Contacts of the helix formed by residues 288 - 301 (chain A) in PDB entry 1BO1
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 VAL 288 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286A HIS* 4.1 19.1 - - + +
287A ASP* 1.3 71.8 - - - +
289A ASP* 1.3 63.0 + - - +
291A ALA* 2.8 28.1 + - + +
292A GLU* 2.9 21.3 + - + +
343A ASP* 4.4 26.7 - - + +
344A PRO* 6.3 2.2 - - + -
359A LYS* 6.0 11.0 - - + -
360A LYS* 3.3 26.0 + - - +
361A GLU* 4.2 5.8 - - - +
362A VAL* 4.6 7.9 - - + -
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Residues in contact with ASP 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A ASP* 3.2 7.7 + - - +
288A VAL* 1.3 83.9 - - - +
290A ARG* 1.3 61.9 + - - +
292A GLU* 3.3 35.7 + - - +
293A GLN* 3.4 16.3 + - - +
359A LYS 5.3 3.6 - - - +
360A LYS* 4.5 19.3 + - - +
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Residues in contact with ARG 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A HIS* 3.8 41.9 + - - +
287A ASP* 3.1 26.1 + - + +
289A ASP* 1.3 73.6 - - - +
291A ALA* 1.3 65.8 + - - +
293A GLN* 3.3 17.6 + - - +
294A GLU* 3.1 42.8 + - + +
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Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A THR* 5.4 2.0 - - - +
212A HIS* 4.0 3.1 - - + +
286A HIS* 3.6 23.6 - - + +
287A ASP 3.0 13.7 + - - +
288A VAL* 2.8 15.2 + - + +
290A ARG* 1.3 77.9 - - - +
292A GLU* 1.3 49.8 + - - +
294A GLU* 3.2 16.4 + - - +
295A GLU* 2.8 38.7 + - - +
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Residues in contact with GLU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A VAL* 2.9 22.1 + - + +
289A ASP* 3.4 32.2 - - - +
291A ALA* 1.3 76.0 - - + +
293A GLN* 1.3 53.4 + - + +
295A GLU* 3.0 15.3 + - - +
296A MET* 2.7 36.8 + - - +
343A ASP* 5.4 5.9 - - - +
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Residues in contact with GLN 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A ASP* 3.4 11.7 - - - +
290A ARG* 3.3 23.5 + - + +
292A GLU* 1.3 74.5 - - + +
294A GLU* 1.3 63.7 + - + +
296A MET* 3.1 12.2 + - - +
297A GLU* 3.0 24.3 + - - +
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Residues in contact with GLU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A THR* 4.5 4.5 + - - -
212A HIS* 2.9 37.8 + - - -
290A ARG* 3.1 31.0 + - + +
291A ALA* 3.5 11.4 - - - +
293A GLN* 1.3 80.2 - - + +
295A GLU* 1.3 62.7 + - - +
297A GLU* 3.6 5.4 + - - +
298A VAL* 3.4 25.1 + - - +
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Residues in contact with GLU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A ALA* 2.8 19.5 + - - +
292A GLU* 3.3 12.4 - - - +
294A GLU* 1.3 75.9 - - - +
296A MET* 1.3 62.4 + - - +
298A VAL* 3.3 11.9 - - + +
299A GLU* 3.2 39.8 + - + +
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Residues in contact with MET 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A GLU 2.7 17.2 + - - +
293A GLN* 3.1 13.7 + - - +
295A GLU* 1.3 70.5 - - - +
297A GLU* 1.3 60.3 + - + +
299A GLU* 2.7 18.7 + - + +
300A GLU* 2.6 51.5 + - + +
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Residues in contact with GLU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A GLN 3.0 15.0 + - - +
294A GLU* 4.0 6.3 - - - +
296A MET* 1.3 78.0 - - + +
298A VAL* 1.3 58.0 + - + +
300A GLU* 3.3 13.2 - - + +
301A ARG* 2.9 65.6 + - + +
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Residues in contact with VAL 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A GLU 3.4 14.8 + - - +
295A GLU* 3.3 13.7 + - + +
296A MET 3.1 0.6 - - - -
297A GLU* 1.3 79.7 - - + +
299A GLU* 1.3 63.1 + - + +
301A ARG* 3.7 14.7 + - - +
302A ALA* 3.9 10.0 + - - +
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Residues in contact with GLU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A GLU* 3.3 34.7 - - + +
296A MET* 2.7 16.9 + - + +
298A VAL* 1.3 78.5 - - + +
300A GLU* 1.3 62.3 + - - +
301A ARG 3.6 0.2 + - - -
302A ALA* 3.6 12.5 + - - +
303A GLU* 3.3 21.6 + - - +
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Residues in contact with GLU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A MET* 2.6 32.5 + - + +
297A GLU* 2.9 19.5 + - - +
299A GLU* 1.3 74.8 - - - +
301A ARG* 1.3 66.5 + - - +
302A ALA 3.3 0.2 - - - -
303A GLU* 3.2 18.1 + - - +
304A ASP* 2.7 54.9 + - - +
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Residues in contact with ARG 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A GLU* 2.9 50.6 + - + +
298A VAL* 4.0 9.2 - - - +
299A GLU 3.4 0.4 - - - -
300A GLU* 1.3 80.4 + - - +
302A ALA* 1.3 56.0 + - - +
303A GLU 3.0 4.7 - - - -
304A ASP* 4.2 1.3 - - - +
305A GLU* 2.8 79.1 + - - +
306A GLU* 3.1 13.1 + - - +
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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