Contacts of the helix formed by residues 227 - 235 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B GLU* 4.9 4.0 + - - +
54B GLY 4.0 6.2 + - - -
55B ASP* 3.3 33.9 - - - +
56B LYS* 5.4 0.3 - - - +
224B PHE* 3.4 28.2 + - + +
225B GLY 3.0 1.2 + - - -
226B PRO* 1.3 85.2 - - + +
228B ALA* 1.3 66.0 + - - -
229B GLY 3.4 0.4 - - - -
230B ALA* 3.4 0.9 + - - +
231B ALA* 2.9 31.5 + - - +
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Residues in contact with ALA 228 (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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54B GLY 3.6 25.5 + - - +
55B ASP* 4.6 2.2 - - - +
59B VAL* 3.6 16.0 - - + +
192B LYS* 4.0 19.3 - - + -
221B VAL* 4.3 6.7 - - + -
223B GLY* 4.6 2.0 - - - -
224B PHE 3.0 11.5 + - - +
227B THR* 1.3 79.9 + - - +
229B GLY* 1.3 63.6 + - - +
231B ALA* 3.2 3.7 + - - +
232B ILE* 3.1 26.5 + - - +
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Residues in contact with GLY 229 (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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165B ILE* 4.3 15.2 - - - +
192B LYS* 3.9 21.8 - - - +
224B PHE 3.3 8.3 + - - -
225B GLY* 3.3 8.2 + - - -
228B ALA* 1.3 76.7 - - - +
230B ALA* 1.3 61.8 + - - +
232B ILE* 3.2 5.7 + - - +
233B ALA* 3.1 22.2 + - - +
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Residues in contact with ALA 230 (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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225B GLY 2.9 9.3 + - - +
226B PRO* 3.3 26.9 - - + +
227B THR 3.9 0.4 - - - +
228B ALA 3.4 0.2 - - - -
229B GLY* 1.3 71.5 - - - +
231B ALA* 1.3 60.7 + - - +
233B ALA* 3.4 7.2 + - - +
234B SER* 2.8 33.3 + - - -
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Residues in contact with ALA 231 (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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56B LYS* 3.9 36.3 - - + -
59B VAL* 3.9 14.1 - - + +
227B THR 2.9 19.0 + - - +
228B ALA 3.5 5.4 - - - +
229B GLY 3.2 0.4 - - - -
230B ALA* 1.3 75.3 - - - +
232B ILE* 1.3 62.8 + - - +
234B SER* 3.5 6.3 + - - -
235B HIS* 3.0 28.4 + - - +
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Residues in contact with ILE 232 (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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59B VAL* 3.8 24.0 - - + -
63B VAL* 5.8 0.4 - - + -
163B GLY* 3.6 28.9 - - - -
165B ILE* 3.9 11.9 - - + -
190B VAL* 3.8 30.5 - - + +
191B MET 4.3 0.9 - - - -
192B LYS* 3.6 34.5 - - + +
221B VAL* 5.4 1.8 - - + -
228B ALA 3.1 14.6 + - - +
229B GLY 3.2 7.6 + - - +
231B ALA* 1.3 80.4 - - - +
233B ALA* 1.3 63.0 + - - +
235B HIS* 3.3 14.1 + - - +
238B VAL* 3.6 18.9 - - + +
241B VAL* 4.6 4.7 - - + +
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Residues in contact with ALA 233 (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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165B ILE* 6.3 0.9 - - + -
229B GLY 3.1 13.0 + - - +
230B ALA* 3.7 8.5 - - - +
231B ALA 3.3 0.2 - - - -
232B ILE* 1.3 80.1 - - - +
234B SER* 1.3 57.5 + - - +
235B HIS 3.9 2.1 + - - +
241B VAL* 4.3 31.1 - - + +
265B VAL* 6.1 0.2 - - - +
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Residues in contact with SER 234 (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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230B ALA 2.8 20.6 + - - -
231B ALA* 3.5 10.4 + - - -
233B ALA* 1.3 76.5 - - - +
235B HIS* 1.3 65.8 + - - +
236B GLU* 3.2 7.8 + - - +
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Residues in contact with HIS 235 (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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56B LYS* 5.0 5.4 - - - -
59B VAL* 4.3 8.7 - - + -
60B ASP* 3.2 35.5 + - - -
63B VAL* 3.5 40.6 - - + +
64B LYS* 6.1 1.3 - - + -
231B ALA 3.0 16.6 + - - +
232B ILE 3.3 3.2 + - - +
233B ALA 4.8 1.7 - - - +
234B SER* 1.3 75.9 - - - +
236B GLU* 1.3 68.3 + - + +
237B ASP* 2.9 36.8 + - + +
238B VAL* 3.4 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