Contacts of the helix formed by residues 404 - 418 (chain B) in PDB entry 2BBT
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 GLY 404 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403B GLU* 1.3 78.1 - - - +
405B PHE* 1.3 66.0 + - - -
406B GLY 3.3 3.1 - - - -
407B GLU* 3.4 8.9 + - - +
408B LEU* 3.2 17.8 + - - +
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Residues in contact with PHE 405 (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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403B GLU 3.9 0.4 + - - -
404B GLY* 1.3 71.6 - - - -
406B GLY* 1.3 55.0 + - - +
408B LEU* 3.0 18.2 + - + +
409B PHE* 2.6 68.5 + + + +
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Residues in contact with GLY 406 (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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404B GLY* 3.3 1.2 - - - -
405B PHE* 1.3 80.4 - - - +
407B GLU* 1.3 55.3 + - - +
409B PHE* 3.6 9.4 - - - +
410B GLU* 3.1 26.2 + - - +
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Residues in contact with GLU 407 (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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403B GLU* 3.3 29.1 - - + +
404B GLY* 3.4 11.9 + - - +
405B PHE 3.2 0.4 - - - -
406B GLY* 1.3 72.8 - - - +
408B LEU* 1.3 66.1 + - - +
410B GLU* 3.2 17.4 + - - +
411B LYS* 3.1 36.2 + - - +
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Residues in contact with LEU 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B GLU* 3.5 53.2 - - + +
404B GLY 3.2 4.8 + - - +
405B PHE* 3.0 23.7 + - + +
407B GLU* 1.3 79.2 - - - +
409B PHE* 1.3 58.1 + - - +
411B LYS* 3.6 13.2 - - + +
412B ALA* 3.0 30.3 + - - +
438B THR 6.2 0.7 - - - +
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Residues in contact with PHE 409 (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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405B PHE* 2.6 50.2 + + + +
406B GLY* 3.6 9.0 - - - +
408B LEU* 1.3 70.9 - - - +
410B GLU* 1.3 66.2 + - - +
412B ALA* 3.4 9.5 + - + +
413B LYS* 3.1 59.6 + - + +
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Residues in contact with GLU 410 (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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406B GLY 3.1 15.6 + - - +
407B GLU* 3.3 22.2 - - - +
409B PHE* 1.3 76.4 - - - +
411B LYS* 1.3 59.8 + - + +
413B LYS* 3.1 22.1 + - - +
414B GLN* 3.1 32.1 + - + +
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Residues in contact with LYS 411 (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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403B GLU* 2.9 31.2 + - - +
407B GLU* 3.3 30.0 + - - +
408B LEU* 3.6 15.7 - - + +
410B GLU* 1.3 77.7 - - + +
412B ALA* 1.3 66.7 + - - +
414B GLN* 3.2 16.2 + - + +
415B ASN* 2.9 33.7 + - - +
438B THR* 4.1 34.1 - - - +
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Residues in contact with ALA 412 (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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408B LEU 3.0 21.2 + - - +
409B PHE* 3.5 10.1 - - + +
411B LYS* 1.3 77.5 - - - +
413B LYS* 1.3 58.3 + - + +
415B ASN* 3.5 5.3 - - - +
416B ASN* 2.9 45.1 + - - +
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Residues in contact with LYS 413 (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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409B PHE* 3.1 49.3 + - + +
410B GLU* 3.1 31.5 + - - +
412B ALA* 1.3 74.8 - - + +
414B GLN* 1.3 64.0 + - + +
416B ASN* 5.0 0.7 - - - -
417B ASN* 3.1 49.2 + - - +
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Residues in contact with GLN 414 (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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410B GLU* 3.1 25.3 + - + +
411B LYS* 3.2 16.1 + - + +
413B LYS* 1.3 76.5 - - + +
415B ASN* 1.3 60.1 + - - +
418B ASN* 2.8 39.3 + - - +
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Residues in contact with ASN 415 (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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411B LYS* 2.9 29.7 + - - +
412B ALA* 3.5 8.1 - - - +
414B GLN* 1.3 76.6 - - - +
416B ASN* 1.3 73.8 + - - +
417B ASN 3.4 1.6 - - - -
418B ASN* 3.2 20.9 - - - +
438B THR* 5.1 7.1 + - - -
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Residues in contact with ASN 416 (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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412B ALA* 2.9 37.2 + - - +
413B LYS* 4.6 1.3 - - - +
415B ASN* 1.3 82.6 + - - +
417B ASN* 1.3 64.2 + - - +
418B ASN 4.6 1.3 - - - +
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Residues in contact with ASN 417 (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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413B LYS* 3.1 46.9 + - - +
416B ASN* 1.3 83.1 - - - +
418B ASN* 1.3 65.8 + - - +
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Residues in contact with ASN 418 (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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413B LYS 5.2 0.4 + - - -
414B GLN* 2.8 31.3 + - - +
415B ASN* 3.2 17.5 - - - +
416B ASN 3.6 1.4 - - - +
417B ASN* 1.3 86.9 - - - +
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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