Contacts of the helix formed by residues 360 - 369 (chain B) in PDB entry 2BWE
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B LEU* 4.2 0.9 - - - -
357B SER* 2.9 32.0 + - - -
358B GLY 3.3 1.6 + - - -
359B GLY* 1.3 75.4 - - - +
361B VAL* 1.3 63.2 + - - +
362B GLN* 3.6 10.0 + - - +
363B GLY* 3.1 16.0 + - - -
364B ALA* 2.9 12.3 + - - +
337C ARG* 3.6 21.0 - - - +
340C ASN* 3.8 20.0 + - - +
341C ASP* 3.8 11.1 + - - -
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Residues in contact with VAL 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B GLN* 3.5 30.1 - - + +
338B GLN* 3.4 46.4 - - + +
339B LEU* 4.3 18.8 - - + -
342B MET* 5.4 4.3 - - - -
354B LEU* 4.4 6.1 - - - -
359B GLY 3.3 2.8 + - - -
360B SER* 1.3 69.7 + - - +
362B GLN* 1.3 68.6 + - - +
363B GLY 3.1 0.3 + - - -
364B ALA* 3.1 2.2 + - - +
365B LEU* 2.9 31.6 + - + +
337C ARG* 5.1 0.4 - - - +
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Residues in contact with GLN 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B SER* 3.7 7.9 - - - +
361B VAL* 1.3 82.1 - - - +
363B GLY* 1.3 60.9 + - - +
365B LEU* 3.4 20.7 - - - +
366B ASP* 3.4 9.4 + - - +
340C ASN 4.5 8.4 + - - +
341C ASP* 4.7 11.4 + - - +
343C GLY* 5.2 3.4 - - - +
345C PHE* 3.7 25.4 - - + -
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Residues in contact with GLY 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357B SER* 4.0 5.2 - - - -
360B SER* 3.1 11.1 + - - -
362B GLN* 1.3 76.9 - - - +
364B ALA* 1.3 65.0 + - - +
366B ASP* 3.1 13.2 + - - +
367B SER* 3.1 14.3 + - - -
340C ASN* 3.4 22.6 - - - +
345C PHE* 3.5 16.9 - - - +
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Residues in contact with ALA 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B LEU* 4.7 7.2 - - + -
353B ALA* 3.7 37.7 - - + +
354B LEU* 3.8 18.6 - - + -
357B SER* 3.7 2.7 - - - +
360B SER 2.9 16.5 + - - +
361B VAL* 3.9 2.7 - - - +
363B GLY* 1.3 71.7 - - - +
365B LEU* 1.3 65.9 + - - +
367B SER* 3.1 6.2 + - - -
368B LEU* 2.7 28.4 + - - +
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Residues in contact with LEU 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B LEU* 4.4 8.8 - - + +
342B MET* 3.8 34.1 - - + -
344B PHE* 3.6 37.0 - - + -
361B VAL* 2.9 16.1 + - + +
362B GLN* 3.4 16.6 - - - +
364B ALA* 1.3 75.0 - - - +
366B ASP* 1.3 65.1 + - - +
368B LEU* 3.0 7.7 + - - +
369B LEU* 2.9 39.9 + - + +
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Residues in contact with ASP 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B GLN 3.4 6.4 + - - +
363B GLY 3.1 10.3 + - - +
365B LEU* 1.3 78.9 - - - +
367B SER* 1.3 59.2 + - - +
369B LEU* 3.2 16.6 + - - +
370B ASN* 2.8 37.4 + - - +
345C PHE* 3.2 46.8 - - + +
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Residues in contact with SER 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B ARG* 5.0 0.2 + - - -
353B ALA* 4.2 17.3 + - - -
356B ARG* 4.4 17.6 + - - +
357B SER* 5.8 0.7 - - - -
363B GLY 3.1 10.2 + - - -
364B ALA* 3.1 14.1 + - - -
366B ASP* 1.3 81.2 + - - +
368B LEU* 1.3 57.4 + - - -
370B ASN* 3.2 6.7 + - - +
371B GLY* 3.0 36.1 + - - +
345C PHE 4.6 10.7 + - - -
347C PHE* 5.9 0.3 - - - +
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Residues in contact with LEU 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B LEU* 3.9 27.1 - - + -
344B PHE* 4.0 27.3 - - + -
349B ARG* 3.2 56.8 + - + +
350B ASN* 3.7 24.5 - - - +
353B ALA* 4.0 18.8 - - + -
364B ALA 2.7 24.9 + - - +
365B LEU* 3.0 5.8 + - - +
367B SER* 1.3 74.5 - - - +
369B LEU* 1.3 62.2 + - - +
370B ASN 3.4 1.0 + - - -
371B GLY 3.9 0.7 + - - -
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Residues in contact with LEU 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344B PHE* 3.5 29.2 - - + -
365B LEU* 2.9 36.6 + - + +
366B ASP* 3.2 8.2 + - - +
368B LEU* 1.3 78.1 - - - +
370B ASN* 1.3 65.5 + - - +
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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