Contacts of the helix formed by residues 895 - 904 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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892B ILE* 5.0 1.9 - - - +
893B PRO* 3.2 25.4 + - + +
894B VAL* 1.3 76.5 - - - +
896B ALA* 1.3 65.2 + - - +
897B ASN* 3.6 24.2 + - - +
898B PHE* 3.1 25.4 + - - +
899B TYR* 3.0 25.0 + - - -
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Residues in contact with ALA 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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895B ASP* 1.3 77.7 + - - +
897B ASN* 1.3 67.1 + - - +
899B TYR* 3.8 10.4 + - - +
900B LYS* 3.5 19.4 + - - +
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Residues in contact with ASN 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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897A ASN* 4.6 15.0 - - - +
892B ILE* 6.5 0.7 - - + -
895B ASP* 3.2 18.3 + - - +
896B ALA* 1.3 82.0 - - - +
898B PHE* 1.3 65.0 + - - +
900B LYS* 3.1 9.4 + - - +
901B LEU* 3.0 35.4 + - + +
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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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852B VAL* 4.7 13.2 - - + -
853B LYS* 3.7 29.8 - - + -
860B LEU* 4.6 12.1 - - + -
889B TYR* 3.6 44.2 - + + -
892B ILE* 3.9 15.2 - - + +
893B PRO 3.4 28.0 - - - +
894B VAL* 4.1 11.2 - - + -
895B ASP* 3.1 17.4 + - - +
897B ASN* 1.3 75.7 - - - +
899B TYR* 1.3 74.8 + + - +
901B LEU* 3.3 21.1 + - + +
902B ILE* 3.3 30.0 + - + +
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Residues in contact with TYR 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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843B VAL* 4.8 1.7 - - - +
844B VAL 5.1 1.6 + - - -
845B ARG* 3.4 37.6 + - - -
852B VAL* 3.9 13.3 - - + +
860B LEU* 3.7 24.0 - - + -
861B PHE* 3.2 38.7 - + + -
894B VAL* 3.3 28.1 - - + +
895B ASP* 3.0 29.8 + - - -
896B ALA* 4.1 9.0 - - - +
897B ASN 3.3 0.2 - - - -
898B PHE* 1.3 81.8 - + - +
900B LYS* 1.3 60.8 + - - +
902B ILE* 3.5 6.6 + - - +
903B GLN* 3.3 21.4 + - - +
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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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891A GLY* 5.3 9.3 + - - -
896B ALA 3.5 11.6 + - - +
897B ASN* 3.1 12.0 + - - +
899B TYR* 1.3 77.4 - - - +
901B LEU* 1.3 67.3 + - + +
903B GLN* 3.4 17.2 + - + +
904B ASN* 3.1 22.2 + - + +
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Residues in contact with LEU 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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892A ILE* 5.9 2.7 - - + -
901A LEU* 4.8 28.5 - - + -
906A PHE* 6.3 0.7 - - + -
892B ILE* 4.2 28.9 - - + -
897B ASN* 3.0 24.9 + - + +
898B PHE* 3.5 16.2 - - + +
899B TYR 3.3 0.4 - - - -
900B LYS* 1.3 76.0 - - + +
902B ILE* 1.3 64.7 + - + +
904B ASN* 3.0 18.8 + - + +
906B PHE* 3.1 50.0 + - + +
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Residues in contact with ILE 902 (chain B).
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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855B MET 5.7 1.1 - - - +
857B PRO* 3.7 36.1 - - + +
860B LEU* 4.7 15.7 - - + -
861B PHE* 6.0 2.0 - - + -
872B TRP* 4.5 12.4 - - + -
889B TYR* 3.5 34.8 - - + +
898B PHE* 3.3 31.9 + - + +
899B TYR* 3.8 7.9 - - - +
900B LYS 3.3 0.2 - - - -
901B LEU* 1.3 75.4 - - + +
903B GLN* 1.3 60.9 + - - +
905B GLY* 3.2 12.8 + - - -
906B PHE* 4.2 16.3 - - + +
928B PHE* 3.6 11.8 - - - -
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Residues in contact with GLN 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 PHE* 5.8 7.2 - - + -
899B TYR 3.3 10.5 + - - +
900B LYS* 3.5 21.7 - - - +
902B ILE* 1.3 80.3 - - - +
904B ASN* 1.3 57.4 + - - +
905B GLY 3.1 3.2 + - - -
928B PHE* 3.9 23.3 - - + -
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Residues in contact with ASN 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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889A TYR* 5.8 1.0 - - - +
892A ILE* 5.4 15.6 - - - +
901A LEU* 5.5 1.6 - - - +
906A PHE* 3.2 37.3 - - + -
907A LYS 4.4 3.5 - - - +
908A MET* 5.9 0.2 - - - -
909A ASP* 4.1 28.7 + - - +
900B LYS* 3.1 12.8 + - + +
901B LEU* 3.0 17.3 + - + +
903B GLN* 1.3 75.6 - - - +
905B GLY* 1.3 62.0 + - - +
906B PHE 3.3 0.8 + - - -
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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