Contacts of the helix formed by residues 227 - 240 (chain B) in PDB entry 4ZTM
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 LYS 227 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226B LEU* 1.4 76.1 - - - +
228B GLN* 1.3 55.4 - - - +
230B PHE* 3.4 25.9 + - + +
231B ASP* 2.9 46.6 + - - +
253B SER* 4.4 16.5 - - - -
258B LEU* 3.9 26.9 - - + +
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Residues in contact with GLN 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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226B LEU 3.4 0.6 - - - -
227B LYS* 1.3 75.3 - - - +
229B GLN* 1.4 64.5 + - + +
231B ASP* 3.3 15.3 + - + +
232B GLN* 3.3 16.6 + - - +
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Residues in contact with GLN 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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226B LEU* 3.2 43.1 + - + +
228B GLN* 1.4 72.1 - - + +
230B PHE* 1.4 60.4 + - - +
231B ASP 3.1 1.3 - - - -
232B GLN* 3.0 28.5 + - - +
233B GLU* 3.7 4.5 + - - +
331B GLY* 4.9 6.4 - - - +
347B ARG* 5.4 6.6 + - - -
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Residues in contact with PHE 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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226B LEU* 2.8 20.7 + - + +
227B LYS* 3.5 26.9 - - - +
229B GLN* 1.4 74.4 - - - +
231B ASP* 1.4 58.3 + - - +
233B GLU* 3.7 8.3 + - - +
234B ILE* 3.4 43.1 + - + +
251B PHE* 3.7 16.4 - + + -
252B SER 3.8 13.2 - - - -
253B SER* 4.7 3.4 - - - -
258B LEU* 3.6 47.8 - - + -
259B CYS 3.2 24.9 - - - -
260B LEU* 4.0 22.7 - - + -
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Residues in contact with ASP 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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227B LYS* 2.9 35.7 + - - +
228B GLN* 3.5 19.2 - - + +
229B GLN 3.1 0.6 - - - -
230B PHE* 1.4 77.1 - - - +
232B GLN* 1.4 54.3 + - - +
233B GLU 3.2 1.3 - - - -
234B ILE* 3.7 22.8 - - - +
235B LYS* 2.8 44.1 + - + +
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Residues in contact with GLN 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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228B GLN 3.3 7.3 + - - +
229B GLN* 3.0 18.4 + - - +
231B ASP* 1.4 74.5 - - - +
233B GLU* 1.3 56.6 + - - +
235B LYS* 4.9 5.4 - - - +
236B VAL* 3.0 58.1 + - + +
307B HIS* 5.6 1.6 + - - -
330B PHE 3.8 7.6 - - - +
331B GLY 3.7 18.8 - - - +
333B ALA 3.4 26.5 + - - +
334B ARG* 4.9 10.5 - - - +
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Residues in contact with GLU 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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213B LYS* 3.3 21.3 + - - +
229B GLN 3.7 3.6 + - - +
230B PHE* 3.7 7.5 + - - +
231B ASP 3.2 0.4 - - - -
232B GLN* 1.3 76.3 - - - +
234B ILE* 1.4 58.6 + - - +
235B LYS 3.3 0.2 + - - -
236B VAL* 5.0 0.4 - - - -
237B MET* 2.9 44.2 + - + +
260B LEU* 3.5 26.2 - - + +
262B TYR* 3.1 28.6 + - - +
329B ASP* 4.0 1.9 + - - -
330B PHE* 3.1 32.8 + - + +
331B GLY* 3.7 22.0 + - - -
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Residues in contact with ILE 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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165B PHE* 6.2 0.9 - - + -
227B LYS* 5.8 0.2 - - - +
230B PHE* 3.4 48.2 + - + +
231B ASP* 3.4 20.6 + - - +
233B GLU* 1.4 73.4 - - - +
235B LYS* 1.4 57.6 + - + +
237B MET* 4.0 0.3 - - - +
238B ALA* 3.0 32.6 + - + +
248B LEU* 4.3 10.4 - - + +
251B PHE* 3.9 37.2 - - + -
260B LEU* 3.9 15.3 - - + -
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Residues in contact with LYS 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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231B ASP* 2.8 29.7 + - + +
232B GLN* 4.2 7.9 - - - +
234B ILE* 1.4 70.9 - - + +
236B VAL* 1.4 65.0 + - - +
238B ALA* 3.2 6.7 + - + +
239B LYS* 3.0 53.7 + - - +
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Residues in contact with VAL 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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232B GLN* 3.0 44.7 + - + +
233B GLU 4.2 0.4 - - - +
235B LYS* 1.4 69.6 - - + +
237B MET* 1.4 53.1 + - - +
239B LYS* 3.4 1.5 + - - -
240B CYS* 2.7 51.1 + - + +
302B LEU* 4.6 2.7 - - + -
307B HIS* 3.9 30.7 - - + +
330B PHE* 3.8 37.0 - - + +
333B ALA* 4.2 14.8 - - + -
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Residues in contact with MET 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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165B PHE* 4.2 5.6 - - - -
233B GLU* 2.9 34.3 + - + +
236B VAL* 1.4 73.0 - - - +
238B ALA* 1.3 63.8 + - - +
240B CYS* 3.4 20.5 - - - +
241B GLN* 3.6 10.7 + - - +
245B LEU* 6.0 0.2 - - - -
246B VAL* 3.4 37.5 - - + +
248B LEU* 3.7 33.7 - - + +
262B TYR* 3.3 31.0 - - + +
330B PHE* 3.5 29.4 - - + -
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Residues in contact with ALA 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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165B PHE* 4.1 17.4 - - + -
234B ILE* 3.0 24.0 + - + +
235B LYS* 3.2 7.2 + - + +
237B MET* 1.3 74.8 - - - +
239B LYS* 1.4 61.6 + - + +
241B GLN* 2.5 27.9 + - - +
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Residues in contact with LYS 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 LYS* 3.0 54.3 + - - +
236B VAL 3.8 2.7 - - - +
238B ALA* 1.4 79.2 - - + +
240B CYS* 1.3 66.1 + - - +
241B GLN* 3.5 6.2 + - - +
301B PHE* 4.7 5.5 - - - -
305B ASN* 5.1 4.7 - - - +
307B HIS* 4.2 20.9 - - + +
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Residues in contact with CYS 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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236B VAL* 2.7 26.6 + - + +
237B MET* 3.4 19.9 - - - +
239B LYS* 1.3 73.0 - - - +
241B GLN* 1.3 60.3 + - - +
242B HIS 4.1 0.4 - - - -
245B LEU* 3.7 24.3 - - + +
246B VAL 5.2 2.1 - - - +
301B PHE* 3.6 20.2 - - + -
302B LEU* 4.0 15.3 - - + -
305B ASN* 4.5 8.3 - - - -
307B HIS* 3.4 35.0 - - - -
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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