Contacts of the helix formed by residues 273 - 278 (chain B) in PDB entry 4FGU
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 LYS 273 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B ASP* 5.2 2.4 - - + +
205B TYR* 3.9 9.6 - - + -
252B HIS* 4.5 6.3 + - + -
269B GLN* 2.8 64.1 + - + +
270B TYR* 4.0 4.8 - - - +
271B GLY 3.2 14.9 + - - +
272B GLN* 1.3 71.6 - - - +
274B THR* 1.3 57.1 + - - +
275B ILE 3.1 0.9 - - - -
276B SER* 2.5 35.1 + - - +
277B THR* 4.8 0.3 - - - +
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Residues in contact with THR 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B GLN* 3.0 25.4 + - - +
273B LYS* 1.3 74.6 - - - +
275B ILE* 1.3 56.3 + - - +
276B SER 3.2 0.4 - - - -
277B THR* 2.6 47.2 + - + +
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Residues in contact with ILE 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B LYS* 3.4 27.6 - - + +
182B MET 4.6 3.8 - - - +
183B VAL* 5.4 0.4 - - + -
203B ASN* 3.4 9.9 - - - +
204B VAL 3.4 30.5 - - - +
205B TYR* 3.6 26.9 - - + +
251B LEU* 3.6 7.0 - - + +
272B GLN* 3.0 23.5 + - + +
274B THR* 1.3 76.1 - - - +
276B SER* 1.3 56.2 + - - +
277B THR* 3.1 2.5 - - - -
278B MET* 2.8 53.0 + - + +
283B PHE* 4.3 13.0 - - + -
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Residues in contact with SER 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B TYR* 3.4 32.9 - - - -
250B THR* 3.5 2.3 - - - -
251B LEU* 2.8 36.1 + - - -
252B HIS* 2.6 46.1 + - - +
273B LYS 2.5 22.9 + - - -
275B ILE* 1.3 75.5 - - - +
277B THR* 1.3 60.5 + - - +
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Residues in contact with THR 277 (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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250B THR* 3.0 26.1 - - - +
252B HIS* 5.4 2.9 - - - +
274B THR* 2.6 42.1 + - + +
276B SER* 1.3 76.5 + - - +
278B MET* 1.3 77.3 + - - +
279B LYS* 3.4 3.3 + - - +
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Residues in contact with MET 278 (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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140B HIS* 4.7 4.9 - - - +
181B LYS* 3.5 38.6 - - + -
251B LEU* 3.1 28.1 + - - +
275B ILE* 2.8 38.5 + - + +
277B THR* 1.3 82.7 + - - +
279B LYS* 1.3 60.8 + - - +
282B GLN* 3.0 30.3 - - - +
283B PHE* 3.6 27.6 - - + -
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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