Contacts of the helix formed by residues 835 - 846 (chain B) in PDB entry 5FLZ
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 ASP 835 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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825B ILE* 3.3 5.5 - - - +
828B ALA* 3.0 23.8 - - + +
829B ASP* 2.8 47.4 + - - +
832B ASN* 3.6 28.6 - - - +
834B GLY* 1.4 71.7 - - - +
836B GLU* 1.3 65.0 + - - +
837B GLU* 3.7 18.0 + - - +
838B LEU* 3.3 11.1 - - - +
839B PHE* 3.1 26.5 - - - -
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Residues in contact with GLU 836 (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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835B ASP* 1.3 76.5 - - - +
837B GLU* 1.3 61.4 + - - +
838B LEU 3.3 0.2 - - - -
839B PHE* 3.0 45.2 + - - +
840B LEU* 3.1 25.3 + - + +
843B LYS* 5.6 2.1 - - - -
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Residues in contact with GLU 837 (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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825B ILE* 3.7 32.3 - - + +
835B ASP* 3.5 14.8 - - - +
836B GLU* 1.3 76.4 - - + +
838B LEU* 1.4 62.8 + - - +
840B LEU* 3.3 28.0 + - - +
841B LEU* 3.2 18.7 + - - +
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Residues in contact with LEU 838 (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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741B PHE* 4.3 12.3 - - + +
742B ALA* 5.4 5.8 - - - -
757B PRO* 4.6 19.1 - - + -
758B TYR* 5.9 0.4 - - + -
825B ILE* 3.4 17.1 - - + +
826B PHE* 4.1 23.8 - - + -
829B ASP* 3.4 30.1 - - + +
835B ASP* 3.3 18.6 + - - +
837B GLU* 1.4 71.6 - - - +
839B PHE* 1.4 76.7 + - + +
841B LEU* 3.0 13.7 + - + +
842B SER* 2.9 29.5 + - - +
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Residues in contact with PHE 839 (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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741B PHE* 3.6 34.1 - + + -
829B ASP* 3.8 10.8 - - - -
834B GLY* 3.5 25.1 - - - -
835B ASP 3.1 25.6 - - - -
836B GLU* 3.0 31.8 + - - +
838B LEU* 1.4 80.7 - - + +
840B LEU* 1.3 59.0 + - + +
842B SER* 2.8 22.3 + - - -
843B LYS* 3.1 27.6 + - - +
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Residues in contact with LEU 840 (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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836B GLU* 3.1 33.5 + - + +
837B GLU* 3.4 32.3 - - - +
838B LEU 3.2 0.2 - - - -
839B PHE* 1.3 78.2 - - - +
841B LEU* 1.3 64.5 + - - +
843B LYS* 3.4 14.6 + - + +
844B SER* 3.0 29.1 + - - +
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Residues in contact with LEU 841 (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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757B PRO* 5.6 4.7 - - + -
822B ARG* 4.4 36.1 - - + +
825B ILE* 4.6 20.4 - - + -
837B GLU* 3.2 10.9 + - - +
838B LEU* 3.0 21.0 + - + +
840B LEU* 1.3 80.8 - - - +
842B SER* 1.4 63.4 + - - +
844B SER* 3.3 8.9 + - - -
845B LEU* 3.3 38.7 + - + +
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Residues in contact with SER 842 (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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741B PHE* 3.3 14.8 - - - -
756B GLN* 4.7 0.5 - - - +
757B PRO* 4.0 20.8 - - - +
838B LEU* 2.9 14.7 + - - -
839B PHE 2.8 18.9 + - - -
841B LEU* 1.4 77.7 - - - +
843B LYS* 1.4 55.8 + - - +
845B LEU* 3.3 13.5 + - - +
846B ARG* 3.0 61.6 + - - +
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Residues in contact with LYS 843 (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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741B PHE* 4.4 15.5 - - - -
836B GLU* 5.6 2.0 - - - -
839B PHE* 3.1 36.4 + - - +
840B LEU* 3.6 15.7 - - + +
842B SER* 1.4 71.8 - - - +
844B SER* 1.4 60.4 + - - +
846B ARG* 3.2 38.9 - - - +
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Residues in contact with SER 844 (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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840B LEU* 3.0 17.3 + - - +
841B LEU* 3.6 14.6 - - - -
843B LYS* 1.4 72.8 - - - +
845B LEU* 1.4 59.5 + - - +
846B ARG 3.0 12.6 - - - +
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Residues in contact with LEU 845 (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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756B GLN* 4.0 15.9 + - + +
757B PRO* 3.9 34.1 - - + -
841B LEU* 3.3 33.2 + - + +
842B SER* 3.3 7.2 + - - +
844B SER* 1.4 72.3 - - - +
846B ARG* 1.4 67.6 - - - +
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Residues in contact with ARG 846 (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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740B LEU 3.6 9.7 + - - -
741B PHE* 2.9 53.3 + - - +
756B GLN* 3.4 41.9 + - - +
842B SER* 3.0 44.3 + - - +
843B LYS* 3.2 32.9 - - - +
844B SER 3.0 12.1 - - - +
845B LEU* 1.4 84.6 - - - +
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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