Contacts of the helix formed by residues 224 - 241 (chain C) in PDB entry 5DO7
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 ASP 224 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195C THR* 5.3 5.0 - - - +
223C LEU* 1.3 80.4 - - - +
225C CYS* 1.3 68.0 + - - +
226C MET* 3.5 28.2 - - + +
227C THR* 2.6 32.7 + - - -
228C ALA* 2.8 25.6 + - - +
251C GLN* 6.0 0.7 - - - -
253C ARG* 4.3 2.0 - - - -
107D SER* 3.3 31.5 - - - +
270D HIS* 4.4 2.7 - - - -
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Residues in contact with CYS 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C ASP* 1.3 72.3 - - + +
226C MET* 1.3 68.4 + - + +
229C ASN* 3.4 26.0 + - - +
253C ARG* 3.0 41.3 - - - +
255C GLU* 5.0 0.5 - - - +
106D SER* 5.3 7.9 - - - -
107D SER* 3.8 17.9 + - - +
270D HIS* 4.8 8.5 - - - -
318D ALA* 5.4 7.0 - - - -
319D ASP* 4.5 25.7 - - + +
322D VAL* 5.2 5.4 - - + -
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Residues in contact with MET 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C ASP* 3.2 22.9 + - - +
225C CYS* 1.3 79.5 - - + +
227C THR* 1.3 64.4 + - - +
229C ASN* 3.5 3.0 + - - +
230C GLN* 2.8 31.6 + - - +
107D SER* 6.1 2.0 - - - +
322D VAL* 3.9 36.3 - - + -
323D ASP 3.4 25.1 - - - +
324D LEU* 5.6 1.1 - - + -
325D THR 5.6 2.0 - - - -
330D ARG* 4.3 13.5 - - - +
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Residues in contact with THR 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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195C THR* 5.4 2.8 - - + +
196C GLY* 3.5 32.9 + - - +
223C LEU* 3.8 14.8 - - + -
224C ASP* 2.6 34.4 + - - -
226C MET* 1.3 75.5 - - - +
228C ALA* 1.3 68.8 + - - +
230C GLN* 2.8 20.6 + - + +
231C ILE* 2.8 22.2 + - + +
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Residues in contact with ALA 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C THR* 4.6 12.0 - - + +
223C LEU* 4.1 21.5 - - + +
224C ASP 2.8 24.0 + - - +
225C CYS 4.3 0.2 - - - +
227C THR* 1.3 69.4 - - - +
229C ASN* 1.3 69.9 + - - +
231C ILE* 2.8 8.1 + - - +
232C VAL* 2.8 26.3 + - - +
251C GLN* 4.2 24.0 - - - +
253C ARG* 5.0 3.4 - - + +
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Residues in contact with ASN 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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225C CYS 3.4 18.3 + - - +
226C MET* 3.5 3.1 + - - +
227C THR 3.3 0.6 - - - -
228C ALA* 1.3 78.7 - - - +
230C GLN* 1.3 66.8 + - - +
232C VAL* 2.9 11.0 + - - +
233C VAL* 2.8 31.0 + - + +
253C ARG* 3.9 20.3 - - - -
255C GLU* 3.4 30.1 + - - +
256C LEU* 4.0 13.8 - - - +
259C LEU* 6.1 1.8 - - - +
319D ASP* 5.2 2.0 + - - +
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Residues in contact with GLN 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C ARG* 3.0 34.7 - - - +
226C MET* 2.8 16.7 + - - +
227C THR* 2.8 23.6 + - + +
229C ASN* 1.3 71.3 - - - +
231C ILE* 1.3 60.5 + - + +
233C VAL* 3.4 14.5 - - + +
234C LEU* 3.3 19.6 - - + +
325D THR* 4.1 22.8 + - - +
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Residues in contact with ILE 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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196C GLY 4.2 19.7 - - - +
199C ARG* 4.5 16.4 - - + -
200C ARG* 4.2 25.4 - - + +
203C ILE* 5.0 13.2 - - + +
219C PRO* 4.3 19.7 - - + +
220C THR* 5.8 0.7 - - + -
223C LEU* 3.9 21.5 - - + -
227C THR* 2.8 27.0 + - + +
228C ALA* 2.8 9.5 + - - +
230C GLN* 1.3 72.6 - - + +
232C VAL* 1.3 68.8 + - + +
234C LEU* 2.8 19.7 + - + +
235C LEU* 3.2 18.7 + - + +
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Residues in contact with VAL 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C THR* 3.6 25.6 - - + -
228C ALA 2.8 14.8 + - - +
229C ASN* 3.5 7.4 - - - +
231C ILE* 1.3 71.4 - - + +
233C VAL* 1.3 67.3 + - - +
235C LEU* 2.8 32.3 + - + +
236C VAL* 3.1 22.6 + - + +
247C LEU* 5.8 2.5 - - + -
249C ILE* 6.2 0.4 - - + -
256C LEU* 3.5 34.8 - - + -
259C LEU* 4.5 15.5 - - + -
260C PHE* 4.9 17.0 - - + -
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Residues in contact with VAL 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C ASN* 2.8 25.7 + - + +
230C GLN* 3.4 13.2 - - + +
232C VAL* 1.3 72.1 - - - +
234C LEU* 1.3 74.5 + - + +
236C VAL* 2.8 23.5 + - - +
237C GLU* 2.8 31.9 + - + +
259C LEU* 6.2 4.3 - - + -
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Residues in contact with LEU 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C LEU* 4.3 26.9 - - + +
176C SER* 4.9 8.5 - - - +
200C ARG* 3.3 47.6 - - + +
203C ILE* 5.5 7.6 - - + -
230C GLN* 3.3 19.1 - - + +
231C ILE* 2.8 16.9 + - + +
233C VAL* 1.3 85.6 - - + +
235C LEU* 1.3 65.3 + - - +
237C GLU* 2.8 16.8 + - + +
238C LEU* 2.8 31.1 + - + +
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Residues in contact with LEU 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ILE* 5.6 0.9 - - + -
203C ILE* 5.4 3.6 - - + +
216C PHE* 3.4 54.1 - - + -
219C PRO* 4.3 11.0 - - + -
231C ILE* 3.2 13.6 + - + +
232C VAL* 2.8 27.0 + - + +
234C LEU* 1.3 78.6 - - - +
236C VAL* 1.3 64.4 + - + +
238C LEU* 2.9 19.9 + - + +
239C ALA 3.0 9.2 + - - -
245C VAL* 4.0 20.2 - - + +
247C LEU* 3.4 35.0 - - + -
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Residues in contact with VAL 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ILE* 3.2 36.1 - - + +
232C VAL* 3.2 30.7 - - + +
233C VAL* 2.8 16.6 + - - +
235C LEU* 1.3 73.6 - - + +
237C GLU* 1.3 54.7 + - + +
239C ALA* 2.8 14.2 + - + +
240C ARG* 2.8 24.0 + - - +
259C LEU* 4.6 12.3 - - + +
260C PHE* 6.0 1.3 - - + -
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Residues in contact with GLU 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 VAL* 2.8 35.7 + - + +
234C LEU* 2.8 22.2 + - + +
236C VAL* 1.3 70.1 - - + +
238C LEU* 1.3 58.1 + - + +
240C ARG* 2.7 62.7 + - - +
241C ARG* 2.8 16.6 + - + +
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Residues in contact with LEU 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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174C GLU* 4.2 15.7 - - + +
175C LEU* 4.9 12.6 - - + -
203C ILE* 4.5 16.8 - - + -
207C LEU* 3.9 22.4 - - + -
214C MET* 3.9 19.5 - - + -
216C PHE* 4.7 4.0 - - + -
234C LEU* 2.8 21.8 + - + +
235C LEU* 3.1 18.8 - - + +
237C GLU* 1.3 75.8 - - + +
239C ALA* 1.3 54.5 + - - +
241C ARG* 2.8 25.6 + - - +
243C ARG* 3.4 44.9 - - + +
245C VAL* 5.0 2.7 - - + -
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Residues in contact with ALA 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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79C GLY* 3.0 41.5 - - - +
80C GLN 3.5 17.0 - - - +
81C ILE* 4.2 6.7 - - + -
235C LEU 3.0 4.8 + - - +
236C VAL* 2.8 19.2 + - + +
238C LEU* 1.3 73.7 - - - +
240C ARG* 1.3 64.2 + - - +
242C ASN 3.2 6.9 + - - -
243C ARG 4.0 10.5 - - - -
245C VAL* 3.7 13.0 - - + +
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Residues in contact with ARG 240 (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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79C GLY 4.6 0.4 + - - -
236C VAL 2.8 6.8 + - - +
237C GLU* 2.7 52.3 + - - +
239C ALA* 1.3 70.3 - - - +
241C ARG* 1.3 92.5 + - - +
242C ASN* 2.9 7.3 + - - +
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Residues in contact with ARG 241 (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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174C GLU* 4.1 24.8 - - + +
212C LYS* 5.5 1.7 - - - +
237C GLU* 2.8 13.0 + - + +
238C LEU* 2.8 22.2 + - - +
240C ARG* 1.3 114.9 + - + +
242C ASN* 1.3 68.8 + - - +
243C ARG* 3.8 12.9 + - - +
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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
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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