Contacts of the helix formed by residues 882 - 897 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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879A TYR 5.0 0.4 - - - -
880A ASN* 3.0 1.8 - - - +
881A PHE* 1.3 80.9 - - - +
883A ASP* 1.3 57.7 + - - +
884A LEU 3.5 1.6 - - - -
885A LEU* 3.8 21.1 - - - +
886A ARG* 2.9 26.2 + - - +
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Residues in contact with ASP 883 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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879A TYR* 2.9 27.0 - - + +
880A ASN 2.9 11.4 + - - +
881A PHE 3.5 0.8 - - - +
882A SER* 1.3 76.0 - - - +
884A LEU* 1.3 59.5 + - - +
886A ARG* 3.4 6.3 + - - +
887A LEU* 3.0 26.2 + - - +
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Residues in contact with LEU 884 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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878A PHE* 3.5 16.4 - - + +
879A TYR* 2.6 46.0 + - - +
883A ASP* 1.3 71.8 - - - +
885A LEU* 1.3 57.4 + - - +
887A LEU* 3.2 10.7 + - - +
888A THR* 2.9 25.2 + - - -
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Residues in contact with LEU 885 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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879A TYR 4.3 0.2 + - - -
882A SER* 3.8 22.2 + - - +
883A ASP 3.3 0.4 - - - -
884A LEU* 1.3 78.8 - - - +
886A ARG* 1.3 57.0 + - - +
888A THR* 2.9 12.7 - - - -
889A LYS* 2.8 24.4 + - - +
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Residues in contact with ARG 886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882A SER 2.9 20.5 + - - +
883A ASP* 3.6 8.5 - - - +
884A LEU 3.2 0.2 - - - -
885A LEU* 1.3 72.9 - - - +
887A LEU* 1.3 55.9 + - - +
888A THR 2.7 13.7 + - - -
889A LYS* 2.8 20.5 + - - +
890A ILE* 3.0 12.3 + - - +
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Residues in contact with LEU 887 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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883A ASP 3.0 13.7 + - - +
884A LEU* 3.2 13.2 + - - +
886A ARG* 1.3 73.5 - - - +
888A THR* 1.3 54.8 + - - +
890A ILE* 4.0 6.6 - - - +
891A LEU* 3.0 26.8 + - - +
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Residues in contact with THR 888 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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884A LEU 2.9 8.6 + - - -
885A LEU* 2.9 22.4 - - - -
886A ARG 2.7 1.4 - - - -
887A LEU* 1.3 75.8 - - - +
889A LYS* 1.3 58.6 + - - -
890A ILE 3.2 1.1 - - - -
891A LEU* 3.5 7.8 - - - +
892A LEU* 2.8 29.3 + - - +
984A VAL* 5.9 6.7 - - - -
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Residues in contact with LYS 889 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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885A LEU 2.8 10.9 + - - +
886A ARG* 2.8 14.5 + - - +
888A THR* 1.3 71.9 - - - +
890A ILE* 1.3 61.8 + - - +
892A LEU* 3.3 20.6 - - - +
893A ALA* 3.7 5.2 + - - +
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Residues in contact with ILE 890 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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886A ARG 3.0 12.0 + - - +
887A LEU* 4.1 7.4 - - - +
889A LYS* 1.3 74.0 - - - +
891A LEU* 1.3 59.7 + - - +
892A LEU 3.0 2.0 - - - -
893A ALA* 2.9 24.7 + - - +
894A ILE* 3.1 11.2 + - - +
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Residues in contact with LEU 891 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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887A LEU 3.0 22.6 + - - +
888A THR* 3.1 8.9 + - - +
890A ILE* 1.3 74.4 - - - +
892A LEU* 1.3 56.8 + - - +
893A ALA 3.2 0.2 - - - -
894A ILE* 3.7 9.8 - - + +
895A LEU* 2.9 32.1 + - - +
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Residues in contact with LEU 892 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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888A THR 2.8 11.7 + - - +
889A LYS* 3.3 16.8 - - - +
890A ILE 3.0 0.4 - - - -
891A LEU* 1.3 77.7 - - - +
893A ALA* 1.3 57.0 + - - +
895A LEU* 3.8 4.7 - - - +
896A ASP* 2.9 27.0 + - - +
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Residues in contact with ALA 893 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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889A LYS 3.7 4.1 + - - +
890A ILE* 2.9 12.3 + - - +
892A LEU* 1.3 79.6 - - - +
894A ILE* 1.3 60.2 + - - +
896A ASP* 3.5 9.7 - - + +
897A CYS* 2.8 30.5 + - - +
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Residues in contact with ILE 894 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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840A VAL* 5.3 18.8 - - + +
841A GLU* 6.5 0.2 - - - -
844A LEU* 5.2 7.0 - - + -
890A ILE 3.1 12.0 + - - +
891A LEU* 3.4 11.0 + - + +
893A ALA* 1.3 76.6 - - - +
895A LEU* 1.4 55.6 + - - +
897A CYS* 2.8 38.4 + - - +
898A VAL* 3.3 5.5 + - - +
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Residues in contact with LEU 895 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891A LEU 2.9 19.6 + - - +
892A LEU* 4.0 5.6 - - - +
894A ILE* 1.4 75.0 - - - +
896A ASP* 1.3 59.8 - - - +
897A CYS 3.3 0.2 - - - -
898A VAL* 4.3 13.4 + - - +
977A ILE* 6.3 3.1 - - + -
981A ILE* 6.4 2.5 - - + -
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Residues in contact with ASP 896 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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892A LEU 2.9 21.1 + - - +
893A ALA* 3.6 11.7 - - - +
894A ILE 3.1 0.2 - - - -
895A LEU* 1.3 78.5 - - - +
897A CYS* 1.4 55.6 + - + +
898A VAL 3.8 1.7 + - - -
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Residues in contact with CYS 897 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843A TYR 5.3 0.3 - - - -
844A LEU* 4.1 19.5 - - + +
847A VAL* 3.5 23.4 - - + +
893A ALA 2.8 15.3 + - - +
894A ILE* 2.8 13.5 + - - +
896A ASP* 1.4 76.0 - - - +
898A VAL* 1.3 57.9 + - - +
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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