Contacts of the helix formed by residues 281 - 285 (chain B) in PDB entry 2UZ1
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 GLY 281 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A THR 3.4 17.9 - - - -
110A ASN* 3.5 7.4 - - - -
279B ARG 3.4 0.4 + - - -
280B PHE* 1.3 74.8 - - - +
282B LEU* 1.3 65.3 + - - -
283B ASN 3.2 2.7 - - - -
284B THR* 3.0 13.4 + - - -
286B HIS* 2.8 33.4 + - - +
417B TYR* 4.0 4.5 - - - -
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Residues in contact with LEU 282 (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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110A ASN 2.9 17.5 + - - +
111A THR* 4.2 1.1 - - - +
112A LEU* 3.9 52.3 - - + +
281B GLY* 1.3 71.9 - - - +
283B ASN* 1.3 72.6 + - - +
284B THR 3.6 0.3 + - - -
285B GLY* 3.9 5.5 + - - -
286B HIS* 3.5 26.7 + - + +
397B TYR* 5.8 3.8 - - - +
416B GLY 4.3 5.2 - - - +
417B TYR* 3.8 23.5 - - + -
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Residues in contact with ASN 283 (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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238B ASP* 3.9 34.1 + - + +
239B TYR* 3.6 29.1 + - + -
257B VAL* 3.2 20.6 - - - +
258B GLN* 5.0 0.5 + - - +
281B GLY 3.2 0.8 - - - -
282B LEU* 1.3 89.1 - - - +
284B THR* 1.3 64.0 + - + +
285B GLY 3.5 0.7 - - - -
291B LEU* 3.8 6.8 - - - +
415B HIS 5.0 1.4 - - - +
416B GLY* 5.0 8.0 - - - -
417B TYR* 3.3 32.0 + - - +
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Residues in contact with THR 284 (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 VAL* 4.8 6.3 - - + -
238B ASP* 5.4 3.6 - - + +
257B VAL* 4.6 12.1 - - + -
275B MET* 4.7 6.1 - - + -
278B ALA* 4.3 19.7 - - + -
279B ARG 2.6 29.6 + - - +
280B PHE* 3.4 5.1 - - - -
281B GLY 3.0 14.1 + - - -
283B ASN* 1.3 86.7 - - + +
285B GLY* 1.3 58.7 + - - +
286B HIS 3.7 4.0 + - - +
291B LEU* 3.8 22.8 + - - +
292B ILE* 3.9 22.6 + - + +
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Residues in contact with GLY 285 (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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281B GLY 3.2 1.8 + - - -
282B LEU 3.9 4.6 + - - -
283B ASN 3.5 2.8 - - - -
284B THR* 1.3 74.6 - - - +
286B HIS* 1.3 79.7 + - - +
288B SER* 2.6 34.4 + - - -
289B GLY 4.3 1.0 + - - -
290B GLN* 5.5 2.7 - - - -
291B LEU* 4.0 14.1 - - - +
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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