Contacts of the helix formed by residues 905 - 914 (chain B) in PDB entry 2O8C
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 LEU 905 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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865B PHE* 4.1 23.8 - - + +
868B MET* 5.0 0.9 - - + -
869B CYS* 3.9 21.9 - - - -
902B PHE* 4.0 9.2 - - + -
903B PRO* 3.2 30.0 + - + +
904B ASP* 1.3 71.4 + - - +
906B THR* 1.3 66.1 + - - +
907B VAL 3.4 0.4 - - - -
908B GLU* 3.2 8.6 + - - +
909B LEU* 2.9 38.7 + - + +
1043B ASN* 5.0 0.7 - - - +
1046B ASP* 3.9 16.2 - - + +
1047B TRP* 3.7 22.7 - - + -
1050B ALA* 3.9 21.8 - - + -
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Residues in contact with THR 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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869B CYS* 4.6 11.5 - - - +
893B LEU* 6.1 0.7 - - - +
904B ASP* 3.2 18.6 + - - -
905B LEU* 1.3 77.2 + - - +
907B VAL* 1.3 62.4 + - + +
909B LEU* 3.8 5.1 - - - +
910B ASN* 2.9 51.1 + - - +
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Residues in contact with VAL 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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904B ASP* 4.3 17.5 + - - +
905B LEU 3.4 0.6 - - - -
906B THR* 1.3 81.2 - - + +
908B GLU* 1.3 58.0 + - - +
910B ASN* 3.2 7.9 + - + +
911B ARG* 3.0 42.4 + - + +
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Residues in contact with GLU 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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904B ASP 4.9 3.2 + - - +
905B LEU* 3.2 11.4 + - - +
907B VAL* 1.3 77.9 - - - +
909B LEU* 1.3 61.1 + - - +
911B ARG* 3.1 35.2 + - - +
912B TRP* 3.1 43.7 + - + -
1039B ASN* 4.8 7.8 - - - +
1043B ASN* 3.4 39.8 - - - +
1046B ASP* 5.7 1.3 - - - +
1047B TRP* 3.8 13.9 - - + -
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Residues in contact with LEU 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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862B LEU* 4.0 35.4 - - + +
865B PHE* 3.9 27.8 - - + +
866B LYS* 4.2 17.5 - - + +
869B CYS* 3.9 9.6 - - - -
905B LEU* 2.9 34.5 + - + +
906B THR* 3.8 4.7 - - - +
908B GLU* 1.3 73.4 - - - +
910B ASN* 1.3 68.7 + - - +
912B TRP* 3.1 14.5 + - - +
913B ASP* 3.1 19.7 + - - +
1047B TRP* 3.6 26.0 - - + -
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Residues in contact with ASN 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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866B LYS* 6.0 0.2 - - - -
906B THR* 2.9 37.6 + - - +
907B VAL* 3.6 8.3 - - + +
909B LEU* 1.3 78.9 - - - +
911B ARG* 1.3 61.6 + - + +
913B ASP* 3.1 25.9 + - + +
914B THR* 3.4 16.8 + - - +
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Residues in contact with ARG 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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907B VAL* 3.0 29.2 + - + +
908B GLU* 3.1 35.3 + - - +
909B LEU 3.2 0.2 - - - -
910B ASN* 1.3 78.7 - - + +
912B TRP* 1.3 58.4 + - + +
914B THR* 3.4 9.6 + - - +
915B ALA* 3.1 25.6 + - - +
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Residues in contact with TRP 912 (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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858B PHE* 3.6 27.6 - + - -
862B LEU* 3.9 28.5 - - + -
908B GLU* 3.1 45.6 + - + +
909B LEU* 3.1 11.2 + - - +
911B ARG* 1.3 77.8 - - + +
913B ASP* 1.3 57.8 + - - +
914B THR 3.3 0.2 - - - -
915B ALA* 3.5 27.1 + - + +
916B PHE* 4.0 17.3 - + - -
918B HIS* 2.8 23.5 + - - -
1036B LEU* 3.6 38.1 - - + -
1039B ASN* 3.6 25.4 - - + -
1040B PHE* 3.7 35.8 - + + +
1047B TRP* 4.5 3.1 - + - -
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Residues in contact with ASP 913 (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 LEU* 6.0 0.7 - - - +
866B LYS* 3.0 40.5 + - - -
909B LEU 3.1 13.0 + - - +
910B ASN* 3.1 21.5 + - - +
912B TRP* 1.3 81.0 - - - +
914B THR* 1.3 59.4 + - + +
916B PHE 3.4 14.2 - - - +
918B HIS* 3.5 20.9 + - + -
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Residues in contact with THR 914 (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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910B ASN 3.4 12.2 + - - +
911B ARG* 3.4 14.7 + - - +
912B TRP 3.3 0.2 - - - -
913B ASP* 1.3 80.5 - - + +
915B ALA* 1.3 63.4 + - - +
916B PHE* 3.3 4.5 + - - -
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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