Contacts of the helix formed by residues 895 - 904 (chain A) in PDB entry 4XUF
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 895 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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892A ILE* 5.1 2.6 - - - +
893A PRO* 3.4 22.5 + - + +
894A VAL* 1.3 76.7 - - - +
896A ALA* 1.3 65.4 + - + +
897A ASN* 3.6 25.4 + - - +
898A PHE* 3.1 24.1 + - - +
899A TYR* 3.0 23.8 - - - -
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Residues in contact with ALA 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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895A ASP* 1.3 77.1 - - - +
897A ASN* 1.3 67.1 + - - +
899A TYR* 3.8 17.0 + - - +
900A LYS* 3.3 22.9 + - + +
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Residues in contact with ASN 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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892A ILE* 6.0 2.9 - - + -
895A ASP* 3.2 18.5 + - - +
896A ALA* 1.3 82.5 - - - +
898A PHE* 1.3 64.8 + - - +
900A LYS* 3.0 37.1 + - - +
901A LEU* 3.0 25.2 - - + +
897B ASN* 4.6 15.6 - - - +
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Residues in contact with PHE 898 (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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852A VAL* 3.6 32.1 - - + -
853A LYS* 3.7 26.7 - - + -
860A LEU* 5.8 1.3 - - + -
889A TYR* 3.8 37.7 - + + -
892A ILE* 4.5 15.3 - - + -
893A PRO 3.6 15.3 - - - +
894A VAL* 4.2 7.4 - - + -
895A ASP* 3.1 30.4 + - - +
897A ASN* 1.3 75.6 - - - +
899A TYR* 1.3 70.4 + + - +
901A LEU* 3.2 20.1 + - + +
902A ILE* 3.1 44.1 + - + +
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Residues in contact with TYR 899 (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 VAL* 4.5 5.2 - - - +
845A ARG* 3.8 52.9 - - + +
852A VAL* 3.7 23.9 - - + +
860A LEU* 4.8 9.0 - - + -
861A PHE* 3.4 31.0 - + + -
894A VAL* 3.4 22.4 - - + +
895A ASP* 3.0 32.3 + - - -
896A ALA* 4.2 9.6 - - - +
897A ASN 3.3 0.6 - - - -
898A PHE* 1.3 82.2 - + - +
900A LYS* 1.3 62.6 + - + +
902A ILE* 3.6 5.7 + - - +
903A GLN* 3.3 21.5 + - - +
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Residues in contact with LYS 900 (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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896A ALA* 3.3 21.5 + - + +
897A ASN* 3.0 29.3 + - - +
899A TYR* 1.3 78.3 - - + +
901A LEU* 1.3 66.1 + - + +
903A GLN* 3.4 16.7 + - - +
904A ASN* 3.0 34.9 + - - +
892B ILE* 6.5 1.1 - - - -
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Residues in contact with LEU 901 (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 ILE* 3.6 30.3 - - + -
897A ASN* 3.0 33.0 - - + +
898A PHE* 3.2 14.0 + - + +
900A LYS* 1.3 78.0 - - + +
902A ILE* 1.3 61.9 + - + +
904A ASN* 2.9 24.6 + - - +
906A PHE* 2.9 58.2 + - + +
901B LEU* 4.8 24.0 - - + -
904B ASN* 5.5 1.3 - - - +
906B PHE* 5.1 6.7 - - + -
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Residues in contact with ILE 902 (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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857A PRO* 3.6 28.3 - - + -
860A LEU* 3.9 24.2 - - + -
861A PHE* 5.6 1.8 - - + -
872A TRP* 4.1 17.6 - - + -
889A TYR* 4.4 18.8 - - + +
898A PHE* 3.1 61.2 - - + +
899A TYR* 3.6 6.2 + - - +
900A LYS 3.4 0.4 - - - -
901A LEU* 1.3 79.5 - - + +
903A GLN* 1.3 61.2 + - - +
905A GLY* 3.0 12.6 + - - -
906A PHE* 4.4 10.3 - - + +
928A PHE* 3.2 11.8 - - - -
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Residues in contact with GLN 903 (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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861A PHE* 4.7 22.1 - - + -
899A TYR 3.3 11.2 + - - +
900A LYS* 3.6 22.6 - - - +
901A LEU 3.2 0.4 - - - -
902A ILE* 1.3 79.9 - - - +
904A ASN* 1.3 61.6 + - - +
905A GLY 3.2 2.0 + - - -
928A PHE* 3.4 25.0 - - + -
909B ASP* 3.2 14.0 - - - +
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Residues in contact with ASN 904 (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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900A LYS* 3.0 25.0 + - - +
901A LEU* 2.9 12.9 + - - +
903A GLN* 1.3 80.6 - - - +
905A GLY* 1.3 61.0 + - - +
906A PHE 3.3 0.8 + - - -
892B ILE* 5.0 9.5 - - - +
906B PHE* 3.9 29.8 - - + -
907B LYS 4.1 7.0 - - - +
908B MET 4.4 0.5 - - - -
909B ASP* 3.7 38.1 + - + +
919B TYR* 4.8 1.9 + - - -
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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