Contacts of the helix formed by residues 225 - 239 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222C PHE* 3.7 0.7 - - - -
224C GLY* 1.3 73.0 - - - -
226C THR* 1.3 54.1 + - - +
227C PRO* 3.5 13.4 - - - +
228C ILE* 3.3 15.6 + - - +
229C ALA* 2.7 35.8 + - - +
247C GLY* 4.1 0.4 - - - -
248C GLY* 4.4 0.9 - - - +
382C GLU* 5.5 0.7 - - - -
501C NAD 2.6 49.6 + - - -
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Residues in contact with THR 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C SER* 1.3 69.9 - - - +
227C PRO* 1.3 75.5 - - - +
229C ALA* 3.8 6.3 - - - -
230C GLU* 2.8 24.9 + - - +
247C GLY* 3.5 1.1 - - - -
248C GLY* 2.8 26.6 + - - +
407C GLU* 5.2 0.2 - - - -
408C TYR* 3.1 23.6 + - + -
454C ARG* 3.3 57.7 + - + +
457C PHE* 4.0 7.6 - - + -
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Residues in contact with PRO 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C SER* 3.5 14.4 - - - +
226C THR* 1.3 97.3 - - + +
228C ILE* 1.3 66.8 - - + +
230C GLU* 3.7 11.7 - - + +
231C TYR* 3.3 18.7 + - - +
408C TYR* 5.1 4.9 - - - +
454C ARG* 5.6 3.8 - - - +
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Residues in contact with ILE 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C PHE* 3.6 21.3 - - + -
225C SER* 3.3 21.9 + - - +
226C THR 3.1 0.6 - - - -
227C PRO* 1.3 79.4 - - + +
229C ALA* 1.3 68.4 + - - +
231C TYR* 2.9 9.6 + - + +
232C ILE* 2.8 37.7 + - + +
501C NAD 3.6 69.1 - - + +
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Residues in contact with ALA 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C PHE* 3.4 23.0 - - + -
225C SER 2.7 22.8 + - - +
226C THR* 3.5 10.1 - - - +
228C ILE* 1.3 72.5 - - - +
230C GLU* 1.3 52.8 + - - +
232C ILE* 3.3 1.1 + - - +
233C TYR* 2.8 35.7 + - - +
245C ALA* 3.4 10.1 - - + +
246C LEU 3.8 13.7 - - - +
247C GLY* 4.0 1.8 - - - -
457C PHE* 4.0 16.8 - - + -
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Residues in contact with GLU 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C THR 2.8 19.7 + - - +
227C PRO* 3.7 9.5 - - - +
229C ALA* 1.3 73.8 - - - +
231C TYR* 1.3 56.5 + - - +
233C TYR* 3.3 3.3 + - - +
234C ARG* 2.9 57.5 + - + +
454C ARG* 3.3 33.0 + - - -
457C PHE* 3.9 24.5 - - + -
238D ALA 5.0 3.9 - - - +
240D GLY* 6.2 0.3 - - - -
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Residues in contact with TYR 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C LYS* 3.4 23.8 + - - -
209C ASP* 2.6 32.4 + - - -
212C LEU* 4.1 11.6 - - + +
213C HIS* 4.9 0.3 - - - -
227C PRO 3.3 11.3 + - - +
228C ILE* 2.9 14.9 + - + +
230C GLU* 1.3 70.8 - - - +
232C ILE* 1.3 86.4 + - + +
234C ARG* 4.1 15.5 - - - +
235C THR* 2.8 55.8 + - - +
501C NAD 3.9 21.8 - + - -
15E GLU 5.6 2.0 - - - -
16E ASN 4.6 4.7 + - - -
17E THR* 4.1 17.3 - - + -
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Residues in contact with ILE 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C ILE* 4.2 6.3 - - + -
208C VAL* 3.4 33.0 - - + -
212C LEU* 3.7 15.5 - - + +
220C VAL* 3.8 28.5 - - + -
222C PHE* 3.9 33.0 - - + -
228C ILE* 2.8 30.0 + - + +
229C ALA 3.6 6.7 - - - +
231C TYR* 1.3 82.4 - - + +
233C TYR* 1.3 57.1 + - - +
235C THR* 4.1 0.3 - - - -
236C ALA* 3.0 29.5 + - - +
243C CYS* 4.2 6.1 - - - -
245C ALA* 4.8 0.2 - - + -
501C NAD 4.7 1.6 - - + +
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Residues in contact with TYR 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C ALA 2.8 22.1 + - - +
230C GLU 3.7 3.4 - - - +
231C TYR 3.2 0.2 - - - -
232C ILE* 1.3 71.4 - - - +
234C ARG* 1.3 57.6 + - - +
236C ALA* 4.1 0.5 - - - +
237C SER* 2.7 44.4 + - - -
243C CYS* 3.5 43.4 + - + -
245C ALA* 4.2 2.0 - - + -
457C PHE* 3.4 46.0 - + + -
458C GLY* 3.5 17.7 + - - -
459C ASP* 6.0 0.5 - - - -
233D TYR* 4.8 8.7 + - - -
237D SER* 3.9 39.9 + - - -
240D GLY 4.7 8.7 - - - -
241D LYS 4.7 1.0 + - - -
242D ARG* 4.6 13.3 - - - +
243D CYS 5.0 1.7 + - - -
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Residues in contact with ARG 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C GLU* 2.9 54.2 + - + +
231C TYR* 4.1 22.8 - - - +
233C TYR* 1.3 72.9 - - - +
235C THR* 1.3 57.7 + - - +
237C SER* 3.4 4.7 + - - -
238C ALA* 2.9 33.2 + - + +
234D ARG* 5.6 2.9 - - + +
237D SER* 4.7 8.5 - - - +
238D ALA* 4.1 39.4 + - + +
15E GLU* 5.8 0.4 - - - -
17E THR* 5.6 10.5 - - - -
38E SER* 5.5 11.4 - - - -
40E LYS* 5.8 6.5 - - - +
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Residues in contact with THR 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C LEU* 3.9 22.7 - - + -
213C HIS* 3.8 29.8 - - + +
231C TYR* 2.8 44.3 + - - +
232C ILE 4.1 1.8 - - - -
234C ARG* 1.3 73.3 - - - +
236C ALA* 1.3 68.0 + - - +
238C ALA* 3.2 12.5 + - - +
239C ASN* 3.3 17.5 + - - +
17E THR* 3.7 25.1 - - - +
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Residues in contact with ALA 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C LEU* 4.3 17.9 - - + +
220C VAL* 4.6 2.5 - - + -
232C ILE 3.0 20.5 + - - +
233C TYR 4.1 0.2 - - - +
235C THR* 1.3 74.9 - - - +
237C SER* 1.3 63.2 + - - +
239C ASN* 3.1 13.8 + - - -
240C GLY 3.5 5.2 + - - -
241C LYS* 3.4 33.5 + - + +
243C CYS* 3.8 27.1 - - + -
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Residues in contact with SER 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C TYR* 2.7 36.4 + - - -
234C ARG 3.7 2.9 - - - -
236C ALA* 1.3 78.7 - - - +
238C ALA* 1.3 59.5 + - - +
240C GLY* 3.3 8.9 + - - -
241C LYS 4.0 4.4 + - - -
243C CYS* 5.0 1.7 - - - +
230D GLU 5.6 0.3 - - - +
233D TYR* 3.5 33.1 + - - -
234D ARG* 4.3 6.7 - - - +
237D SER* 3.3 35.8 + - - -
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Residues in contact with ALA 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C ARG* 2.9 20.6 + - + +
235C THR* 3.6 8.5 - - - +
236C ALA 3.2 0.4 - - - -
237C SER* 1.3 77.5 - - - +
239C ASN* 1.3 63.6 + - - +
240C GLY 3.3 2.0 + - - -
230D GLU* 4.6 4.7 - - - +
234D ARG* 4.0 37.0 + - + +
17E THR* 4.5 7.9 - - - +
18E ARG* 4.0 24.5 - - + +
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Residues in contact with ASN 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C LEU 3.8 19.0 - - - +
213C HIS* 3.4 27.3 + - - +
215C ASP* 5.4 3.5 - - - +
235C THR* 3.3 9.2 + - - +
236C ALA 3.1 9.6 + - - +
238C ALA* 1.3 76.9 - - - +
240C GLY* 1.3 57.8 + - - +
241C LYS* 3.3 16.6 + - - -
230D GLU* 6.1 0.7 - - - -
17E THR 3.1 26.1 + - - -
18E ARG* 4.6 6.0 - - - +
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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