Contacts of the strand formed by residues 225 - 232 (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 GLY 225 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220C VAL* 4.8 0.5 - - - +
221C ARG* 3.7 7.2 - - - -
222C GLY* 2.2 51.8 + - - -
223C GLN 3.0 3.2 + - - -
224C ALA* 1.3 72.8 - - - +
226C GLY* 1.3 60.8 + - - -
227C LYS* 3.7 5.1 + - - +
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Residues in contact with GLY 226 (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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220C VAL 2.8 12.6 - - - -
221C ARG* 3.5 17.1 - - - +
225C GLY* 1.3 71.5 - - - -
227C LYS* 1.3 64.5 + - - +
249C ASP* 3.1 13.9 - - - +
250C VAL* 3.0 32.9 + - - +
252C PHE* 4.0 5.1 - - - -
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Residues in contact with LYS 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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218C PHE 4.1 0.2 - - - +
219C ALA* 3.3 3.8 - - - -
220C VAL* 2.7 35.4 + - + +
224C ALA* 3.0 32.7 + - + +
225C GLY* 3.7 7.5 + - - +
226C GLY* 1.3 75.0 + - - +
228C LEU* 1.3 59.7 + - - +
229C HIS* 3.8 25.8 - - + +
247C ALA* 5.6 2.2 - - + -
248C VAL 3.2 11.9 - - - +
249C ASP* 3.3 43.3 + - + +
250C VAL* 3.4 8.7 - - - +
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Residues in contact with LEU 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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217C CYS* 3.4 26.0 - - - -
218C PHE 3.4 7.2 - - - +
219C ALA* 3.8 7.0 - - + -
227C LYS* 1.3 76.0 - - - +
229C HIS* 1.3 63.4 + - - +
230C ILE* 4.2 20.8 + - + +
247C ALA* 3.1 4.9 - - - -
248C VAL* 2.6 42.5 + - + +
250C VAL* 3.7 12.3 - - + +
264C MET* 3.6 21.1 - - + -
273C VAL* 4.3 7.4 - - + -
275C LEU* 5.1 1.3 - - + -
285C TYR* 3.9 41.5 - - + -
290C GLY* 4.7 6.7 - - - +
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Residues in contact with HIS 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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216C PHE 3.7 1.2 - - - +
217C CYS* 3.0 7.3 - - - -
218C PHE* 2.7 83.3 + + + -
220C VAL* 4.9 4.5 - - + +
227C LYS* 3.8 28.1 - - + +
228C LEU* 1.3 76.2 - - - +
230C ILE* 1.3 63.1 + - - +
231C ILE* 4.1 3.4 - - + -
245C LYS* 3.3 13.8 + - - +
246C LYS 3.3 4.7 - - - +
247C ALA* 3.3 27.0 - - + +
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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
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215C LEU* 4.0 19.1 - - + -
216C PHE 3.7 3.8 - - - +
217C CYS* 3.6 20.6 - - + +
228C LEU* 4.2 11.9 - - + +
229C HIS* 1.3 76.0 - - - +
231C ILE* 1.3 61.0 + - - +
243C PHE* 3.9 17.4 - - + -
245C LYS* 3.4 1.9 - - - -
246C LYS* 2.6 47.4 + - + +
248C VAL* 6.1 0.2 - - + -
273C VAL* 4.9 1.1 - - + -
286C ASP 4.0 1.6 - - - +
287C LEU* 3.3 40.4 - - + +
290C GLY* 3.7 29.8 - - - +
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Residues in contact with ILE 231 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183C LEU* 5.8 1.1 - - + -
194C ILE* 5.9 1.3 - - + -
215C LEU* 3.5 5.3 - - - -
216C PHE* 2.9 71.5 + - + +
218C PHE* 4.4 9.2 - - + -
229C HIS* 4.6 3.1 - - + -
230C ILE* 1.3 82.4 - - - +
232C GLU* 1.3 70.9 + - - +
233C VAL* 4.8 4.0 - - + -
243C PHE* 4.9 1.3 - - - -
245C LYS* 3.8 41.1 - - + +
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Residues in contact with GLU 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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213C SER* 3.7 26.8 + - - -
214C THR 3.5 13.1 + - - +
215C LEU* 3.9 5.9 - - + +
231C ILE* 1.3 83.4 - - - +
233C VAL* 1.3 70.4 + - - +
234C GLY 4.1 6.6 + - - +
235C THR 4.8 0.2 - - - -
236C PRO* 3.6 32.9 - - - +
237C PRO* 4.4 2.1 - - - +
240C ASN* 5.8 0.2 - - - +
241C GLN 5.3 1.1 - - - +
242C PRO* 3.7 10.5 - - - +
243C PHE* 2.9 47.2 + - + +
245C LYS* 5.1 0.6 - - - +
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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