Contacts of the helix formed by residues 238 - 248 (chain B) in PDB entry 5OF4
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ARG* 3.1 17.5 + - - +
237B HIS* 1.3 75.2 - - - +
239B ILE* 1.3 64.4 + - - +
240B ASP* 3.2 9.0 - - - -
241B ASN* 3.1 26.4 + - + +
242B VAL* 2.9 27.6 + - + +
606B GLU* 5.1 0.5 - - - +
658B ARG* 3.9 16.3 - - - +
659B HIS* 4.1 12.5 + - - -
662B GLN* 2.6 42.7 + - - -
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Residues in contact with ILE 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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75B ARG* 3.4 18.8 - - - +
209B TYR* 3.2 30.7 - - + +
233B PHE* 5.0 5.4 - - + -
236B ALA* 3.6 32.5 - - + +
237B HIS 3.2 5.0 + - - +
238B ASN* 1.3 77.3 - - - +
240B ASP* 1.3 64.5 + - - +
242B VAL* 3.4 1.7 + - - +
243B CYS* 3.1 33.9 + - - -
440B ALA* 6.2 0.4 - - + -
444B ILE* 3.7 29.2 - - + -
456B ILE* 3.8 15.5 - - + -
470B ILE* 4.0 17.0 - - + -
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Residues in contact with ASP 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ASN 3.7 2.8 - - - -
239B ILE* 1.3 77.0 - - - +
241B ASN* 1.3 75.2 + - - -
243B CYS* 3.3 2.8 + - - +
244B ILE* 2.9 35.1 + - - +
440B ALA* 4.4 13.2 - - + -
469B LYS* 3.7 29.6 - - + +
470B ILE* 5.7 2.3 - - + +
636B ARG* 2.4 29.5 + - - +
651B PHE* 3.3 8.8 - - - -
658B ARG* 2.8 39.8 + - - +
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Residues in contact with ASN 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ASN* 3.1 26.5 + - + +
240B ASP* 1.3 88.7 + - - +
242B VAL* 1.3 57.9 + - + +
244B ILE* 3.9 7.4 - - - +
245B ASP* 2.9 33.8 + - - +
636B ARG* 3.2 27.2 + - - -
658B ARG* 3.0 20.8 - - - +
659B HIS* 4.5 9.9 + - - -
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Residues in contact with VAL 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ARG* 4.9 4.0 - - - +
209B TYR* 3.5 46.0 - - + +
210B HIS* 4.0 24.2 - - + -
213B LEU* 4.2 14.8 - - + +
238B ASN* 2.9 25.7 + - + +
239B ILE 3.7 2.0 - - - +
241B ASN* 1.3 74.7 - - + +
243B CYS* 1.3 60.6 + - - +
245B ASP* 4.5 1.5 - - - +
246B SER* 2.8 34.0 + - - -
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Residues in contact with CYS 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B LEU* 3.6 30.5 - - - -
239B ILE* 3.1 25.3 + - - +
240B ASP* 3.7 5.4 - - - +
242B VAL* 1.3 76.9 - - - +
244B ILE* 1.3 62.6 + - - +
246B SER* 2.7 20.6 + - - -
247B MET* 3.0 19.2 + - - +
437B CYS* 6.1 0.2 - - - -
439B ASP 5.5 1.3 - - - +
440B ALA* 4.2 16.4 - - - +
443B ALA* 3.6 29.7 - - + +
444B ILE* 4.2 8.1 - - - -
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Residues in contact with ILE 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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240B ASP 2.9 21.7 + - - +
241B ASN* 3.9 6.1 - - - +
243B CYS* 1.3 78.1 - - + +
245B ASP* 1.3 58.1 + - + +
247B MET* 3.1 2.5 + - - +
248B SER* 2.7 39.7 + - - +
436B SER* 4.5 18.1 - - - -
437B CYS* 4.2 22.1 + - + +
438B MET* 3.8 26.9 - - + +
439B ASP 5.3 2.7 - - - +
440B ALA* 5.6 1.3 - - - -
469B LYS* 4.1 12.8 - - - +
632B ILE* 6.1 2.7 - - + -
636B ARG* 4.1 22.2 - - - +
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Residues in contact with ASP 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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210B HIS* 4.8 5.5 + - + +
216B LYS* 3.9 20.4 + - - -
241B ASN 2.9 19.6 + - - +
242B VAL* 4.5 1.8 - - - +
244B ILE* 1.3 80.3 - - + +
246B SER* 1.3 57.8 + - - +
247B MET 3.4 0.4 + - - -
248B SER* 3.6 14.5 + - - -
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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
----------------------------------------------------------
210B HIS* 3.4 18.6 + - - -
213B LEU 3.4 22.4 + - - -
214B ASP* 3.3 8.7 - - - +
215B PRO* 3.3 13.7 - - - +
216B LYS* 3.2 30.5 + - - +
242B VAL 2.8 16.8 + - - -
243B CYS* 2.7 24.9 + - - -
245B ASP* 1.3 79.4 - - - +
247B MET* 1.3 56.6 + - - +
443B ALA* 4.9 0.5 - - - +
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Residues in contact with MET 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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215B PRO* 3.5 27.8 - - + +
216B LYS* 4.8 3.1 - - - +
243B CYS* 3.0 11.7 + - + +
244B ILE 4.2 0.7 - - - +
246B SER* 1.3 80.7 - - - +
248B SER* 1.3 65.0 + - - +
249B VAL* 3.7 11.1 + - - +
406B LEU* 3.9 19.4 - - + +
410B TYR* 4.4 9.0 - - - -
414B PHE* 3.5 24.4 - - + -
435B PHE* 3.8 5.0 - - - +
436B SER* 5.3 0.2 - - - -
437B CYS* 3.6 37.5 - - + -
439B ASP 4.6 1.6 - - - +
442B LEU 4.2 15.3 - - - +
443B ALA* 4.0 20.9 - - + +
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Residues in contact with SER 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B LYS* 3.3 24.6 + - - -
244B ILE* 2.7 26.0 + - - +
245B ASP* 3.6 18.7 + - - +
247B MET* 1.3 76.6 - - - +
249B VAL* 1.3 61.3 + - - +
434B HIS* 5.9 2.5 - - - -
435B PHE 2.7 17.3 - - - -
436B SER* 3.7 19.2 - - - +
437B CYS 5.0 0.2 - - - +
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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