Contacts of the helix formed by residues 218 - 224 (chain f) in PDB entry 5T0J
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 VAL 218 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203f GLY 5.7 3.1 - - - +
204f SER* 5.9 5.4 - - - +
207f ASP* 3.3 26.7 - - + +
214f ALA* 3.2 19.3 - - + +
216f SER 2.9 3.2 + - - -
217f PHE* 1.3 86.2 - - + +
219f ASN* 1.3 67.1 + - + +
220f GLY 3.3 0.9 - - - -
221f PHE* 3.2 3.0 + - - +
222f VAL* 3.1 31.0 + - + +
238f LYS* 4.3 26.0 - - - +
240f LEU* 5.4 7.4 - - + -
248f MET* 5.0 4.0 - - + -
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Residues in contact with ASN 219 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215f SER* 3.0 32.6 + - - +
218f VAL* 1.3 78.5 - - + +
220f GLY* 1.3 52.3 + - - +
222f VAL* 3.3 13.5 - - - +
223f ASN* 2.7 29.0 + - - +
248f MET* 3.6 34.0 - - + +
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Residues in contact with GLY 220 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215f SER 3.2 9.2 + - - -
216f SER* 5.3 1.1 - - - -
217f PHE* 4.8 6.7 - - - -
218f VAL 3.3 1.0 - - - +
219f ASN* 1.3 77.2 - - - +
221f PHE* 1.3 59.6 + - - +
223f ASN* 2.8 27.1 - - - +
224f ALA* 3.6 10.7 - - - +
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Residues in contact with PHE 221 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189f ILE* 5.3 14.6 - - + -
217f PHE* 3.2 40.7 - + - +
218f VAL* 3.2 8.9 + - - +
220f GLY* 1.3 78.1 - - - +
222f VAL* 1.3 76.5 + - + +
224f ALA* 3.5 3.4 + - - +
225f ALA* 3.2 26.7 + - + +
230f LYS* 4.0 36.6 - - + -
231f LEU* 5.9 0.2 - - + -
234f ASP* 3.7 22.4 - - - -
666f MET* 4.2 24.5 - - - -
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Residues in contact with VAL 222 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218f VAL* 3.4 13.5 - - + +
219f ASN* 3.3 21.5 - - - +
221f PHE* 1.3 87.0 - - + +
223f ASN* 1.3 64.3 + - + +
225f ALA* 3.6 20.5 + - - +
231f LEU* 3.8 30.8 - - + +
234f ASP* 6.0 4.0 - - + +
238f LYS* 4.2 8.5 - - - +
248f MET* 4.1 17.3 - - + +
249f LEU* 3.8 22.2 - - + -
251f ALA* 5.4 0.9 - - - +
254f SER* 4.0 16.9 - - - +
255f LEU* 6.0 0.2 - - - +
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Residues in contact with ASN 223 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219f ASN* 2.7 27.8 + - - +
220f GLY* 2.8 21.4 - - - +
222f VAL* 1.3 81.9 - - + +
224f ALA* 1.3 77.0 + - - +
225f ALA 3.3 1.6 + - - +
254f SER* 3.8 22.2 - - - +
255f LEU* 4.1 9.5 - - - +
258f ILE* 3.3 47.8 - - + +
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Residues in contact with ALA 224 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220f GLY 3.6 15.5 - - - +
221f PHE* 3.5 4.3 + - - +
222f VAL 3.4 0.6 - - - -
223f ASN* 1.3 81.7 + - - +
225f ALA* 1.3 59.1 + - - +
226f PHE* 3.7 6.9 + - - +
230f LYS* 5.5 0.5 + - - -
258f ILE* 5.4 0.7 - - - -
666f MET* 5.8 2.9 - - - +
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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