Contacts of the helix formed by residues 234 - 246 (chain B) in PDB entry 5ZCS
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 TYR 234 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B LEU* 3.6 42.1 + - + -
220B THR* 3.6 21.1 - - + -
221B THR* 3.0 26.9 + - - +
233B TRP* 1.3 79.2 - - - +
235B ARG* 1.3 61.4 + - - +
236B HIS 3.6 0.7 - - - -
237B THR* 3.8 16.6 + - - -
238B PHE* 4.2 1.9 + - - +
271B LEU* 5.4 11.9 - - + +
274B ILE* 4.1 8.6 - - + +
275B SER* 3.9 27.8 - - - -
356B LEU* 3.4 37.0 - - + +
357B VAL* 3.4 18.1 - - + +
358B GLU* 4.9 9.4 - - + +
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Residues in contact with ARG 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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233B TRP* 3.3 5.6 - - + -
234B TYR* 1.3 75.4 - - - +
236B HIS* 1.3 73.6 + - + +
237B THR 3.2 3.6 + - - -
238B PHE* 3.4 40.7 + - - +
239B GLU* 3.2 51.5 + - - +
242B GLU* 5.3 1.0 + - - -
356B LEU* 4.3 9.3 - - + +
357B VAL* 3.5 23.2 - - - +
361B CYS* 5.5 5.3 - - - +
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Residues in contact with HIS 236 (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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191B PHE* 5.9 4.9 - - + -
195B PHE* 3.3 27.7 - - + -
233B TRP* 4.0 40.8 + + + +
234B TYR 3.6 0.4 - - - -
235B ARG* 1.3 82.2 - - + +
237B THR* 1.3 60.3 + - - +
238B PHE 3.5 0.2 - - - -
239B GLU* 3.9 28.1 + - - +
240B GLU* 4.1 6.2 + - - +
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Residues in contact with THR 237 (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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191B PHE* 6.0 2.1 - - - -
195B PHE* 3.7 22.5 - - + -
213B LEU* 5.2 11.2 - - + -
217B LEU* 5.0 11.9 - - + +
233B TRP 4.7 7.3 + - - -
234B TYR* 3.8 11.1 + - - -
235B ARG 3.2 1.0 - - - -
236B HIS* 1.3 78.7 - - - +
238B PHE* 1.3 64.9 + - - +
239B GLU 3.4 0.5 + - - -
240B GLU* 3.7 4.2 + - - +
241B ALA* 3.6 17.3 + - - +
267B ILE* 3.7 32.9 - - + +
271B LEU* 4.5 15.3 - - + -
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Residues in contact with PHE 238 (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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234B TYR 4.2 1.2 + - - +
235B ARG* 3.4 29.7 + - - +
237B THR* 1.3 77.9 - - - +
239B GLU* 1.3 59.2 + - - +
240B GLU 3.4 0.2 - - - -
241B ALA* 3.7 9.9 - - + -
242B GLU* 2.9 66.4 + - + +
267B ILE* 6.3 0.2 - - - -
268B LEU* 5.4 3.1 - - + -
271B LEU* 5.0 17.5 - - + +
357B VAL* 4.0 17.3 - - + -
361B CYS* 4.9 13.9 - - + -
364B ASP* 4.1 29.2 - - + -
365B LEU* 4.2 24.9 - - + -
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Residues in contact with GLU 239 (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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235B ARG* 3.2 52.5 + - - +
236B HIS* 3.9 27.2 + - - +
237B THR 3.3 0.8 - - - -
238B PHE* 1.3 80.0 - - - +
240B GLU* 1.3 66.1 + - + +
241B ALA 3.5 0.2 + - - -
242B GLU* 4.4 4.2 - - - +
243B LYS* 3.7 31.3 + - - +
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Residues in contact with GLU 240 (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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195B PHE* 3.7 42.4 - - + +
199B TRP* 3.3 32.0 + - - +
236B HIS 4.1 2.8 + - - +
237B THR 3.7 7.0 + - - +
238B PHE 3.4 0.2 - - - -
239B GLU* 1.3 80.6 - - + +
241B ALA* 1.3 60.5 + - - +
243B LYS* 4.5 3.3 - - - +
244B GLY* 3.7 8.5 + - - -
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Residues in contact with ALA 241 (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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199B TRP* 3.7 9.8 - - - +
237B THR 3.6 12.5 + - - +
238B PHE* 3.2 18.2 + - + +
240B GLU* 1.3 79.9 - - - +
242B GLU* 1.3 60.7 + - - +
243B LYS 3.4 0.2 - - - -
245B PHE* 2.9 34.1 + - - +
264B ALA* 4.0 17.9 - - + +
267B ILE* 4.2 17.9 - - + -
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Residues in contact with GLU 242 (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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235B ARG* 5.3 1.4 + - - -
238B PHE* 2.9 50.4 + - + +
239B GLU* 3.8 5.4 + - - +
240B GLU 3.6 0.2 - - - -
241B ALA* 1.3 78.4 - - - +
243B LYS* 1.3 61.3 + - + +
245B PHE* 4.9 2.0 - - - -
246B ASP* 3.1 45.5 + - + +
364B ASP* 5.2 5.9 - - + +
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Residues in contact with LYS 243 (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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239B GLU* 3.7 21.5 + - - +
240B GLU* 5.0 3.1 - - - +
241B ALA 3.4 0.2 - - - -
242B GLU* 1.3 80.3 - - + +
244B GLY* 1.3 60.5 + - - +
246B ASP* 4.2 11.5 - - - +
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Residues in contact with GLY 244 (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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199B TRP* 3.5 31.8 - - - -
240B GLU 3.7 6.9 + - - -
241B ALA 3.5 2.6 + - - -
242B GLU 3.3 0.6 - - - -
243B LYS* 1.3 80.4 - - - +
245B PHE* 1.3 62.1 + - - +
246B ASP 4.4 2.4 - - - +
260B ARG 4.9 4.5 - - - +
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Residues in contact with PHE 245 (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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199B TRP* 3.7 3.5 - + - -
241B ALA 2.9 20.2 + - - +
242B GLU* 4.4 2.2 - - - +
244B GLY* 1.3 79.6 - - - +
246B ASP* 1.3 83.3 + - - +
260B ARG 5.4 2.9 - - - -
261B ILE* 3.8 39.3 - - + -
264B ALA* 3.9 17.0 - - + -
265B LEU* 4.1 19.3 - - + -
368B GLU* 3.3 40.6 - - + -
372B GLN* 3.7 17.7 - - + -
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Residues in contact with ASP 246 (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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242B GLU* 3.1 32.7 + - + +
243B LYS* 4.2 13.0 - - - +
244B GLY 4.4 2.8 - - - +
245B PHE* 1.3 102.8 - - - +
368B GLU* 4.4 12.0 - - - +
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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