Contacts of the helix formed by residues 863 - 869 (chain B) in PDB entry 3BBT
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 ALA 863 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861B TRP 3.8 1.6 + - - -
862B MET* 1.3 77.1 - - - +
864B LEU* 1.3 61.7 + - - +
865B GLU* 3.2 12.1 - - + -
866B CYS* 2.9 22.6 + - - +
867B ILE* 3.2 10.6 + - - +
876B SER* 4.0 13.6 + - - -
879B TRP* 3.6 35.2 - - + +
939B ARG* 3.8 20.6 - - - +
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Residues in contact with LEU 864 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862B MET 4.0 0.4 + - - -
863B ALA* 1.3 72.8 - - - +
865B GLU* 1.3 61.7 + - - +
866B CYS 3.3 0.3 + - - -
867B ILE* 3.4 13.6 + - + +
868B HIS* 3.3 57.2 + - + +
879B TRP* 4.4 19.2 - - + -
905B PRO* 3.8 27.1 - - + +
908B LEU* 4.3 17.3 - - + -
909B GLU* 3.6 29.8 - - + +
913B ARG* 5.8 0.4 - - - +
934B ILE* 3.7 28.9 - - + +
939B ARG* 4.8 2.2 - - - +
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Residues in contact with GLU 865 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863B ALA* 3.8 5.6 - - + -
864B LEU* 1.3 76.5 - - - +
866B CYS* 1.3 71.4 + - - +
869B TYR* 2.9 42.9 + - + +
870B ARG 3.2 4.3 + - - -
871B LYS* 3.4 25.4 + - + +
873B THR* 3.3 23.4 - - - +
876B SER* 4.1 5.6 - - - -
934B ILE 5.1 1.2 - - - +
936B ALA* 3.4 14.5 - - - +
939B ARG* 2.8 39.8 + - - +
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Residues in contact with CYS 866 (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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862B MET* 3.4 24.8 - - + +
863B ALA* 2.9 17.2 + - - +
865B GLU* 1.3 78.3 - - - +
867B ILE* 1.3 66.4 + - - +
870B ARG* 3.2 30.6 + - - +
871B LYS 3.4 21.8 - - - +
872B PHE* 3.9 23.1 - - + -
876B SER* 3.4 28.0 - - - -
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Residues in contact with ILE 867 (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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859B ILE* 4.3 27.8 - - + +
862B MET* 3.9 30.1 - - + +
863B ALA 3.2 15.0 + - - +
864B LEU* 3.4 28.2 + - + +
866B CYS* 1.3 80.1 - - - +
868B HIS* 1.3 65.3 + - + +
870B ARG* 5.1 3.8 + - - +
904B ILE* 4.6 8.5 - - + -
905B PRO* 3.9 24.2 - - + -
908B LEU* 4.4 11.0 - - + -
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Residues in contact with HIS 868 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864B LEU* 3.3 46.4 + - + +
867B ILE* 1.3 85.2 + - + +
869B TYR* 1.3 91.0 + + + +
870B ARG* 3.5 2.9 + - - +
905B PRO* 4.0 20.7 - - + +
906B ASP* 5.8 0.9 - - - -
909B GLU* 4.4 14.7 + - - -
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Residues in contact with TYR 869 (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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865B GLU* 2.9 26.5 + - + +
868B HIS* 1.3 95.1 - + + +
870B ARG* 1.3 70.2 + - - +
871B LYS* 3.2 10.4 + - + +
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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
------------------------------------------------------------
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