Contacts of the helix formed by residues 221 - 237 (chain C) in PDB entry 3IZ0
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 HIS 221 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213C GLU* 3.1 29.9 + - + +
214C GLU* 5.1 0.2 - - - +
220C MET* 1.3 93.6 + - + +
222C ASN* 1.3 59.3 + - - +
223C LYS 3.2 3.4 - - - -
224C LEU* 2.9 29.7 + - + +
225C PHE* 3.1 9.2 + - - +
257C LEU* 3.9 33.4 - - + +
258C PHE* 4.3 17.2 - + - -
138D TYR* 3.4 9.0 + - - +
142D LEU* 4.0 14.0 - - + +
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Residues in contact with ASN 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C GLY 3.6 7.1 + - - +
213C GLU 2.8 25.5 + - - +
214C GLU* 4.1 1.1 - - - +
215C THR* 3.1 28.3 + - - +
219C ILE* 3.9 10.9 - - + +
220C MET 3.5 0.4 - - - -
221C HIS* 1.3 71.3 - - - +
223C LYS* 1.3 55.6 + - - +
225C PHE* 3.9 14.5 - - - -
226C LEU* 2.8 45.2 + - - +
56D VAL 3.3 21.7 + - - +
57D TYR* 3.5 22.0 + - - +
58D GLY* 3.8 1.8 - - - +
131D ARG* 4.2 0.3 + - - -
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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
----------------------------------------------------------
212C GLY 4.6 4.3 + - - +
213C GLU* 3.6 26.2 + - - +
221C HIS 3.2 0.2 - - - -
222C ASN* 1.3 77.2 - - - +
224C LEU* 1.3 62.2 + - + +
226C LEU* 4.4 6.9 - - - +
227C ASP* 3.5 23.0 + - - +
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Residues in contact with LEU 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C GLU* 4.7 0.4 + - - -
221C HIS* 2.9 20.2 + - + +
223C LYS* 1.3 81.7 - - + +
225C PHE* 1.3 59.6 + - - +
227C ASP* 3.5 3.1 + - + +
228C TYR* 3.1 26.1 + - + +
250C LEU* 4.0 17.9 - - + -
253C LYS* 3.5 46.9 - - + +
254C LEU* 4.0 24.7 - - + -
257C LEU* 4.7 9.9 - - + -
138D TYR* 3.9 13.9 - - - +
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Residues in contact with PHE 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C ILE* 3.3 44.4 - - + -
221C HIS 3.1 7.6 + - - +
222C ASN* 3.2 16.8 + - - +
224C LEU* 1.3 74.5 - - - +
226C LEU* 1.3 57.7 + - + +
228C TYR* 3.1 5.8 + + - +
229C THR* 2.6 61.7 + - - -
131D ARG* 3.5 42.8 - - + -
134D CYS* 3.6 11.0 - - + -
135D ARG* 3.5 27.4 - - + -
138D TYR* 3.5 32.9 - + + -
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Residues in contact with LEU 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C ASN* 2.8 35.4 + - - +
223C LYS* 4.4 6.1 - - - +
225C PHE* 1.3 77.0 - - + +
227C ASP* 1.3 57.8 + - - +
229C THR* 4.3 5.4 - - - -
230C ILE* 2.8 57.0 + - + +
56D VAL* 3.7 35.4 - - + +
57D TYR* 3.5 36.1 - - + +
98D ILE* 5.5 1.6 - - + -
127D PHE* 4.8 8.7 - - + -
131D ARG* 5.8 2.5 - - - +
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Residues in contact with ASP 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C LYS* 3.5 20.0 + - - +
224C LEU* 3.7 6.5 - - + +
225C PHE 3.2 0.4 - - - -
226C LEU* 1.3 78.0 - - - +
228C TYR* 1.3 64.8 + - - +
230C ILE* 4.0 6.8 - - - +
231C LYS* 3.1 58.8 + - - +
249C GLU* 4.5 0.5 - - - +
253C LYS* 2.9 29.5 + - - +
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Residues in contact with TYR 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C LEU* 3.1 13.0 + - + +
225C PHE* 3.3 22.9 - + - +
227C ASP* 1.3 81.4 + - - +
229C THR* 1.3 59.0 + - - +
231C LYS* 3.2 8.3 + - - +
232C CYS* 2.9 54.0 + - - -
243C PHE* 5.1 1.6 - - - +
246C MET* 3.8 24.9 - - + -
247C ASN* 2.7 29.3 + - - -
250C LEU* 3.9 31.0 - - + -
134D CYS* 3.9 29.8 - - + -
137D THR* 3.1 18.1 - - + +
138D TYR* 4.3 7.6 - + + -
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Residues in contact with THR 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C PHE* 2.6 54.6 + - - -
226C LEU* 3.9 7.2 - - - -
228C TYR* 1.3 72.8 - - - +
230C ILE* 1.3 66.9 + - - +
232C CYS* 3.4 3.3 + - - +
233C TYR* 2.9 21.7 + - - +
127D PHE* 4.0 18.4 - - + -
130D PHE* 4.0 3.2 - - + -
131D ARG* 3.4 35.9 - - + -
134D CYS* 3.9 13.9 - - - +
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Residues in contact with ILE 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C LEU* 2.8 43.1 + - + +
227C ASP* 4.0 5.8 - - - +
229C THR* 1.3 71.8 - - - +
231C LYS* 1.3 66.8 + - + +
233C TYR* 2.9 17.8 + - - +
234C GLU* 3.1 31.5 + - + +
57D TYR* 6.1 1.3 - - + -
98D ILE* 3.7 46.2 - - + -
127D PHE* 5.2 3.4 - - + -
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Residues in contact with LYS 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C ASP* 3.1 48.8 + - - +
228C TYR* 3.5 5.4 - - - +
230C ILE* 1.3 79.7 - - + +
232C CYS* 1.3 61.6 + - - +
234C GLU* 3.3 11.0 + - + +
235C SER* 3.3 19.9 + - - -
246C MET* 4.1 22.3 - - + +
249C GLU* 2.9 40.4 + - - +
253C LYS* 4.0 1.6 - - - +
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Residues in contact with CYS 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C TYR* 2.9 54.1 + - - +
229C THR 3.6 7.6 - - - +
231C LYS* 1.3 75.8 - - - +
233C TYR* 1.3 57.4 + - - +
235C SER* 3.3 1.1 + - - -
236C PHE* 2.8 30.5 + - - +
243C PHE* 3.4 28.6 - - + -
246C MET* 3.7 16.1 - - - +
130D PHE* 3.7 15.7 - - + -
134D CYS* 4.1 6.5 - - - -
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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
----------------------------------------------------------
229C THR 2.9 12.2 + - - +
230C ILE* 2.9 13.8 + - + +
232C CYS* 1.3 76.1 - - - +
234C GLU* 1.3 52.5 + - + +
236C PHE* 3.2 21.4 + + - +
237C MET* 2.7 51.5 + - - +
98D ILE* 3.5 27.1 - - + -
99D CYS* 4.7 1.3 + - - -
100D ARG* 4.2 22.9 - - + +
123D GLY 4.8 0.9 + - - -
126D ASN* 3.8 13.0 - - - +
127D PHE* 3.7 41.6 + + + -
130D PHE* 3.2 42.6 - + + -
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Residues in contact with GLU 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 ILE* 3.1 31.4 + - + +
231C LYS* 3.3 9.8 + - + +
233C TYR* 1.3 74.8 - - + +
235C SER* 1.3 61.7 + - - +
237C MET* 3.3 3.8 + - - +
238C SER* 2.8 27.1 + - - -
100D ARG* 2.7 35.0 + - - +
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Residues in contact with SER 235 (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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231C LYS 3.3 9.4 + - - -
232C CYS 3.5 8.1 - - - -
234C GLU* 1.3 77.2 - - - +
236C PHE* 1.3 58.3 + - - +
238C SER* 2.8 27.0 + - - -
240C ALA* 3.1 33.5 + - - +
242C SER 5.2 0.4 + - - -
243C PHE* 4.4 4.0 - - - -
246C MET* 3.1 31.6 - - - +
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Residues in contact with PHE 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C CYS 2.8 21.1 + - - +
233C TYR* 3.4 28.0 - + - +
235C SER* 1.3 72.9 - - - +
237C MET* 1.3 72.0 + - + +
239C GLY* 2.9 22.0 + - - -
240C ALA 3.9 14.8 + - - -
243C PHE* 4.0 13.1 - + + -
130D PHE* 3.5 31.0 - + + -
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Residues in contact with MET 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 35.6 + - - +
234C GLU 3.6 6.5 - - - +
235C SER 3.2 0.2 - - - -
236C PHE* 1.3 90.3 - - + +
238C SER* 1.3 58.7 + - - +
239C GLY 3.4 0.4 - - - -
100D ARG* 3.5 58.9 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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