Contacts of the helix formed by residues 903 - 911 (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 GLU 903 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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899B ILE* 4.6 9.0 - - + +
900B PRO* 3.5 37.0 + - + +
901B THR 3.2 1.0 - - - -
902B ARG* 1.3 80.1 - - + +
904B ILE* 1.3 63.9 + - - +
905B PRO* 3.6 1.8 - - - -
906B ASP* 3.9 8.3 + - + +
907B LEU* 3.3 24.2 + - + +
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Residues in contact with ILE 904 (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* 4.2 22.4 - - + +
860B LYS* 3.9 24.9 - - + -
867B ILE* 4.6 3.1 - - + -
896B TYR* 3.7 43.1 - - + -
899B ILE* 4.3 6.5 - - + -
900B PRO 3.6 11.0 - - - +
901B THR* 3.3 21.1 - - - +
903B GLU* 1.3 75.1 - - - +
905B PRO* 1.4 70.8 - - + +
907B LEU* 3.2 8.9 + - + +
908B LEU* 3.0 41.8 + - + +
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Residues in contact with PRO 905 (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* 5.4 0.9 - - + -
864B LEU* 3.8 13.0 - - + +
867B ILE* 3.9 26.0 - - + -
868B HIS* 4.0 26.7 - - + +
901B THR 3.9 4.9 - - - +
902B ARG* 3.6 14.4 - - - +
903B GLU 3.6 3.4 - - - -
904B ILE* 1.4 96.4 - - + +
906B ASP* 1.3 68.1 + - - +
908B LEU* 3.2 5.1 + - + +
909B GLU* 3.1 29.7 + - - +
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Residues in contact with ASP 906 (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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868B HIS* 5.8 1.2 - - - -
902B ARG 4.7 6.9 - - - +
903B GLU* 3.9 8.0 + - + +
904B ILE 3.4 0.4 - - - -
905B PRO* 1.3 83.3 - - - +
907B LEU* 1.3 65.5 + - - +
909B GLU* 3.4 11.2 + - - +
910B LYS* 3.3 38.5 + - - +
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Residues in contact with LEU 907 (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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896B TYR* 3.9 26.9 - - + -
899B ILE* 3.9 38.8 - - + -
903B GLU* 3.3 13.5 + - + +
904B ILE* 3.2 14.1 + - + +
906B ASP* 1.3 78.7 - - - +
908B LEU* 1.3 64.6 + - + +
910B LYS* 3.4 20.9 + - - +
911B GLY 3.7 0.2 + - - -
912B GLU* 3.4 60.1 + - + +
913B ARG* 5.2 0.4 - - - -
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Residues in contact with LEU 908 (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 4.9 2.2 - - - +
864B LEU* 4.3 17.4 - - + +
867B ILE* 4.4 16.2 - - + -
879B TRP* 3.7 32.3 - - + -
896B TYR* 3.6 25.4 - - + +
904B ILE* 3.0 35.4 + - + +
905B PRO 3.2 6.3 + - - +
907B LEU* 1.3 78.5 - - + +
909B GLU* 1.3 60.5 + - - +
910B LYS 3.4 0.2 - - - -
911B GLY* 3.5 3.3 + - - -
912B GLU 3.7 15.0 - - - +
913B ARG* 2.8 40.5 + - + +
934B ILE* 5.5 1.4 - - - +
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Residues in contact with GLU 909 (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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864B LEU* 3.6 23.4 - - + +
868B HIS* 4.4 14.2 + - - -
905B PRO 3.1 21.1 + - - +
906B ASP* 3.8 11.6 - - - +
907B LEU 3.3 0.4 - - - -
908B LEU* 1.3 72.9 - - - +
910B LYS* 1.3 64.1 + - - +
911B GLY* 3.2 3.3 + - - -
934B ILE* 5.4 6.0 - - + +
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Residues in contact with LYS 910 (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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906B ASP* 3.3 27.1 + - - +
907B LEU* 3.7 12.4 - - - +
908B LEU 3.4 0.4 - - - -
909B GLU* 1.3 76.9 - - + +
911B GLY* 1.3 56.8 + - - +
912B GLU* 3.4 28.7 - - + +
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Residues in contact with GLY 911 (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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908B LEU 3.5 3.7 + - - -
909B GLU 3.2 4.4 - - - -
910B LYS* 1.3 79.1 - - - +
912B GLU* 1.3 64.7 + - - +
913B ARG* 3.4 26.4 + - - -
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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
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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