Contacts of the helix formed by residues 227 - 240 (chain C) in PDB entry 4OGB
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 227 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209C ASN* 4.1 3.2 - - - +
225C ASP 4.1 1.4 + - - -
226C SER* 1.3 71.8 - - - +
228C VAL* 1.3 66.1 + - - +
230C GLU* 3.3 22.1 + - - -
231C ASN* 2.9 30.0 + - - -
269C LEU* 4.4 8.5 - - - -
272C ASP* 2.5 30.6 + - - +
275C LYS* 3.6 20.3 + - - -
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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
----------------------------------------------------------
209C ASN* 3.4 14.3 + - + +
212C LEU* 4.3 13.5 - - + -
213C ILE* 4.3 9.0 - - + -
219C LEU* 3.6 21.5 - - + +
220C ALA* 3.6 35.7 - - + +
223C TYR* 3.8 9.8 - - + -
225C ASP* 3.6 37.5 - - - +
226C SER 3.7 3.4 - - - +
227C SER* 1.3 76.6 - - - +
229C LEU* 1.3 65.1 + - - +
231C ASN* 3.7 2.6 - - - +
232C HIS* 3.0 20.4 + - - +
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Residues in contact with LEU 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C HIS* 3.8 19.3 - - + +
205C PRO* 3.5 24.2 - - + -
207C VAL 3.2 27.1 - - - +
208C SER* 4.5 0.9 - - - -
209C ASN* 2.6 35.5 + - - +
212C LEU* 3.6 20.6 - - + -
219C LEU* 4.3 11.7 - - + -
228C VAL* 1.3 73.9 - - - +
230C GLU* 1.3 57.8 + - - +
232C HIS* 3.0 9.2 + - + +
233C HIS* 2.7 55.2 + - + +
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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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209C ASN* 3.0 28.8 + - - -
227C SER* 3.3 15.8 + - - +
229C LEU* 1.3 75.1 - - - +
231C ASN* 1.3 64.9 + - - +
233C HIS* 3.3 13.5 + - + +
234C LEU* 3.1 27.0 + - - +
268C VAL* 3.8 9.7 - - - +
269C LEU* 4.0 18.4 - - + -
271C THR* 3.7 19.4 - - - +
272C ASP* 3.5 33.5 - - + +
273C MET 4.8 0.5 + - - -
511C ZN 4.1 13.0 - - - -
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Residues in contact with ASN 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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223C TYR* 3.6 39.3 + - + +
226C SER* 3.0 27.1 + - - -
227C SER* 2.9 19.8 + - - +
228C VAL 3.7 0.4 - - - +
230C GLU* 1.3 74.4 - - - +
232C HIS* 1.3 62.7 + - - +
234C LEU* 3.2 7.5 + - - +
235C ALA* 3.0 22.3 + - - +
269C LEU* 3.8 11.2 - - - +
222D MET 5.1 0.9 - - - +
223D TYR* 5.5 1.9 - - - -
224D ASN* 2.9 29.6 + - - -
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Residues in contact with HIS 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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502A EDO 4.8 11.0 - - - -
202C VAL 4.4 2.7 - - - -
203C ASP* 2.7 46.3 + - + -
219C LEU* 3.7 43.0 - - + +
223C TYR* 3.9 9.8 + - + -
228C VAL 3.0 13.9 + - - +
229C LEU* 3.0 15.5 + - + +
231C ASN* 1.3 77.0 - - - +
233C HIS* 1.3 65.8 + - - +
235C ALA* 3.1 6.3 + - - +
236C VAL* 3.0 40.8 + - + +
512C EDO 5.8 0.8 - - - -
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Residues in contact with HIS 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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199C ILE* 3.5 15.0 - - - +
200C HIS* 2.9 30.7 - - - +
201C ASP* 3.2 26.6 + - - -
202C VAL* 2.6 37.9 + - - +
203C ASP 4.5 0.7 - - - -
204C HIS* 3.7 24.1 - + + -
229C LEU* 2.7 48.6 + - + +
230C GLU* 3.3 12.3 + - + +
232C HIS* 1.3 73.0 - + - +
234C LEU* 1.3 57.5 + - - +
237C GLY* 2.9 27.0 + - - -
268C VAL* 4.5 2.0 - - + -
511C ZN 4.2 4.8 - - - -
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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
----------------------------------------------------------
199C ILE* 4.3 4.9 - - + +
230C GLU 3.1 12.9 + - - +
231C ASN* 3.4 8.3 - - - +
233C HIS* 1.3 78.5 - - - +
235C ALA* 1.3 63.0 + - - +
237C GLY* 3.9 0.2 - - - -
238C PHE* 3.1 51.1 + - + -
264C VAL* 3.9 6.7 - - + +
265C ILE* 3.8 26.5 - - + +
268C VAL* 3.6 31.4 - - + +
269C LEU* 3.7 36.8 - - + -
224D ASN* 4.2 20.2 - - - +
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Residues in contact with ALA 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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502A EDO 4.0 24.6 + - - -
223C TYR* 3.7 23.1 - - - +
231C ASN 3.0 8.6 + - - +
232C HIS* 3.1 8.9 + - - +
234C LEU* 1.3 77.3 - - - +
236C VAL* 1.3 56.8 + - - +
238C PHE* 4.1 4.8 - - - +
239C LYS* 3.0 32.0 + - - +
222D MET* 6.5 0.9 - - - -
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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
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502A EDO 4.3 10.3 - - - +
152C HIS* 4.5 9.9 - - + +
202C VAL* 3.8 26.2 - - + -
203C ASP* 4.2 10.1 - - + +
232C HIS* 3.0 41.4 + - + +
235C ALA* 1.3 73.4 - - - +
237C GLY* 1.3 67.0 + - - +
239C LYS* 4.3 4.7 - - - -
240C LEU* 2.9 48.7 + - + +
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Residues in contact with GLY 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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145C TYR* 2.8 30.4 + - - -
149C LEU* 4.6 4.3 - - - -
195C PHE* 4.1 2.9 - - - -
199C ILE* 3.9 24.7 - - - -
202C VAL* 3.8 3.8 - - - +
233C HIS 2.9 18.3 + - - -
234C LEU 3.9 0.9 - - - -
236C VAL* 1.3 78.5 - - - +
238C PHE* 1.3 62.5 + - - +
240C LEU* 3.8 1.0 + - - +
241C LEU* 4.0 1.9 + - - +
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Residues in contact with PHE 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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195C PHE* 3.9 26.2 - + - -
199C ILE* 4.8 1.3 - - + -
234C LEU* 3.1 32.4 + - + +
235C ALA* 4.1 3.8 - - - +
237C GLY* 1.3 72.2 - - - +
239C LYS* 1.3 60.4 + - - +
240C LEU 3.1 0.2 - - - -
241C LEU* 2.8 44.7 + - + +
242C GLN* 4.2 6.2 + - - +
249C PHE* 5.8 1.6 - + - -
260C LEU* 6.2 1.3 - - + -
261C ARG* 4.1 39.3 - - + -
264C VAL* 3.9 24.2 - - + -
265C ILE* 3.9 20.4 - - + -
224D ASN* 5.4 1.3 - - - -
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Residues in contact with LYS 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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218A GLU* 4.0 42.0 - - + +
221A LEU* 5.1 10.5 - - - +
502A EDO 3.3 19.5 - - - +
239B LYS* 5.6 7.5 - - - +
242B GLN* 5.1 7.1 + - - +
235C ALA 3.0 21.9 + - - +
236C VAL* 3.8 4.7 - - - +
238C PHE* 1.3 76.0 - - - +
240C LEU* 1.3 65.6 + - + +
242C GLN* 2.4 59.4 + - - +
243C GLU* 4.2 3.3 + - - +
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Residues in contact with LEU 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C TYR* 3.8 16.2 - - + -
148C THR* 4.0 9.4 - - + +
149C LEU* 3.8 25.4 - - + -
152C HIS* 3.5 55.2 - - + +
236C VAL* 2.9 32.2 + - + +
237C GLY 4.0 0.4 - - - +
238C PHE 3.1 0.2 - - - -
239C LYS* 1.3 80.3 - - + +
241C LEU* 1.3 61.2 + - - +
242C GLN 3.1 1.0 + - - -
243C GLU* 3.3 29.4 + - + +
246C CYS* 3.3 18.0 - - - +
501C EDO 4.5 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