Contacts of the helix formed by residues 241 - 248 (chain E) in PDB entry 5FHK
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 241 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E ILE* 4.0 15.3 - - + -
165E VAL* 3.5 35.9 - - + -
224E ARG* 4.3 13.5 - - + -
236E MET* 3.8 34.3 - - + -
237E PRO 3.7 7.4 - - - +
238E ASP* 3.1 11.6 + - - +
240E MET* 1.3 83.1 - - + +
242E LYS* 1.3 66.0 + - - +
243E GLU 3.2 2.7 - - - +
244E TYR* 3.0 27.5 + - + +
245E ILE* 3.0 16.7 + - + +
250E LEU* 3.9 19.5 - - + -
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Residues in contact with LYS 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238E ASP* 3.2 27.8 + - - +
239E VAL* 4.1 26.7 + - - +
240E MET 3.7 2.0 - - - -
241E ILE* 1.3 76.1 - - - +
243E GLU* 1.3 63.4 + - - +
245E ILE* 3.3 9.0 + - + +
246E ALA* 3.0 25.1 + - + +
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Residues in contact with GLU 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E ARG* 2.8 43.6 + - - +
240E MET 6.1 0.4 - - - +
241E ILE 3.2 0.8 - - - -
242E LYS* 1.3 79.3 - - - +
244E TYR* 1.3 81.7 + - + +
246E ALA* 3.5 5.9 + - - +
247E ASP* 3.0 33.8 + - + +
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Residues in contact with TYR 244 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E LYS* 5.8 0.5 + - - -
104E ARG* 4.4 9.0 + - - -
224E ARG* 3.5 46.8 + - - -
228E SER* 5.0 2.9 - - - -
240E MET 4.1 11.9 - - - -
241E ILE* 3.0 27.2 + - + +
243E GLU* 1.3 101.5 + - + +
245E ILE* 1.3 61.6 + - - +
247E ASP* 2.7 25.1 - - - +
248E GLY 3.0 10.0 + - - -
249E SER* 3.2 25.1 + - - +
250E LEU* 3.2 25.6 + - + +
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Residues in contact with ILE 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E ILE* 4.7 9.9 - - + -
165E VAL* 4.0 17.9 - - + -
238E ASP 6.0 0.2 - - - +
241E ILE* 3.0 22.9 + - + +
242E LYS* 3.6 11.0 - - + +
244E TYR* 1.3 75.5 - - - +
246E ALA* 1.3 64.4 + - - +
248E GLY* 3.3 10.7 + - - -
250E LEU* 3.6 20.7 - - + +
252E ARG* 3.7 28.9 - - + +
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Residues in contact with ALA 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242E LYS* 3.0 19.0 + - + +
243E GLU* 3.8 6.5 - - - +
244E TYR 3.3 0.2 - - - -
245E ILE* 1.3 79.9 - - - +
247E ASP* 1.3 61.3 + - - +
248E GLY 3.5 0.5 + - - -
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Residues in contact with ASP 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243E GLU* 3.0 26.1 + - + +
244E TYR* 2.7 32.0 - - - +
246E ALA* 1.3 77.6 - - + +
248E GLY* 1.3 58.1 - - - +
249E SER* 2.7 25.3 + - - -
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Residues in contact with GLY 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E PRO* 3.2 24.3 - - - +
244E TYR 3.0 5.8 + - - -
245E ILE 3.3 7.1 + - - -
246E ALA 3.3 4.2 + - - -
247E ASP* 1.3 78.9 + - - +
249E SER* 1.3 59.8 + - - +
250E LEU 3.2 9.5 + - - +
251E VAL* 4.2 3.7 - - - +
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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