Contacts of the strand formed by residues 286 - 293 (chain C) in PDB entry 3BFO
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 286 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262C LYS* 4.6 1.1 - - - -
263C ASN* 3.6 13.2 - - - -
284C HIS 3.4 2.0 + - - -
285C GLN* 1.3 77.7 - - - +
287C THR* 1.3 63.2 + - - -
288C TYR* 3.5 12.4 - - - -
305C GLU* 3.5 7.7 - - - +
306C ILE 2.9 34.1 + - - -
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Residues in contact with THR 287 (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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261C PHE 3.9 0.2 - - - +
262C LYS* 3.3 1.9 - - - -
263C ASN* 2.7 44.9 + - - -
264C GLU* 5.8 1.8 - - - +
286C GLY* 1.3 74.0 - - - -
288C TYR* 1.3 61.3 + - - +
289C TRP* 4.8 3.8 - - + -
303C LYS* 4.0 33.7 - - + -
304C VAL 3.3 12.6 - - - +
305C GLU* 4.5 10.7 + - - +
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Residues in contact with TYR 288 (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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244C LEU* 3.9 12.3 - - + +
246C LEU* 3.5 24.7 - - + -
260C TRP* 4.7 5.8 - + + -
261C PHE 3.1 13.9 - - - +
262C LYS* 3.3 31.6 - - + +
267C LEU* 3.9 9.6 - - + -
275C TYR* 3.6 27.2 + + - -
284C HIS* 2.6 38.1 + - - +
286C GLY 3.5 16.4 - - - -
287C THR* 1.3 74.9 - - - +
289C TRP* 1.3 67.5 + - - +
303C LYS* 3.4 1.6 - - - -
304C VAL* 2.9 40.6 + - + +
306C ILE* 3.6 22.7 - - + -
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Residues in contact with TRP 289 (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 PRO* 5.3 0.2 - - - -
260C TRP* 3.5 10.7 - - - -
261C PHE* 2.8 73.5 + + + +
264C GLU* 3.2 34.1 + - - +
287C THR* 4.8 4.9 - - + -
288C TYR* 1.3 82.8 - - - +
290C CYS* 1.3 78.8 + - - +
291C HIS* 3.8 15.0 - + + -
300C ASP* 3.1 41.1 - - + -
301C SER* 3.4 15.5 - - - +
302C LYS 3.7 7.0 - - - +
303C LYS* 3.8 30.0 - - + +
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Residues in contact with CYS 290 (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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248C CYS* 3.9 10.3 - - + -
258C TYR* 3.8 39.3 - - - -
259C GLN 3.4 10.5 - - - -
260C TRP* 3.8 38.1 - - + -
289C TRP* 1.3 80.2 - - - +
291C HIS* 1.3 65.7 + - - +
292C VAL* 3.8 3.8 + - - +
300C ASP* 3.6 1.0 - - - -
301C SER* 2.8 40.1 + - - +
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Residues in contact with HIS 291 (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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257C HIS 3.7 0.5 - - - +
258C TYR* 3.3 5.9 - - - -
259C GLN* 2.9 34.5 + - + +
261C PHE* 3.8 22.9 - + + -
289C TRP* 3.8 5.9 - + + -
290C CYS* 1.3 72.5 - - - +
292C VAL* 1.3 59.7 + - - +
293C TYR* 3.6 32.2 - + + +
298C SER* 3.5 37.0 + - - -
299C GLN 3.7 5.3 + - - -
300C ASP* 2.6 30.4 + - - +
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Residues in contact with VAL 292 (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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227C LEU* 4.1 9.0 - - + +
229C ILE* 3.7 16.2 - - + -
248C CYS* 3.7 30.7 - - - -
250C ALA* 3.5 28.9 - - + -
256C PRO* 3.7 15.0 - - + -
257C HIS 3.2 6.3 - - - +
258C TYR* 3.8 12.6 - - + -
290C CYS* 4.0 5.2 - - - +
291C HIS* 1.3 78.1 - - - +
293C TYR* 1.3 65.7 + - - +
298C SER* 3.2 4.0 - - - -
299C GLN 2.9 37.9 + - - +
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Residues in contact with TYR 293 (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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227C LEU* 3.6 7.0 - - - -
257C HIS* 2.8 76.8 + + + +
258C TYR 4.1 12.1 + - - -
259C GLN* 4.7 6.6 - - + +
291C HIS* 3.6 27.8 - + - +
292C VAL* 1.3 79.9 - - - +
294C ASN* 1.3 73.5 + - - +
297C ASP 3.5 5.8 - - - +
298C SER* 3.6 16.4 - - - -
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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