Contacts of the helix formed by residues 882 - 893 (chain B) in PDB entry 5XA0
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 SER 882 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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879B TYR 4.4 0.2 - - - -
880B ASN 3.2 2.2 + - - -
881B PHE* 1.3 86.0 - - - +
883B ASP* 1.3 60.6 + - - +
884B LEU 3.4 1.6 - - - -
885B LEU* 3.6 13.2 - - - -
886B ARG* 2.6 38.9 + - - +
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Residues in contact with ASP 883 (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 SER 5.2 5.4 - - - +
879B TYR* 3.3 20.2 + - + +
881B PHE* 5.3 0.2 - - - +
882B SER* 1.3 75.9 - - - +
884B LEU* 1.3 63.7 + - - +
886B ARG* 4.0 3.5 - - - +
887B LEU* 2.9 25.5 + - - +
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Residues in contact with LEU 884 (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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878B PHE* 3.5 18.4 - - + +
879B TYR 2.6 44.7 + - - +
880B ASN* 5.0 0.4 - - - -
883B ASP* 1.3 76.1 - - - +
885B LEU* 1.3 55.1 + - - +
887B LEU* 3.2 10.2 - - - +
888B THR* 2.9 25.2 + - - -
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Residues in contact with LEU 885 (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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879B TYR 3.4 2.8 + - - -
880B ASN 4.2 10.5 - - - +
881B PHE 4.7 1.6 - - - +
882B SER* 3.4 18.3 + - - -
883B ASP 3.2 0.6 - - - -
884B LEU* 1.3 77.7 - - - +
886B ARG* 1.3 53.8 + - - +
888B THR* 2.4 37.8 + - - -
889B LYS* 2.9 5.7 + - - +
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Residues in contact with ARG 886 (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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882B SER* 2.6 26.5 + - - +
883B ASP* 4.0 3.1 - - - +
885B LEU* 1.3 67.6 - - - +
887B LEU* 1.3 63.3 + - - +
888B THR 2.9 4.5 + - - -
889B LYS* 3.2 10.4 + - - +
890B ILE* 3.1 20.4 + - - +
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Residues in contact with LEU 887 (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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883B ASP 2.9 20.2 + - - +
884B LEU* 3.2 11.9 - - - +
886B ARG* 1.3 76.4 - - - +
888B THR* 1.3 49.2 + - - +
890B ILE* 3.4 9.6 - - - +
891B LEU* 2.7 33.0 + - - +
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Residues in contact with THR 888 (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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884B LEU 2.9 12.0 + - - -
885B LEU* 2.4 35.8 + - - -
887B LEU* 1.3 67.3 - - - +
889B LYS* 1.3 57.7 + - - -
891B LEU* 3.6 8.7 - - - +
892B LEU* 3.0 26.5 + - - +
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Residues in contact with LYS 889 (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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885B LEU 2.9 7.9 + - - +
886B ARG* 3.2 9.2 + - - +
888B THR* 1.3 73.6 - - - +
890B ILE* 1.3 63.9 + - - +
892B LEU* 3.3 8.6 + - - +
893B ALA* 3.1 21.1 + - - +
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Residues in contact with ILE 890 (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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837B MET* 5.8 10.1 - - + +
841B GLU* 6.4 1.8 - - + -
886B ARG 3.1 11.9 + - - +
887B LEU* 3.4 13.5 - - - +
889B LYS* 1.3 75.7 - - - +
891B LEU* 1.3 57.8 + - - +
893B ALA* 3.3 8.9 + - - +
894B ILE* 2.9 24.7 + - - +
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Residues in contact with LEU 891 (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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887B LEU 2.7 19.0 + - - +
888B THR* 3.7 11.2 - - - +
889B LYS 3.1 0.4 - - - -
890B ILE* 1.3 72.1 - - - +
892B LEU* 1.3 60.0 + - - +
894B ILE* 2.7 34.8 + - + +
895B LEU* 3.9 2.9 + - - +
984B VAL* 5.8 9.0 - - + -
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Residues in contact with LEU 892 (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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888B THR 3.0 13.4 + - - +
889B LYS* 3.5 11.4 - - - +
891B LEU* 1.3 77.9 - - - +
893B ALA* 1.3 57.0 + - - +
894B ILE 3.4 1.4 + - - -
895B LEU 4.3 1.2 + - - -
896B ASP* 4.2 12.1 + - - +
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Residues in contact with ALA 893 (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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844B LEU* 3.9 16.6 - - - +
889B LYS 3.1 13.8 + - - +
890B ILE* 3.3 9.6 - - - +
891B LEU 3.1 0.2 - - - -
892B LEU* 1.3 74.0 - - - +
894B ILE* 1.3 62.8 + - - +
895B LEU 3.6 0.2 - - - -
896B ASP* 4.1 18.3 + - + +
897B CYS 4.8 0.7 + - - -
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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