Contacts of the helix formed by residues 219 - 234 (chain C) in PDB entry 4Z07
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 219 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A PHE* 6.0 0.2 - - - -
188A TYR* 4.8 6.6 + - - +
123C GLU* 3.5 20.6 - - - +
126C GLN* 3.5 24.7 - - - +
216C MET 3.5 11.9 - - - +
217C MET 3.0 5.1 + - - -
218C ARG* 1.3 74.7 - - - +
220C GLY* 1.3 65.5 + - - +
221C LEU* 3.5 8.0 + - - +
222C ILE* 3.1 28.8 + - + +
223C LYS* 2.9 23.3 + - - +
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Residues in contact with GLY 220 (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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123C GLU* 3.0 18.8 + - - -
219C THR* 1.3 71.7 - - - +
221C LEU* 1.3 56.9 + - - +
223C LYS* 3.3 6.2 + - - +
224C HIS* 2.8 32.0 + - - +
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Residues in contact with LEU 221 (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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117A ASP* 3.6 41.7 - - + +
118A PHE* 3.5 35.2 - - + -
123C GLU* 4.9 1.4 + - - +
219C THR* 3.2 8.6 + - - +
220C GLY* 1.3 77.2 - - - +
222C ILE* 1.3 51.7 + - - +
224C HIS* 3.6 10.7 + - + +
225C THR* 2.6 42.3 + - - +
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Residues in contact with ILE 222 (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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118A PHE* 4.1 16.4 - - + -
184A LEU* 5.7 2.5 - - + -
188A TYR* 3.7 34.8 - - + +
217C MET* 3.1 55.4 - - + +
218C ARG* 5.3 0.9 - - - -
219C THR* 3.1 20.6 + - + +
221C LEU* 1.3 74.6 - - - +
223C LYS* 1.3 65.3 + - - +
225C THR* 3.1 7.3 + - - -
226C GLU* 2.9 42.7 + - + +
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Residues in contact with LYS 223 (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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218C ARG 6.3 0.2 - - - -
219C THR 2.9 15.8 + - - +
220C GLY* 3.7 6.7 - - - +
222C ILE* 1.3 75.7 - - - +
224C HIS* 1.3 62.7 + - - +
226C GLU* 3.1 16.6 + - - +
227C TYR* 3.0 38.7 + - + -
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Residues in contact with HIS 224 (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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220C GLY 2.8 18.3 + - - +
221C LEU* 3.6 15.1 + - + +
223C LYS* 1.3 77.1 - - - +
225C THR* 1.3 63.1 + - - +
227C TYR* 3.3 11.3 + - - +
228C MET* 3.0 49.8 + - + +
246C SER* 3.2 30.5 + - - -
249C ALA* 3.5 15.5 - - + +
250C ASP* 2.8 30.4 + - - -
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Residues in contact with THR 225 (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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118A PHE* 4.4 12.8 - - + -
184A LEU* 6.1 2.2 - - + -
401A PCG 3.9 21.8 - - + +
221C LEU* 2.6 32.5 + - - +
222C ILE* 3.1 9.7 + - - -
224C HIS* 1.3 77.9 + - - +
226C GLU* 1.3 58.9 + - - +
228C MET* 3.2 11.1 + - + +
229C GLU* 2.8 45.4 + - - +
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Residues in contact with GLU 226 (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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217C MET* 6.1 0.9 - - - +
222C ILE* 2.9 34.5 + - + +
223C LYS* 3.6 14.1 - - - +
225C THR* 1.3 73.9 - - - +
227C TYR* 1.3 62.8 + - + +
229C GLU* 3.2 17.7 + - - +
230C PHE* 2.9 30.2 + - - +
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Residues in contact with TYR 227 (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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223C LYS* 3.0 29.7 + - + -
224C HIS* 3.5 9.2 - - - +
226C GLU* 1.3 78.7 - - + +
228C MET* 1.3 58.2 + - - +
230C PHE* 3.3 5.7 + - + +
231C LEU* 2.9 35.8 + - - +
249C ALA* 3.6 30.1 - - + -
252C LEU* 3.9 29.7 + - + -
254C GLU* 3.8 31.0 + - - +
329C LEU* 3.8 33.4 - - + -
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Residues in contact with MET 228 (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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401A PCG 6.0 0.7 - - - +
224C HIS* 3.0 32.1 + - + +
225C THR* 3.3 12.6 - - + +
227C TYR* 1.3 72.6 - - - +
229C GLU* 1.3 65.8 + - + +
231C LEU* 3.3 6.7 + - - +
232C LYS* 2.9 42.1 + - - +
242C GLU* 3.3 37.9 - - + +
245C LEU* 3.7 24.0 - - + +
246C SER* 3.6 32.3 - - - +
249C ALA* 3.8 2.2 - - + -
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Residues in contact with GLU 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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167A LYS* 3.4 29.8 + - + -
170A VAL* 5.3 2.1 - - - +
172A LEU* 4.1 25.7 - - + +
401A PCG 2.7 47.6 + - - +
225C THR* 2.8 32.3 + - - +
226C GLU* 3.2 17.4 + - - +
228C MET* 1.3 73.0 - - + +
230C PHE* 1.3 63.3 + - - +
232C LYS* 3.3 5.6 + - + +
233C SER* 3.2 19.2 + - - -
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Residues in contact with PHE 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 GLU 2.9 14.1 + - - +
227C TYR* 3.6 9.0 - - + +
229C GLU* 1.3 76.6 - - - +
231C LEU* 1.3 67.7 + - + +
233C SER* 2.2 43.5 + - - -
234C VAL* 3.4 16.1 + - + +
275C ILE* 3.6 25.1 - - + -
276C ILE 3.5 21.3 - - - -
277C SER* 3.6 23.8 - - - -
301C LYS* 3.9 23.8 - - + -
302C GLY* 4.5 1.3 - - - -
329C LEU* 3.4 30.1 - - + -
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Residues in contact with LEU 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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227C TYR 2.9 24.3 + - - +
228C MET* 3.3 6.0 + - - +
230C PHE* 1.3 85.1 - - + +
232C LYS* 1.3 57.5 + - - +
234C VAL* 2.9 30.3 + - - +
237C PHE* 3.8 16.7 - - + +
238C GLN* 3.7 5.4 + - - -
245C LEU* 3.8 42.2 - - + +
248C LEU* 3.9 20.6 - - + -
249C ALA* 4.2 3.4 - - + +
252C LEU* 4.0 21.5 - - + -
275C ILE* 4.2 24.7 - - + -
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Residues in contact with LYS 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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170A VAL* 5.0 4.0 - - + +
171A LYS 4.2 11.2 - - - +
172A LEU* 3.3 44.2 + - + +
173A CYS* 5.2 1.6 - - - +
401A PCG 4.4 14.1 + - - -
228C MET* 2.9 35.5 + - - +
229C GLU* 3.6 6.2 - - - +
230C PHE 3.2 0.2 - - - -
231C LEU* 1.3 76.0 - - - +
233C SER* 1.3 58.2 + - - +
234C VAL 3.2 0.2 - - - -
238C GLN* 2.7 49.0 + - + +
242C GLU* 3.1 37.3 + - - -
245C LEU* 4.0 19.1 - - + -
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Residues in contact with SER 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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170A VAL* 4.6 17.0 - - - +
229C GLU 3.2 9.5 + - - -
230C PHE* 2.2 40.7 + - - -
232C LYS* 1.3 78.5 - - - +
234C VAL* 1.3 59.9 + - - +
235C PRO* 3.5 10.3 - - - +
238C GLN* 4.9 1.3 - - - -
301C LYS* 5.5 1.9 - - - -
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Residues in contact with VAL 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 PHE* 3.7 41.3 - - + +
231C LEU* 2.9 9.5 + - + +
233C SER* 1.3 78.3 - - - +
235C PRO* 1.3 58.8 - - + -
236C THR* 3.9 9.4 - - - +
237C PHE* 2.7 54.0 + - + -
238C GLN* 2.8 16.6 + - - -
275C ILE* 4.5 4.5 - - + -
302C GLY* 3.3 33.7 - - - +
304C TRP* 4.7 0.2 - - + -
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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