Contacts of the helix formed by residues 894 - 904 (chain B) in PDB entry 4OL0
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 GLN 894 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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889B THR 5.2 0.5 - - - +
890B VAL* 3.8 4.3 - - + +
891B THR* 3.4 42.2 + - + +
892B HIS 3.0 2.2 - - - -
893B LYS* 1.3 79.7 - - - +
895B LEU* 1.3 62.2 + - - +
896B THR 3.4 0.4 - - - -
897B ASP* 4.4 3.5 - - - +
898B PHE* 3.1 28.9 + - - +
918B PHE* 3.7 7.8 - - - -
921B LEU* 3.2 45.5 - - + +
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Residues in contact with LEU 895 (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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876B LEU* 3.9 24.3 - - + +
879B LEU* 4.8 0.2 - - + -
881B LYS* 3.7 37.0 - - + -
890B VAL* 4.2 11.7 - - + +
891B THR 3.5 18.1 + - - +
892B HIS* 4.7 15.5 - - + +
894B GLN* 1.3 76.4 - - - +
896B THR* 1.3 60.7 + - - +
898B PHE* 3.3 2.5 + - - +
899B HIS* 2.8 32.1 + - - +
918B PHE* 3.7 31.4 - - + -
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Residues in contact with THR 896 (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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892B HIS* 2.9 37.1 + - + +
893B LYS* 4.0 12.1 - - + +
894B GLN 3.4 1.0 - - - +
895B LEU* 1.3 78.5 - - - +
897B ASP* 1.3 60.8 + - - +
899B HIS* 3.3 6.1 + - - +
900B LYS* 2.8 56.3 + - + +
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Residues in contact with ASP 897 (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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893B LYS* 2.8 33.1 - - - +
894B GLN* 4.0 4.5 - - - +
895B LEU 3.4 0.4 - - - -
896B THR* 1.3 84.0 - - - +
898B PHE* 1.3 57.9 + - - +
900B LYS* 3.9 8.3 - - - +
901B GLN* 2.8 49.9 + - + +
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Residues in contact with PHE 898 (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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838B LEU* 3.8 21.1 - - + -
857B LEU* 5.9 1.8 - - + -
872B LEU* 3.8 24.5 - - + -
876B LEU* 3.7 34.8 - - + -
894B GLN 3.1 21.8 + - - +
895B LEU 3.5 2.7 - - - +
896B THR 3.2 0.2 - - - -
897B ASP* 1.3 74.3 - - - +
899B HIS* 1.3 62.5 + - - +
901B GLN* 3.2 7.4 + - - +
902B VAL* 2.9 58.7 + - + +
914B ALA 3.9 9.6 - - - -
915B LEU* 3.9 23.6 - - + -
918B PHE* 3.5 33.9 - + + -
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Residues in contact with HIS 899 (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* 2.8 34.6 + - + -
872B LEU* 3.5 33.0 - - + -
873B GLU* 3.5 32.7 + - + +
876B LEU* 3.7 11.2 - - + -
895B LEU 2.8 19.8 + - - +
896B THR* 3.7 5.8 - - + +
898B PHE* 1.3 74.0 - - - +
900B LYS* 1.3 54.6 + - - +
902B VAL* 3.9 0.2 - - - +
903B THR* 2.6 60.1 + - + +
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Residues in contact with LYS 900 (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 THR* 2.8 40.4 + - + +
897B ASP* 3.9 9.0 - - - +
899B HIS* 1.3 74.8 + - - +
901B GLN* 1.3 59.2 + - + +
903B THR* 3.6 5.4 - - - +
904B SER* 2.5 42.6 + - - +
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Residues in contact with GLN 901 (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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897B ASP* 2.8 40.6 + - - +
898B PHE* 3.6 5.1 + - - +
900B LYS* 1.3 73.0 - - - +
902B VAL* 1.3 65.1 + - - +
904B SER* 3.6 5.7 + - - -
905B ALA* 3.3 19.2 + - - +
910B GLN* 4.6 8.4 + - - +
913B TRP* 5.6 1.0 - - - +
914B ALA* 3.4 35.5 - - + +
917B ASP* 4.0 16.6 + - - +
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Residues in contact with VAL 902 (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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857B LEU* 5.3 3.4 - - + -
861B MET* 3.4 28.6 - - + +
868B PHE* 3.8 18.8 - - + -
872B LEU* 3.9 9.4 - - + -
898B PHE* 2.9 48.6 + - + +
899B HIS 3.9 2.2 - - - +
901B GLN* 1.3 76.3 - - - +
903B THR* 1.3 64.2 + - - +
905B ALA* 3.1 22.3 + - - +
911B VAL* 4.2 19.5 - - + +
914B ALA* 3.7 15.0 - - + -
915B LEU* 5.4 0.9 - - + -
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Residues in contact with THR 903 (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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861B MET* 4.1 7.0 - - - -
865B ARG* 2.9 29.3 + - - -
868B PHE* 4.3 5.6 - - + -
869B CYS* 3.6 36.1 - - - -
872B LEU* 3.9 12.8 - - + -
899B HIS* 2.6 53.0 + - + +
900B LYS* 3.4 8.0 + - - +
902B VAL* 1.3 71.0 - - - +
904B SER* 1.3 59.9 + - - +
905B ALA 3.3 0.4 - - - -
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Residues in contact with SER 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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865B ARG* 4.3 1.1 - - - +
900B LYS* 2.5 29.7 + - - +
901B GLN* 3.6 5.5 + - - -
903B THR* 1.3 76.9 - - - +
905B ALA* 1.3 64.2 + - - +
906B GLU* 3.7 14.1 + - - +
910B GLN* 4.4 3.3 + - - +
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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