Contacts of the helix formed by residues 666 - 674 (chain B) in PDB entry 4BEJ
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 LYS 666 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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662B GLY 4.3 9.0 - - - +
663B GLN* 3.7 22.7 - - - +
664B LEU 2.7 11.4 + - - +
665B TYR* 1.3 78.5 - - - +
667B SER* 1.3 67.3 + - - +
668B SER* 3.2 12.8 + - - +
669B LEU* 2.9 20.2 + - + +
670B LEU* 3.0 11.8 + - - +
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Residues in contact with SER 667 (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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665B TYR 4.2 0.2 - - - -
666B LYS* 1.3 71.1 - - - +
668B SER* 1.3 64.3 + - - +
670B LEU* 3.2 33.5 + - - +
671B ASP 4.5 1.0 + - - -
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Residues in contact with SER 668 (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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666B LYS* 3.2 13.8 + - - +
667B SER* 1.3 83.4 + - - +
669B LEU* 1.3 75.3 + - - +
671B ASP* 3.0 20.6 - - - +
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Residues in contact with LEU 669 (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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463B ALA* 5.9 2.9 - - + -
663B GLN 5.5 6.1 - - - +
664B LEU* 4.8 12.8 - - + +
666B LYS* 2.9 12.9 + - + +
668B SER* 1.3 85.4 + - - +
670B LEU* 1.3 64.0 + - - +
671B ASP* 3.3 2.7 - - - -
672B ASP* 3.2 21.8 + - + +
673B LEU* 3.1 43.7 + - + +
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Residues in contact with LEU 670 (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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329B LYS* 4.0 10.8 - - + +
330B SER* 3.4 41.7 - - - +
333B LEU* 3.6 29.2 - - + -
664B LEU 4.3 0.7 - - - +
665B TYR* 4.6 5.2 - - + -
666B LYS 3.0 37.0 - - - +
667B SER* 3.2 22.2 + - - +
669B LEU* 1.3 75.3 - - - +
671B ASP* 1.3 65.7 + - - +
672B ASP 3.2 0.2 + - - -
673B LEU* 3.2 3.0 + - - +
674B LEU* 3.1 39.8 + - + +
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Residues in contact with ASP 671 (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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329B LYS* 4.4 23.4 - - - +
667B SER 4.5 0.8 + - - -
668B SER 3.0 26.0 + - - +
669B LEU* 4.2 0.7 - - - -
670B LEU* 1.3 79.1 - - - +
672B ASP* 1.3 71.0 + - - +
674B LEU* 4.0 1.6 + - - +
675B THR* 3.1 19.9 + - - -
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Residues in contact with ASP 672 (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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459B LYS* 3.1 62.7 + - - +
669B LEU* 3.2 26.1 + - + +
671B ASP* 1.3 90.5 - - - +
673B LEU* 1.3 74.9 + - - +
675B THR* 3.1 12.4 + - - -
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Residues in contact with LEU 673 (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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333B LEU* 3.7 26.5 - - + -
457B PHE* 3.4 12.1 - - - +
459B LYS* 3.9 20.4 - - - +
460B LEU* 3.4 37.7 + - + +
463B ALA* 4.2 11.0 - - + -
664B LEU* 3.4 34.1 - - + +
669B LEU* 3.1 28.0 + - + +
670B LEU 3.2 4.0 + - - +
672B ASP* 1.3 92.0 - - - +
674B LEU* 1.3 63.0 + - + +
675B THR 3.2 4.0 + - - +
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Residues in contact with LEU 674 (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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326B VAL* 5.1 13.3 - - + +
329B LYS* 3.5 46.2 - - + +
332B THR* 3.6 24.7 - - + +
333B LEU* 4.7 8.1 - - + +
336B LEU* 5.7 0.2 - - + -
457B PHE* 3.6 36.2 - - + -
460B LEU* 4.2 9.0 - - + -
670B LEU* 3.1 37.1 + - + +
671B ASP 4.3 2.5 - - - +
673B LEU* 1.3 80.6 - - + +
675B THR* 1.3 64.1 + - - +
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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