Contacts of the helix formed by residues 360 - 370 (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 SER 360 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354G LEU* 3.9 1.3 - - - +
357G SER* 2.8 36.6 + - - -
359G GLY* 1.3 76.5 - - - +
361G VAL* 1.3 57.7 + - - +
362G GLN* 3.5 2.8 + - - +
363G GLY 3.2 15.6 + - - -
364G ALA* 3.0 17.0 + - - +
337H ARG* 3.4 11.3 - - - +
340H ASN* 3.4 18.5 - - - +
341H ASP* 2.7 29.9 + - - -
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Residues in contact with VAL 361 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335G GLN* 3.5 35.2 - - + +
338G GLN* 3.3 42.2 - - + +
339G LEU* 4.4 9.6 - - + +
342G MET* 5.1 2.7 - - - -
354G LEU* 4.6 0.9 - - + -
359G GLY 3.7 0.6 + - - -
360G SER* 1.3 71.1 + - - +
362G GLN* 1.3 59.0 + - + +
364G ALA* 3.3 6.6 + - - +
365G LEU* 2.8 53.4 + - + +
341H ASP* 4.5 1.0 + - - -
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Residues in contact with GLN 362 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360G SER* 3.8 7.4 - - - +
361G VAL* 1.3 82.2 - - + +
363G GLY* 1.3 56.9 + - - +
365G LEU* 3.5 10.8 + - + +
366G ASP* 3.1 25.5 + - - +
340H ASN 3.3 17.9 - - - +
341H ASP* 3.5 20.4 + - - +
343H GLY* 4.2 4.5 + - - -
345H PHE* 4.0 16.5 - - + -
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Residues in contact with GLY 363 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357G SER* 3.9 6.7 - - - -
360G SER* 3.2 10.6 + - - -
362G GLN* 1.3 76.2 - - - +
364G ALA* 1.3 65.7 + - - +
366G ASP* 3.2 4.2 + - - +
367G SER* 3.1 22.7 + - - -
340H ASN* 3.4 27.7 + - - -
345H PHE* 3.6 13.8 - - - +
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Residues in contact with ALA 364 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339G LEU* 4.3 11.0 - - + -
353G ALA* 3.8 25.5 - - + +
354G LEU* 4.0 18.6 - - + -
357G SER* 3.6 8.0 - - - +
360G SER 3.0 18.4 + - - +
361G VAL* 3.5 5.6 - - - +
363G GLY* 1.3 74.6 - - - +
365G LEU* 1.3 58.2 + - - +
367G SER* 3.1 4.8 + - - -
368G LEU* 2.9 33.7 + - - +
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Residues in contact with LEU 365 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339G LEU* 3.8 13.2 - - + -
342G MET* 3.6 35.4 - - + -
344G PHE* 3.3 41.7 - - + -
361G VAL* 2.8 36.2 + - + +
362G GLN* 3.6 10.3 - - + +
364G ALA* 1.3 72.0 - - - +
366G ASP* 1.3 63.1 + - - +
368G LEU* 3.4 5.8 + - + +
369G LEU* 3.0 40.5 + - + +
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Residues in contact with ASP 366 (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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362G GLN 3.1 14.4 + - - +
363G GLY 3.2 9.6 + - - +
365G LEU* 1.3 75.0 - - - +
367G SER* 1.3 59.9 + - - +
369G LEU* 3.8 5.5 - - - -
370G ASN* 2.9 56.7 + - - +
345H PHE* 3.1 48.7 - - + +
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Residues in contact with SER 367 (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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349G ARG* 4.6 3.1 + - - -
353G ALA* 4.1 20.5 - - - +
356G ARG* 4.4 18.4 + - - -
363G GLY 3.1 12.2 + - - -
364G ALA* 3.1 8.5 + - - -
366G ASP* 1.3 80.4 + - - +
368G LEU* 1.3 55.0 + - - +
370G ASN* 2.7 28.5 - - - +
371G GLY 4.1 7.0 - - - +
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Residues in contact with LEU 368 (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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339G LEU* 4.0 24.5 - - + -
344G PHE* 4.1 29.8 - - + -
349G ARG* 3.1 68.6 + - + +
350G ASN* 3.5 26.9 - - - +
353G ALA* 4.1 7.9 - - + -
364G ALA 2.9 22.6 + - - +
365G LEU* 3.8 5.8 - - - +
367G SER* 1.3 75.8 - - - +
369G LEU* 1.3 61.0 + - - +
370G ASN 4.1 1.0 - - - +
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Residues in contact with LEU 369 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344G PHE* 3.9 27.8 - - + -
365G LEU* 3.0 31.9 + - + +
366G ASP* 3.9 5.6 - - - +
368G LEU* 1.3 78.0 - - - +
370G ASN* 1.3 63.9 + - - +
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Residues in contact with ASN 370 (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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349G ARG* 5.1 0.9 + - - -
366G ASP* 2.9 46.9 + - - +
367G SER* 2.7 18.6 - - - +
368G LEU 4.1 2.8 - - - +
369G LEU* 1.3 83.6 - - - +
371G GLY* 1.3 70.7 + - - +
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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