Contacts of the helix formed by residues 768 - 773 (chain B) in PDB entry 2BKU
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 768 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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715B ALA* 4.2 32.7 - - + +
718B ILE* 4.6 5.6 - - + -
764B GLY 5.6 0.9 - - - +
765B LEU* 2.9 36.2 + - + +
767B ASP* 1.3 105.5 + - + +
769B PRO* 1.3 65.4 - - - +
770B GLU* 3.3 22.0 - - - +
771B ALA* 3.4 15.8 + - + +
772B LEU* 3.6 6.9 + - - +
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Residues in contact with PRO 769 (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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765B LEU 3.9 0.4 - - - -
766B HIS 4.2 6.1 - - - +
767B ASP 3.3 9.9 - - - +
768B LYS* 1.3 87.2 - - - +
770B GLU* 1.3 68.0 + - - +
772B LEU* 3.0 2.6 + - - -
773B PHE* 2.8 31.5 + - - +
812B MET* 3.6 35.7 - - + +
813B PHE* 3.4 29.1 - - + -
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Residues in contact with GLU 770 (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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767B ASP 4.5 1.0 - - - +
768B LYS* 3.5 35.0 - - - +
769B PRO* 1.3 89.6 - - - +
771B ALA* 1.3 63.9 + - + +
773B PHE* 3.4 8.2 + - - +
774B PRO* 3.3 19.4 - - - +
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Residues in contact with ALA 771 (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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718B ILE* 3.7 42.8 - - + -
721B LEU* 3.3 18.7 - - + +
765B LEU* 4.4 6.7 - - + -
768B LYS* 3.4 12.3 + - + +
769B PRO 3.1 0.6 - - - -
770B GLU* 1.3 83.7 - - + +
772B LEU* 1.3 61.3 + - - +
774B PRO* 3.4 10.3 - - - +
775B TYR* 3.7 5.0 - - - -
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Residues in contact with LEU 772 (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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721B LEU* 4.7 1.1 - - + -
725B MET* 5.9 0.7 - - - -
761B ILE* 3.9 28.0 - - + -
762B VAL* 4.1 19.3 - - + -
765B LEU* 4.4 9.4 - - + +
768B LYS 3.6 4.1 + - - +
769B PRO 3.0 7.4 + - - +
771B ALA* 1.3 78.1 - - - +
773B PHE* 1.3 66.3 + - - +
774B PRO* 3.2 1.3 - - - -
775B TYR* 2.8 29.3 + - + +
776B VAL* 3.6 5.9 + - + +
779B ILE* 3.9 22.0 - - + -
809B ILE* 4.7 8.3 - - + -
812B MET* 3.7 35.7 - - + -
813B PHE* 4.3 12.1 - - + -
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Residues in contact with PHE 773 (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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769B PRO 2.8 14.8 + - - +
770B GLU* 3.5 9.9 - - - +
772B LEU* 1.3 76.3 - - - +
774B PRO* 1.3 70.6 - - + +
775B TYR 2.8 6.8 + - - -
776B VAL* 3.3 15.9 + - - +
813B PHE* 3.7 27.4 - + + -
817B SER* 3.7 35.4 - - - -
818B ILE* 3.9 11.2 - - + -
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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