Contacts of the helix formed by residues 227 - 239 (chain C) in PDB entry 5DQZ
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 227 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187C LEU* 5.5 0.7 - - + -
223C ILE* 2.9 31.4 + - - +
224C LYS* 5.1 0.4 - - - -
225C PHE 3.2 1.0 - - - -
226C ASP* 1.3 84.0 + - - +
228C VAL* 1.3 67.2 + - - +
229C VAL 3.6 1.8 - - - -
230C PRO* 3.7 10.7 - - - +
231C LYS* 4.1 8.8 + - - +
254C ILE* 3.6 45.6 - - + +
255C PHE* 3.7 24.2 - - + -
258C SER* 4.4 7.3 + - - +
260C THR* 4.4 7.6 + - + +
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Residues in contact with VAL 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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183C ALA* 3.8 34.0 - - + +
184C THR* 4.2 4.0 - - - +
187C LEU* 3.9 28.7 - - + -
224C LYS* 3.0 16.1 + - + +
227C THR* 1.3 81.3 - - + +
229C VAL* 1.3 72.1 + - + +
231C LYS* 3.4 7.5 + - - +
232C ALA* 3.0 24.4 + - - +
251C CYS* 4.3 8.6 - - - -
254C ILE* 4.8 2.9 - - + -
255C PHE* 3.7 36.3 - - + -
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Residues in contact with VAL 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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149C TYR* 4.2 11.4 - - + +
152C LEU* 3.7 11.9 - - + -
180C ILE* 4.6 19.7 - - + -
183C ALA* 5.5 0.2 - - - -
184C THR* 5.0 0.9 - - - +
224C LYS* 3.3 34.5 + - + +
225C PHE* 4.1 18.4 - - + -
228C VAL* 1.3 76.9 - - + +
230C PRO* 1.4 73.3 - - + +
231C LYS 3.1 0.9 - - - -
232C ALA* 3.0 8.9 + - - +
233C PHE* 2.9 43.9 + - + -
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Residues in contact with PRO 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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152C LEU* 4.1 28.0 - - + -
156C TYR* 3.5 28.0 - - + +
225C PHE* 3.2 28.7 - - - +
226C ASP 4.7 4.5 - - - +
227C THR 3.7 12.8 - - - +
229C VAL* 1.4 94.7 - - + +
231C LYS* 1.3 56.9 + - + +
233C PHE* 3.2 3.2 + - + +
234C GLU* 2.9 23.4 + - - +
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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
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156C TYR* 5.9 0.9 - - - +
227C THR 4.1 7.4 + - - +
228C VAL* 3.4 11.3 + - - +
229C VAL 3.1 0.6 - - - -
230C PRO* 1.3 78.6 - - + +
232C ALA* 1.3 60.9 + - - +
234C GLU* 3.3 26.8 + - - +
235C ILE* 3.0 35.7 + - + +
250C ALA* 3.5 48.9 - - + +
251C CYS* 5.4 3.6 - - - +
253C ASP* 5.2 5.0 - - - +
254C ILE* 4.1 32.4 - - + +
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Residues in contact with ALA 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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176C ILE* 4.1 2.2 - - - -
179C CYS* 3.7 17.2 - - + +
180C ILE* 3.9 35.2 - - + +
183C ALA* 4.4 4.7 - - + +
228C VAL 3.0 12.8 + - - +
229C VAL* 3.0 15.0 + - - +
231C LYS* 1.3 77.7 - - - +
233C PHE* 1.3 56.5 + - - +
235C ILE* 3.5 4.6 + - - -
236C ALA* 2.9 28.2 + - - +
247C VAL* 5.5 2.2 - - - -
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Residues in contact with PHE 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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149C TYR* 4.1 23.6 - + - -
152C LEU* 3.9 26.0 - - + -
153C ALA* 3.5 22.2 - - + -
156C TYR* 3.8 18.5 - - + +
158C VAL* 3.8 23.1 - - + +
160C TRP* 4.1 14.6 - + - -
176C ILE* 3.6 35.4 - - + -
180C ILE* 4.3 2.2 - - + -
229C VAL* 2.9 44.9 + - + -
230C PRO 3.2 7.8 + - - +
232C ALA* 1.3 74.4 - - - +
234C GLU* 1.3 66.0 + - - +
236C ALA* 3.2 1.7 + - - +
237C ARG* 2.9 24.8 + - - +
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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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156C TYR* 3.6 30.9 + - + -
230C PRO 2.9 9.3 + - - +
231C LYS* 3.4 40.1 + - - +
233C PHE* 1.3 76.7 - - - +
235C ILE* 1.3 58.5 + - - +
237C ARG* 3.2 4.5 + - - +
238C ARG* 3.0 58.1 + - + +
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Residues in contact with ILE 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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179C CYS* 4.0 14.1 - - - -
231C LYS 3.0 19.3 + - - +
232C ALA 3.9 3.4 - - - +
234C GLU* 1.3 73.6 - - + +
236C ALA* 1.3 66.6 + - - +
238C ARG* 3.0 19.4 + - - +
239C ASN 2.9 18.2 + - - -
240C PRO* 3.5 25.3 - - + +
243C PRO 4.5 2.2 - - - +
246C GLU* 3.2 45.1 - - + +
247C VAL* 3.4 25.6 - - + -
250C ALA* 3.5 15.0 - - + -
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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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158C VAL* 4.3 9.2 - - + -
175C THR* 4.2 17.0 - - + +
176C ILE* 3.8 38.1 - - + +
179C CYS* 4.2 2.4 - - - -
232C ALA 2.9 19.0 + - - +
233C PHE* 3.4 6.3 - - - +
235C ILE* 1.3 76.4 - - - +
237C ARG* 1.3 61.2 + - - +
239C ASN* 3.0 18.2 + - - +
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Residues in contact with ARG 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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156C TYR* 2.9 19.6 + - + +
157C GLY* 2.6 46.2 + - - -
158C VAL* 3.9 10.9 - - + +
233C PHE 2.9 13.0 + - - +
234C GLU* 3.7 8.5 - - - +
236C ALA* 1.3 77.0 - - - +
238C ARG* 1.3 63.3 + - + +
239C ASN* 3.2 5.9 + - - +
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Residues in contact with ARG 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 GLU* 3.0 46.9 + - + +
235C ILE* 3.0 22.6 + - - +
237C ARG* 1.3 78.9 - - + +
239C ASN* 1.3 68.6 + - - +
240C PRO* 3.7 3.0 - - + +
246C GLU* 2.4 36.6 + - - +
250C ALA* 5.6 3.8 - - - +
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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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175C THR* 4.6 13.2 + - - -
235C ILE 2.9 8.5 + - - -
236C ALA 3.0 14.4 + - - +
237C ARG 3.9 5.8 - - - +
238C ARG* 1.3 81.4 - - - +
240C PRO* 1.3 70.0 - - - +
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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