
240B ILE 3.2 0.4 - - - -
241B VAL* 1.3 79.3 - - - +
243B GLU* 1.3 63.5 + - - +
245B PHE* 3.4 4.3 + - - +
246B SER* 3.2 21.0 + - - -
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Residues in contact with GLU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B MET* 3.4 15.6 - - + +
198B ARG* 3.1 16.5 + - - -
232B TYR* 2.7 30.7 + - - -
239B ASP 3.3 13.6 + - - +
242B HIS* 1.3 77.7 - - - +
244B MET* 1.3 69.4 + - - +
246B SER* 2.6 30.8 + - - +
247B TYR* 2.5 37.4 + - - +
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Residues in contact with MET 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B VAL* 3.8 27.6 - - + -
194B MET* 3.9 17.2 - - + -
197B MET* 3.7 24.2 - - + -
213B TYR* 3.0 30.3 + - + -
218B CYS* 3.8 28.3 - - + +
221B ASN* 3.7 25.4 - - - +
222B ALA* 4.2 15.0 - - - -
225B ILE* 4.3 2.2 - - + -
240B ILE 3.0 18.3 + - - +
241B VAL* 3.3 13.7 - - - +
243B GLU* 1.3 78.5 - - - +
245B PHE* 1.3 66.0 + - + +
246B SER 3.4 0.2 + - - -
247B TYR* 3.4 6.3 + - - -
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Residues in contact with PHE 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B PHE* 3.4 47.1 - + - +
90B PHE* 3.4 31.4 - + + -
213B TYR* 3.7 24.7 - + - -
215B ALA* 3.4 34.5 - - + -
218B CYS* 4.0 13.7 - - + -
241B VAL* 3.1 43.3 + - + +
242B HIS 3.4 1.3 + - - +
243B GLU 3.2 0.4 - - - -
244B MET* 1.3 81.2 - - + +
246B SER* 1.3 57.8 + - - +
247B TYR 2.9 10.4 + - - -
248B ALA* 3.0 19.5 + - - +
251B CYS* 4.1 12.8 - - + -
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Residues in contact with SER 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B HIS* 4.6 8.1 + - - -
242B HIS* 3.2 16.8 + - - -
243B GLU* 2.6 32.8 + - - +
245B PHE* 1.3 76.6 - - - +
247B TYR* 1.3 71.3 + - - +
248B ALA 3.4 4.1 + - - +
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Residues in contact with TYR 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B MET* 3.9 10.5 - - + -
197B MET* 4.0 8.9 - - + +
198B ARG* 3.0 53.0 + - + -
201B HIS* 3.6 55.4 + + + +
211B ILE* 3.8 13.0 - - - +
213B TYR* 3.5 15.9 + - - +
243B GLU* 2.5 52.6 + - - +
244B MET 3.4 6.3 + - - -
245B PHE 2.9 1.4 - - - -
246B SER* 1.3 91.4 - - - +
248B ALA* 1.3 57.9 + - - +
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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