Contacts of the helix formed by residues 227 - 235 (chain J) in PDB entry 1ZUM
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 THR 227 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53J GLU* 4.9 7.5 + - - +
54J GLY 3.9 4.3 + - - -
55J ASP* 3.6 37.4 - - - +
56J LYS* 5.4 0.3 - - - +
224J PHE* 3.0 31.7 + - + +
225J GLY 2.9 0.8 + - - -
226J PRO* 1.3 87.5 - - + +
228J ALA* 1.3 66.8 + - - -
229J GLY 3.4 0.4 - - - -
230J ALA* 3.5 1.2 + - - +
231J ALA* 3.0 30.0 + - - +
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Residues in contact with ALA 228 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54J GLY 3.5 24.0 + - - +
55J ASP* 4.5 2.2 - - - +
59J VAL* 3.7 15.7 - - + +
192J LYS* 3.7 23.1 - - + -
221J VAL* 4.5 5.4 - - + -
223J GLY* 4.5 1.3 - - - -
224J PHE 3.0 11.1 + - - +
227J THR* 1.3 79.9 + - - +
229J GLY* 1.3 64.0 + - - +
231J ALA* 3.3 4.5 + - - +
232J ILE* 3.2 27.0 + - - +
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Residues in contact with GLY 229 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165J ILE* 3.7 28.1 - - - +
192J LYS* 3.9 16.6 - - - +
224J PHE 3.3 4.0 + - - -
225J GLY* 3.2 13.3 + - - -
228J ALA* 1.3 78.6 - - - +
230J ALA* 1.3 61.4 + - - +
232J ILE* 3.3 3.8 + - - +
233J ALA* 3.3 18.4 + - - +
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Residues in contact with ALA 230 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225J GLY 2.9 7.5 + - - +
226J PRO* 3.4 28.5 - - + +
227J THR 3.5 0.4 + - - +
228J ALA 3.4 0.2 - - - -
229J GLY* 1.3 74.2 - - - +
231J ALA* 1.3 57.5 + - - +
233J ALA* 3.4 6.7 + - - +
234J SER* 2.8 37.4 + - - +
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Residues in contact with ALA 231 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56J LYS* 3.8 47.3 + - + +
59J VAL* 4.0 13.5 - - + +
227J THR 3.0 18.4 + - - +
228J ALA 3.5 6.3 - - - +
229J GLY 3.2 0.4 - - - -
230J ALA* 1.3 76.7 - - - +
232J ILE* 1.3 55.8 + - - +
234J SER* 3.8 1.8 - - - -
235J HIS* 3.0 31.2 + - - +
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Residues in contact with ILE 232 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59J VAL* 3.5 24.0 - - + -
163J GLY* 3.5 31.9 - - - -
165J ILE* 4.9 7.4 - - + -
190J VAL* 3.9 26.2 - - + +
191J MET 4.5 1.1 - - - -
192J LYS* 3.6 37.2 - - + +
221J VAL* 5.5 1.6 - - + -
228J ALA 3.2 11.2 + - - +
229J GLY 3.7 5.8 - - - +
230J ALA 3.3 0.2 - - - -
231J ALA* 1.3 76.0 - - - +
233J ALA* 1.3 64.2 + - - +
234J SER 3.3 0.5 + - - -
235J HIS* 3.4 9.5 + - - -
238J VAL* 3.6 26.7 - - + +
241J VAL* 4.8 5.4 - - + -
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Residues in contact with ALA 233 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165J ILE* 5.1 3.6 - - + -
229J GLY 3.3 13.1 + - - +
230J ALA* 3.8 7.2 - - - +
232J ILE* 1.3 79.8 - - - +
234J SER* 1.3 60.8 + - - +
235J HIS 3.5 2.6 - - - +
238J VAL* 6.0 0.2 - - - +
241J VAL* 4.2 32.6 - - + +
265J VAL* 6.1 0.3 - - - +
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Residues in contact with SER 234 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56J LYS* 4.9 9.9 - - - -
230J ALA* 2.8 24.1 + - - +
231J ALA* 4.1 5.2 - - - -
233J ALA* 1.3 79.2 - - - +
235J HIS* 1.3 64.8 + - - +
236J GLU* 3.3 13.9 + - - +
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Residues in contact with HIS 235 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56J LYS* 5.8 6.5 - - + +
59J VAL* 4.9 2.5 - - + -
60J ASP* 2.9 36.9 + - + -
63J VAL* 3.6 30.0 - - + +
64J LYS* 5.7 4.5 - - + -
231J ALA 3.0 18.6 + - - +
232J ILE* 3.4 3.5 + - - +
233J ALA 4.6 2.4 - - - +
234J SER* 1.3 76.8 - - - +
236J GLU* 1.3 69.2 + - + +
237J ASP* 2.7 45.6 + - + +
238J VAL* 3.5 33.1 + - + +
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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