Contacts of the helix formed by residues 360 - 370 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354E LEU* 4.2 1.6 - - - -
357E SER* 2.8 28.4 + - - -
358E GLY 3.5 0.6 - - - -
359E GLY* 1.3 75.4 - - - +
361E VAL* 1.3 58.6 + - - +
362E GLN* 3.4 5.5 + - - -
363E GLY 3.2 9.4 + - - -
364E ALA* 2.9 15.6 + - - +
337F ARG* 3.8 9.6 - - - +
340F ASN* 3.2 33.0 - - - +
341F ASP* 3.0 27.2 + - - -
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Residues in contact with VAL 361 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335E GLN* 3.3 43.1 - - + +
338E GLN* 3.6 37.9 - - + +
339E LEU* 4.2 11.2 - - + +
342E MET* 5.1 1.8 - - - -
354E LEU* 4.6 1.1 - - + -
359E GLY 3.7 0.6 + - - -
360E SER* 1.3 69.8 + - - +
362E GLN* 1.3 61.4 + - + +
364E ALA* 3.6 5.9 - - - +
365E LEU* 2.8 53.3 + - + +
337F ARG* 5.4 1.1 - - - +
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Residues in contact with GLN 362 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360E SER* 3.4 4.9 + - - +
361E VAL* 1.3 84.0 - - + +
363E GLY* 1.3 61.2 + - - +
365E LEU* 3.5 11.2 + - + +
366E ASP* 3.1 17.3 + - - +
340F ASN 4.0 8.7 - - - +
341F ASP* 2.8 46.6 + - - +
345F PHE* 3.6 17.4 - - + -
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Residues in contact with GLY 363 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357E SER* 3.8 6.1 - - - -
360E SER* 3.2 10.0 + - - -
362E GLN* 1.3 75.4 - - - +
364E ALA* 1.3 66.8 + - - +
366E ASP* 3.0 5.7 + - - +
367E SER* 2.9 22.7 + - - -
340F ASN* 3.3 15.0 - - - +
345F PHE* 3.2 25.7 - - - +
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Residues in contact with ALA 364 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339E LEU* 4.4 11.0 - - + -
353E ALA* 3.8 28.5 - - + +
354E LEU* 4.0 17.0 - - + +
357E SER* 3.4 7.8 + - - +
360E SER 2.9 17.0 + - - +
361E VAL* 3.6 5.8 - - - +
363E GLY* 1.3 74.8 - - - +
365E LEU* 1.3 57.8 + - - +
367E SER* 3.1 5.3 + - - -
368E LEU* 2.9 33.9 + - - +
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Residues in contact with LEU 365 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339E LEU* 3.8 10.1 - - + +
342E MET* 3.7 31.2 - - + -
344E PHE* 3.3 39.5 - - + -
361E VAL* 2.8 43.4 + - + +
362E GLN* 3.6 10.5 - - + +
364E ALA* 1.3 73.8 - - - +
366E ASP* 1.3 61.0 + - - +
368E LEU* 3.4 6.1 + - - +
369E LEU* 3.0 38.9 + - + +
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Residues in contact with ASP 366 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362E GLN 3.1 8.7 + - - +
363E GLY 3.0 9.7 + - - +
365E LEU* 1.3 75.6 - - - +
367E SER* 1.3 60.9 + - - +
369E LEU* 3.3 6.4 + - - +
370E ASN* 2.6 65.0 + - - +
345F PHE* 2.9 51.9 - - + +
346F ASP* 5.7 0.2 - - - -
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Residues in contact with SER 367 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349E ARG* 4.9 1.6 + - - -
353E ALA* 4.1 20.9 - - - +
356E ARG* 4.7 15.0 + - - -
363E GLY 2.9 11.4 + - - -
364E ALA* 3.1 8.5 + - - -
366E ASP* 1.3 81.6 + - - +
368E LEU* 1.3 56.3 + - - +
370E ASN* 2.6 29.3 - - - +
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Residues in contact with LEU 368 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339E LEU* 3.8 28.5 - - + -
344E PHE* 4.0 31.8 - - + -
349E ARG* 3.2 62.4 + - + +
350E ASN* 3.7 22.7 - - - +
353E ALA* 4.0 8.3 - - + -
364E ALA 2.9 22.1 + - - +
365E LEU* 3.8 6.1 - - - +
367E SER* 1.3 76.3 - - - +
369E LEU* 1.3 61.7 + - - +
370E ASN 4.3 1.2 - - - +
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Residues in contact with LEU 369 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344E PHE* 3.9 24.0 - - + -
365E LEU* 3.0 33.4 + - + +
366E ASP* 3.9 5.6 - - - +
368E LEU* 1.3 79.6 - - - +
370E ASN* 1.3 68.0 + - - +
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Residues in contact with ASN 370 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349E ARG* 5.6 0.7 + - - -
366E ASP* 2.6 45.0 + - - +
367E SER* 2.6 25.1 - - - +
368E LEU 4.3 1.7 - - - +
369E LEU* 1.3 89.1 - - - +
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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