Contacts of the helix formed by residues 225 - 239 (chain L) in PDB entry 4ZZ7
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 SER 225 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222L PHE* 3.8 0.2 - - - -
224L GLY* 1.3 73.7 - - - -
226L THR* 1.3 53.6 + - - +
227L PRO* 3.6 13.4 - - - +
228L ILE* 3.5 14.9 - - - +
229L ALA* 2.7 35.3 + - - +
247L GLY* 4.1 1.6 - - - -
248L GLY 4.4 0.4 - - - +
382L GLU* 5.4 0.7 - - - -
501L NAD 2.7 51.5 + - - -
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Residues in contact with THR 226 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225L SER* 1.3 68.9 - - - +
227L PRO* 1.3 75.4 - - + +
229L ALA* 3.4 7.2 - - - +
230L GLU* 2.8 25.2 + - - +
247L GLY* 3.7 1.0 - - - -
248L GLY* 2.9 25.8 + - - +
407L GLU* 4.3 4.9 - - - +
408L TYR* 3.1 18.6 + - + -
454L ARG* 3.1 59.8 + - - +
457L PHE* 4.2 6.3 - - + -
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Residues in contact with PRO 227 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225L SER* 3.6 13.7 - - - +
226L THR* 1.3 96.1 - - + +
228L ILE* 1.3 62.7 + - + +
230L GLU* 3.6 9.7 + - + +
231L TYR* 3.2 24.1 + - - +
408L TYR* 5.1 4.3 - - - +
454L ARG* 5.7 1.6 - - - +
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Residues in contact with ILE 228 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222L PHE* 3.6 20.6 - - + -
225L SER* 3.4 14.5 + - - +
226L THR 3.2 0.4 - - - -
227L PRO* 1.3 79.2 - - + +
229L ALA* 1.3 56.6 + - - +
231L TYR* 3.0 10.5 + - + -
232L ILE* 2.7 45.3 + - + +
501L NAD 3.4 76.1 - - + +
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Residues in contact with ALA 229 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222L PHE* 3.6 13.8 - - + -
225L SER 2.7 22.9 + - - +
226L THR* 3.4 7.9 - - - +
228L ILE* 1.3 72.0 - - - +
230L GLU* 1.3 52.1 + - - +
232L ILE* 3.1 2.2 + - - +
233L TYR* 2.7 37.2 + - - +
245L ALA* 3.6 13.7 - - + +
246L LEU 3.9 16.8 - - - +
457L PHE* 3.8 21.3 - - + -
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Residues in contact with GLU 230 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237I SER 5.6 3.3 - - - +
238I ALA* 4.3 8.4 - - - +
239I ASN 6.0 0.2 - - - -
240I GLY* 5.8 2.9 + - - -
226L THR 2.8 19.1 + - - +
227L PRO* 3.7 8.1 - - - +
229L ALA* 1.3 69.2 - - - +
231L TYR* 1.3 61.2 + - - +
233L TYR* 4.0 4.4 - - - +
234L ARG* 2.9 60.9 + - + +
454L ARG* 2.8 38.0 + - - -
457L PHE* 3.9 20.6 - - + -
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Residues in contact with TYR 231 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205L LYS* 3.5 24.5 + - - -
209L ASP* 2.5 36.8 + - - -
212L LEU* 4.1 11.7 - - + -
213L HIS* 4.7 2.3 - - - -
227L PRO 3.2 11.9 + - - +
228L ILE* 3.0 15.5 + - + +
230L GLU* 1.3 77.0 - - - +
232L ILE* 1.3 73.1 + - + +
234L ARG* 3.7 18.0 - - + +
235L THR* 2.8 64.6 + - + +
501L NAD 4.4 11.2 - + - -
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Residues in contact with ILE 232 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145L ILE* 4.2 6.1 - - + -
208L VAL* 3.3 33.7 - - + -
212L LEU* 3.7 15.6 - - + +
220L VAL* 3.9 28.5 - - + -
222L PHE* 3.6 37.2 - - + -
228L ILE* 2.7 30.3 + - + +
229L ALA 3.6 3.4 - - - +
231L TYR* 1.3 83.7 - - + +
233L TYR* 1.3 57.0 + - - +
235L THR* 3.9 0.7 - - - -
236L ALA* 2.8 34.3 + - - +
243L CYS* 4.3 5.6 - - - -
245L ALA* 5.0 0.2 - - + -
501L NAD 4.5 1.1 - - + -
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Residues in contact with TYR 233 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233I TYR* 4.7 9.4 + - - -
237I SER* 3.5 45.5 + - - -
240I GLY 4.8 7.6 - - - -
241I LYS 4.8 1.1 - - - -
242I ARG* 4.4 13.2 - - - +
243I CYS 5.0 1.9 + - - -
229L ALA 2.7 19.9 + - - +
230L GLU* 4.0 4.0 - - - +
232L ILE* 1.3 72.5 - - - +
234L ARG* 1.3 59.0 + - - +
236L ALA* 4.0 0.7 - - - +
237L SER* 2.7 40.5 + - - -
243L CYS* 3.4 44.6 - - + -
245L ALA* 4.2 2.0 - - + -
457L PHE* 3.5 34.5 - + + -
458L GLY* 3.5 28.2 + - - -
459L ASP* 6.1 0.2 - - - -
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Residues in contact with ARG 234 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234I ARG* 5.2 5.8 - - + +
237I SER 4.7 7.6 - - - +
238I ALA* 4.0 39.9 + - + +
230L GLU* 2.9 62.3 + - - +
231L TYR* 3.7 20.7 - - - +
233L TYR* 1.3 79.5 - - - +
235L THR* 1.3 59.3 + - - +
237L SER* 3.6 3.6 - - - -
238L ALA* 2.8 32.9 + - + +
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Residues in contact with THR 235 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212L LEU* 3.8 26.2 - - + -
213L HIS* 3.8 29.8 - - + +
231L TYR* 2.8 46.8 + - + +
234L ARG* 1.3 78.8 - - - +
236L ALA* 1.3 60.9 + - - +
238L ALA* 3.5 4.8 + - - +
239L ASN* 2.9 38.3 + - - +
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Residues in contact with ALA 236 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212L LEU* 4.4 16.7 - - + +
220L VAL* 4.6 2.9 - - + -
232L ILE 2.8 19.2 + - - +
233L TYR 4.0 0.7 - - - +
235L THR* 1.3 77.3 - - - +
237L SER* 1.3 56.8 + - - +
239L ASN* 3.3 3.9 + - - -
240L GLY 3.1 21.1 + - - -
241L LYS* 3.2 34.4 + - + +
243L CYS* 3.7 28.0 - - + -
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Residues in contact with SER 237 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230I GLU* 5.5 2.3 - - - +
233I TYR* 3.7 32.5 + - - -
234I ARG* 4.5 7.7 - - - +
237I SER* 3.3 35.2 + - - -
457I PHE* 5.4 0.2 - - - -
233L TYR* 2.7 32.9 + - - -
234L ARG 3.6 2.7 - - - -
236L ALA* 1.3 75.0 - - - +
238L ALA* 1.3 65.7 + - - +
240L GLY* 3.1 13.7 + - - -
241L LYS 4.0 2.1 + - - -
243L CYS* 5.2 1.6 - - - +
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Residues in contact with ALA 238 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230I GLU* 4.2 9.9 - - - +
234I ARG* 3.9 45.0 + - + +
234L ARG* 2.8 22.9 + - + +
235L THR* 3.7 9.0 - - + +
236L ALA 3.4 0.2 - - - -
237L SER* 1.3 73.2 - - - +
239L ASN* 1.3 66.9 + - - +
240L GLY* 3.2 1.6 + - - -
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Residues in contact with ASN 239 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230I GLU* 5.5 2.0 - - - -
212L LEU 3.5 22.3 - - - +
213L HIS* 3.5 32.3 + - - +
215L ASP* 5.4 2.9 - - - +
235L THR* 2.9 39.0 + - - +
236L ALA 3.7 4.5 - - - +
238L ALA* 1.3 79.1 - - - +
240L GLY* 1.3 55.2 + - - +
241L LYS* 3.4 16.4 + - - -
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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