Contacts of the helix formed by residues 332 - 342 (chain G) in PDB entry 2BWB
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 TYR 332 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328G PRO* 2.7 44.6 + - + +
329G GLU 4.1 0.4 - - - -
331G ARG* 1.3 110.8 + - + +
333G GLU* 1.3 58.2 + - - +
335G GLN* 3.2 24.8 + - - +
336G LEU* 2.8 34.0 + - + +
351G VAL* 4.5 9.4 - - + -
354G LEU* 3.9 31.9 + - + -
355G ARG* 3.8 35.9 + - + +
358G GLY 5.3 0.3 - - - -
359G GLY* 4.0 22.5 + - - -
333H GLU* 4.0 12.8 + - - +
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Residues in contact with GLU 333 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331F ARG* 3.2 41.7 + - - -
332F TYR* 4.2 10.0 + - - +
358F GLY* 3.5 31.5 - - - +
329G GLU 3.3 18.9 + - - +
330G GLU* 3.3 17.5 + - - +
331G ARG 3.5 1.0 + - - -
332G TYR* 1.3 76.9 - - - +
334G HIS* 1.3 85.0 + - + +
336G LEU* 3.4 0.8 + - - -
337G ARG* 3.1 19.9 + - - +
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Residues in contact with HIS 334 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332G TYR 3.4 0.6 - - - -
333G GLU* 1.3 99.3 + - + +
335G GLN* 1.3 69.0 + - - +
337G ARG* 3.5 11.7 + - - +
338G GLN* 3.2 32.3 + - - +
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Residues in contact with GLN 335 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331G ARG 4.1 5.3 + - - +
332G TYR* 3.3 31.0 - - - +
333G GLU 3.9 0.2 + - - -
334G HIS* 1.3 83.1 + - + +
336G LEU* 1.3 58.2 + - - +
338G GLN* 3.4 4.4 + - - +
339G LEU* 3.0 35.8 + - - +
354G LEU* 3.6 18.6 - - + -
359G GLY* 3.1 36.0 + - - +
361G VAL* 3.5 25.9 - - + +
337H ARG* 4.1 18.3 - - - +
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Residues in contact with LEU 336 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355F ARG 4.5 4.3 - - - +
356F ARG 3.9 19.5 - - - +
357F SER 3.6 2.9 - - - -
358F GLY 4.2 9.6 - - - +
328G PRO 3.9 17.5 - - - +
329G GLU* 4.1 11.2 - - - +
332G TYR* 2.8 27.3 + - + +
333G GLU* 3.7 4.3 - - - +
335G GLN* 1.3 73.5 - - - +
337G ARG* 1.3 60.5 + - - +
339G LEU* 3.5 3.3 + - - +
340G ASN* 2.5 37.7 + - - +
347G PHE* 4.0 20.9 - - + -
350G ASN* 3.7 33.4 - - + +
351G VAL* 4.5 6.3 - - + -
354G LEU* 4.3 8.5 - - + -
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Residues in contact with ARG 337 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335F GLN* 3.0 28.9 + - - +
357F SER 3.4 9.8 + - - -
358F GLY 3.4 23.4 + - - +
359F GLY* 3.1 12.4 + - - -
360F SER* 4.2 10.5 - - - -
333G GLU 3.1 7.8 + - - +
334G HIS* 3.6 15.3 - - - +
335G GLN 3.2 0.2 - - - -
336G LEU* 1.3 73.6 - - - +
338G GLN* 1.3 60.3 + - + +
340G ASN* 3.4 1.4 + - - +
341G ASP* 2.9 49.7 + - - +
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Residues in contact with GLN 338 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334G HIS* 3.2 20.9 + - - +
335G GLN* 3.6 8.2 - - - +
337G ARG* 1.3 78.0 - - + +
339G LEU* 1.3 64.0 + - - +
341G ASP* 3.4 7.7 + - - +
342G MET* 3.1 33.5 + - - +
361G VAL* 3.3 38.8 - - + +
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Residues in contact with LEU 339 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335G GLN 3.0 21.9 + - - +
336G LEU* 3.8 4.5 - - - +
338G GLN* 1.3 75.4 - - - +
340G ASN* 1.3 59.7 + - - +
342G MET* 3.1 10.4 + - - -
343G GLY 3.3 0.5 + - - -
344G PHE* 2.9 30.3 + - + +
350G ASN* 3.8 33.4 - - + +
354G LEU* 3.9 31.0 - - + -
361G VAL* 4.4 16.2 - - + +
364G ALA* 4.3 4.7 - - + -
365G LEU* 3.8 35.9 - - + +
368G LEU* 4.0 15.9 - - + -
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Residues in contact with ASN 340 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356F ARG 4.4 2.9 + - - +
357F SER* 3.6 20.8 + - - +
360F SER* 3.6 23.3 - - - +
362F GLN* 3.3 5.5 + - - +
363F GLY* 3.4 21.4 - - - -
336G LEU* 2.5 35.9 + - - +
339G LEU* 1.3 71.6 - - - +
341G ASP* 1.3 63.7 + - - +
342G MET 3.1 1.8 - - - -
343G GLY 3.1 10.0 + - - -
344G PHE 3.5 15.1 + - - -
345G PHE* 3.2 34.6 + - - +
350G ASN* 3.6 11.7 + - - -
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Residues in contact with ASP 341 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360F SER* 2.8 24.5 + - - -
361F VAL 5.1 0.3 + - - -
362F GLN* 3.4 29.6 + - - +
337G ARG* 2.9 36.3 + - - +
338G GLN* 3.7 7.5 - - - +
340G ASN* 1.3 75.4 - - - +
342G MET* 1.3 60.1 + - + +
343G GLY 3.4 0.4 - - - -
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Residues in contact with MET 342 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338G GLN* 3.1 22.8 + - - +
339G LEU* 3.1 6.6 + - - +
340G ASN 3.1 0.6 - - - -
341G ASP* 1.3 79.8 - - + +
343G GLY* 1.3 57.6 + - - +
344G PHE* 3.5 24.1 - - + -
361G VAL* 5.1 4.7 - - - -
365G LEU* 3.6 39.3 - - + -
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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