Contacts of the helix formed by residues 227 - 235 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53G GLU* 5.0 7.1 + - - +
54G GLY 3.9 5.5 + - - -
55G ASP* 3.6 34.2 - - - +
56G LYS* 5.4 0.3 - - - +
224G PHE* 3.1 29.4 + - + +
225G GLY 3.0 0.8 + - - -
226G PRO* 1.3 86.3 - - + +
228G ALA* 1.3 71.5 + - - -
229G GLY 3.4 0.2 - - - -
230G ALA* 3.5 0.9 + - - +
231G ALA* 3.0 25.5 + - - +
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Residues in contact with ALA 228 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G GLY 3.7 21.9 + - - +
55G ASP* 4.6 2.4 - - - +
59G VAL* 3.7 16.4 - - + +
192G LYS* 3.7 23.6 - - + -
221G VAL* 4.4 6.7 - - + +
223G GLY* 4.6 0.9 - - - -
224G PHE 2.9 12.6 + - - +
227G THR* 1.3 79.5 + - - +
229G GLY* 1.3 64.8 + - - +
231G ALA* 3.2 4.4 + - - +
232G ILE* 3.1 26.0 + - - +
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Residues in contact with GLY 229 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165G ILE* 3.8 22.2 - - - +
192G LYS* 4.0 15.7 - - - +
224G PHE 3.3 3.8 + - - -
225G GLY* 3.2 13.1 + - - -
228G ALA* 1.3 77.9 - - - +
230G ALA* 1.3 61.9 + - - +
232G ILE* 3.2 6.6 + - - +
233G ALA* 3.1 22.1 + - - +
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Residues in contact with ALA 230 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225G GLY 3.0 9.5 + - - +
226G PRO* 3.4 25.4 - - + +
227G THR 3.5 0.4 + - - +
228G ALA 3.4 0.4 - - - -
229G GLY* 1.3 75.0 - - - +
231G ALA* 1.3 57.4 + - - +
233G ALA* 3.4 6.0 + - - +
234G SER* 2.9 38.9 + - - +
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Residues in contact with ALA 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56G LYS* 3.8 38.8 - - + +
59G VAL* 4.1 13.1 - - + +
227G THR 3.0 19.2 + - - +
228G ALA 3.2 5.1 + - - +
230G ALA* 1.3 77.4 - - - +
232G ILE* 1.3 57.6 + - - +
234G SER* 3.8 3.8 - - - -
235G HIS* 2.9 31.5 + - - +
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Residues in contact with ILE 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59G VAL* 3.5 25.6 - - + -
163G GLY* 3.6 32.5 - - - -
165G ILE* 4.9 6.5 - - + -
190G VAL* 3.9 28.3 - - + +
191G MET 4.5 1.3 - - - +
192G LYS* 3.7 32.8 - - + +
221G VAL* 5.3 1.6 - - + -
228G ALA 3.1 13.0 + - - +
229G GLY 3.2 7.4 + - - +
231G ALA* 1.3 77.2 - - - +
233G ALA* 1.3 63.1 + - - +
234G SER 3.3 0.7 + - - -
235G HIS* 3.4 10.0 + - - -
238G VAL* 3.8 24.6 - - + +
241G VAL* 4.6 6.7 - - + -
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Residues in contact with ALA 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165G ILE* 4.9 4.0 - - + -
229G GLY 3.1 12.8 + - - +
230G ALA* 3.4 7.2 + - - +
232G ILE* 1.3 79.3 - - - +
234G SER* 1.3 59.5 + - - +
241G VAL* 4.1 29.0 - - + +
263G LYS* 3.3 23.0 + - - +
265G VAL* 6.0 0.2 - - - +
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Residues in contact with SER 234 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230G ALA* 2.9 24.2 + - - +
231G ALA* 4.1 4.5 - - - -
233G ALA* 1.3 80.2 - - - +
235G HIS* 1.3 66.2 + - - +
236G GLU* 3.3 4.0 + - - +
263G LYS* 4.0 5.8 + - - +
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Residues in contact with HIS 235 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56G LYS* 5.8 4.3 - - + -
59G VAL* 4.7 3.6 - - + -
60G ASP* 2.7 35.1 + - + -
63G VAL* 3.6 31.3 - - + +
64G LYS* 5.8 3.4 - - + -
231G ALA* 2.9 19.3 + - + +
232G ILE* 3.4 2.0 + - - -
234G SER* 1.3 73.9 - - - +
236G GLU* 1.3 69.5 + - + +
237G ASP* 3.0 41.4 + - + +
238G VAL* 3.5 20.1 + - + -
263G LYS* 3.1 25.5 + - - -
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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