Contacts of the strand formed by residues 213 - 222 (chain C) in PDB entry 1BPO
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 213 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203C GLN* 3.1 7.8 - - - +
204C PHE* 2.6 39.3 + - - -
206C MET* 3.3 27.6 + - - +
209C ASN* 5.3 0.9 + - - -
211C GLU 3.7 1.9 + - - -
212C GLU* 1.3 76.9 - - - +
214C THR* 1.3 61.7 + - - +
215C LEU* 3.5 20.4 - - - -
232C GLU* 3.7 21.6 + - - -
237C PRO* 5.0 4.4 - - - +
240C ASN* 5.1 2.9 + - - +
241C GLN 5.3 1.0 + - - -
243C PHE* 4.6 0.9 - - - -
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Residues in contact with THR 214 (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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159C ASP* 4.1 27.8 + - + +
161C LYS* 4.5 9.5 + - - +
164C TRP* 4.5 2.0 - - + -
201C PHE* 4.7 1.1 - - + -
202C ALA 3.6 3.4 - - - +
203C GLN* 2.9 25.4 + - - +
212C GLU 5.2 0.2 + - - -
213C SER* 1.3 73.2 - - - +
215C LEU* 1.3 68.3 + - - +
232C GLU* 3.5 5.9 + - - +
233C VAL* 2.9 55.4 + - + -
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Residues in contact with LEU 215 (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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201C PHE* 3.2 12.6 - - - +
202C ALA* 2.7 41.4 + - + +
204C PHE* 3.7 24.0 - - + -
213C SER* 3.5 22.7 - - - -
214C THR* 1.3 84.5 - - - +
216C PHE* 1.3 62.6 + - - +
217C CYS* 4.2 0.7 - - + -
230C ILE* 4.0 20.9 - - + -
231C ILE 3.5 4.9 - - - +
232C GLU* 3.9 14.6 - - - +
243C PHE* 3.7 35.4 - - + -
287C LEU* 4.3 13.0 - - + -
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Residues in contact with PHE 216 (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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166C LEU* 3.2 44.9 - - + -
181C MET* 4.2 5.6 - - + -
183C LEU* 4.1 13.5 - - + -
194C ILE* 3.9 16.8 - - + -
199C ALA* 3.9 6.7 - - + -
200C SER 3.7 5.4 - - - -
201C PHE* 3.4 32.3 - + + -
215C LEU* 1.3 74.4 - - - +
217C CYS* 1.3 64.0 + - - +
218C PHE* 3.3 35.0 - + + -
229C HIS 3.7 0.3 - - - +
230C ILE* 3.7 0.7 - - - -
231C ILE* 2.9 60.0 + - + +
233C VAL* 4.1 11.0 - - + -
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Residues in contact with CYS 217 (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 ALA* 2.8 21.8 - - - +
200C SER 2.8 21.2 + - - +
215C LEU* 4.2 1.3 - - + -
216C PHE* 1.3 75.2 - - - +
218C PHE* 1.3 66.4 + - - +
228C LEU* 3.4 28.7 - - - -
229C HIS 3.0 10.5 - - - +
230C ILE* 3.6 23.1 - - + -
264C MET* 3.8 13.5 - - - -
266C ILE* 4.4 10.1 - - + -
273C VAL* 4.0 13.2 - - + -
287C LEU* 4.9 2.7 - - + -
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Residues in contact with PHE 218 (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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181C MET* 3.2 22.4 - - + -
194C ILE* 3.6 19.1 - - + -
195C GLU 3.5 21.3 - - - -
196C GLY* 4.1 2.0 - - - -
198C ALA 3.2 6.3 - - - +
199C ALA* 3.1 17.3 - - + +
216C PHE* 3.3 29.4 - + + -
217C CYS* 1.3 79.3 - - - +
219C ALA* 1.3 62.4 + - - +
220C VAL* 4.7 4.3 - - + -
227C LYS 4.1 0.2 - - - +
228C LEU* 3.4 3.1 - - - +
229C HIS* 2.7 80.1 + + + -
231C ILE* 4.4 8.5 - - + -
264C MET* 4.2 3.6 - - - -
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Residues in contact with ALA 219 (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 3.6 0.2 - - - -
197C HIS* 2.6 33.3 + - - +
198C ALA 2.6 16.6 + - - +
218C PHE* 1.3 76.9 - - - +
220C VAL* 1.3 57.5 + - - +
227C LYS 3.3 11.2 - - - +
228C LEU* 3.8 14.1 - - + -
250C VAL* 4.7 1.6 - - + -
261C PRO* 4.0 7.0 - - + -
264C MET* 3.9 1.6 - - + -
275C LEU* 3.7 33.4 - - + -
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Residues in contact with VAL 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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179C GLY 5.5 0.9 - - - +
195C GLU* 3.7 45.5 - - + +
196C GLY* 3.9 7.0 - - - +
197C HIS* 3.4 19.5 - - + +
218C PHE* 4.7 8.3 - - + -
219C ALA* 1.3 78.3 - - - +
221C ARG* 1.3 73.3 + - - +
222C GLY* 3.9 9.6 - - - +
225C GLY 4.8 0.2 - - - +
226C GLY* 2.8 3.3 - - - -
227C LYS* 2.7 50.7 + - + +
229C HIS* 4.9 3.8 - - - +
250C VAL* 4.8 0.3 - - - +
261C PRO* 4.0 6.3 - - - +
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Residues in contact with ARG 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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176C ARG* 3.4 22.0 + - - +
195C GLU* 4.4 3.3 - - - +
197C HIS* 3.0 27.2 + - + +
220C VAL* 1.3 75.5 - - - +
222C GLY* 1.3 62.5 + - - +
225C GLY* 4.2 3.8 - - - -
226C GLY* 3.5 10.9 - - - +
252C PHE* 3.4 52.8 + - + +
253C PRO 5.2 0.6 + - - -
256C ALA 3.6 4.0 + - - -
257C GLN 3.0 20.0 + - - -
258C ASN* 3.5 2.8 - - - +
259C ASP* 2.6 54.3 + - - +
260C PHE* 4.3 1.8 - - + -
261C PRO* 4.2 6.1 - - + -
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Residues in contact with GLY 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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195C GLU* 4.0 21.8 - - - -
220C VAL* 3.5 9.5 - - - +
221C ARG* 1.3 76.8 - - - +
223C GLN* 1.3 52.4 + - - -
224C ALA* 2.6 11.7 + - - -
225C GLY* 2.2 42.9 + - - -
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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
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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