Contacts of the helix formed by residues 893 - 906 (chain A) in PDB entry 2KFZ
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 VAL 893 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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700A VAL* 3.6 26.2 - - + -
702A VAL* 4.5 8.9 - - + +
888A VAL* 4.0 8.3 - - + -
889A HIS 3.2 10.8 + - - +
890A LYS* 3.2 22.6 + - - +
891A ASP 3.7 1.0 - - - -
892A ASP* 1.3 76.4 - - - +
894A ASP* 1.3 63.2 + - - +
896A VAL* 3.9 0.7 - - - +
897A ALA* 2.9 33.6 + - + +
920A SER* 4.1 26.0 - - - +
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Residues in contact with ASP 894 (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 ASP 5.7 0.2 - - - -
892A ASP 3.1 1.4 + - - -
893A VAL* 1.3 78.4 - - - +
895A ALA* 1.3 67.0 + - - +
897A ALA* 3.2 15.1 + - - +
898A LYS* 3.2 17.4 + - - +
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Residues in contact with ALA 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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892A ASP* 3.4 8.5 + - - +
894A ASP* 1.3 78.6 - - - +
896A VAL* 1.3 64.0 + - + +
898A LYS* 3.4 10.8 + - - +
899A GLN* 3.2 21.9 + - - +
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Residues in contact with VAL 896 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A VAL* 6.1 1.3 - - + -
866A TRP* 4.1 17.7 - - + -
872A PRO* 5.0 4.9 - - + -
873A ARG 5.7 0.9 - - - +
874A VAL* 4.2 17.3 - - + -
888A VAL* 3.8 33.7 - - + -
892A ASP* 3.1 31.4 + - + +
893A VAL 4.0 0.9 - - - +
895A ALA* 1.3 75.6 - - + +
897A ALA* 1.3 61.0 + - - +
899A GLN* 3.2 7.7 + - - +
900A ILE* 2.9 42.0 + - + +
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Residues in contact with ALA 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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702A VAL* 5.5 5.2 - - + -
893A VAL* 2.9 24.6 + - + +
894A ASP* 3.2 6.0 + - - +
896A VAL* 1.3 74.6 - - - +
898A LYS* 1.3 66.0 + - - +
900A ILE* 4.1 4.4 - - - +
901A HIS* 3.1 26.5 + - - +
918A VAL* 4.2 26.2 - - + +
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Residues in contact with LYS 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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894A ASP 3.2 10.6 + - - +
895A ALA* 3.5 13.2 - - - +
896A VAL 3.3 0.2 - - - -
897A ALA* 1.3 78.7 - - - +
899A GLN* 1.3 57.9 + - - +
901A HIS* 3.5 6.1 - - - +
902A GLN* 3.0 49.8 + - - +
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Residues in contact with GLN 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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866A TRP* 3.4 49.5 - - + +
870A GLU* 5.7 1.1 - - - -
895A ALA 3.2 10.4 + - - +
896A VAL* 3.4 8.5 - - - +
897A ALA 3.1 0.4 - - - -
898A LYS* 1.3 77.7 - - - +
900A ILE* 1.3 65.2 + - - +
901A HIS 3.1 1.1 - - - -
902A GLN* 3.2 15.4 + - - +
903A LEU* 3.0 41.5 + - + +
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Residues in contact with ILE 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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702A VAL* 5.6 5.2 - - + -
704A ALA* 3.8 15.9 - - + -
863A VAL* 3.8 19.1 - - + -
866A TRP* 3.4 28.5 - - + -
874A VAL* 5.1 0.9 - - + -
886A PHE* 3.9 28.5 - - + -
888A VAL* 6.1 0.2 - - + -
896A VAL* 2.9 34.4 + - + +
897A ALA* 4.1 4.9 - - - +
899A GLN* 1.3 70.9 - - - +
901A HIS* 1.3 57.5 + - - +
903A LEU* 3.3 7.1 + - - +
904A MET* 3.0 54.9 + - + +
918A VAL* 5.1 4.5 - - + -
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Residues in contact with HIS 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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3A ZN 2.4 32.6 - - - -
897A ALA 3.1 17.8 + - - +
898A LYS* 3.5 6.5 - - - +
900A ILE* 1.3 80.8 - - - +
902A GLN* 1.3 70.2 + - + +
904A MET* 3.6 1.0 + - - +
905A GLU* 3.2 45.8 + - + +
915A LEU* 5.2 3.4 - - + -
916A VAL* 3.0 38.9 + - - +
918A VAL* 3.9 16.9 - - + +
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Residues in contact with GLN 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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898A LYS* 3.0 36.9 + - - +
899A GLN* 3.2 15.9 + - - +
901A HIS* 1.3 82.4 - - + +
903A LEU* 1.3 63.6 + - + +
906A ASN* 3.0 48.1 + - + +
907A CYS* 3.8 3.9 + - - -
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Residues in contact with LEU 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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859A ALA* 5.2 0.6 - - - -
862A ALA* 4.2 19.3 - - + +
863A VAL* 3.9 24.2 - - + -
866A TRP* 3.6 45.3 - - + -
899A GLN* 3.0 34.8 + - - +
900A ILE* 3.6 4.7 - - - +
902A GLN* 1.3 77.2 - - + +
904A MET* 1.3 57.3 + - - +
907A CYS* 3.1 52.4 + - + +
908A THR* 4.0 1.6 + - - -
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Residues in contact with MET 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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704A ALA* 3.4 46.2 - - + +
706A TYR* 2.4 54.1 + - + +
859A ALA* 4.0 14.6 - - + -
863A VAL* 4.1 10.3 - - + -
882A ASP 5.2 0.7 - - - +
884A LEU* 3.9 25.8 - - + -
900A ILE* 3.0 27.8 + - - +
901A HIS 4.2 0.9 - - - +
903A LEU* 1.3 79.4 - - - +
905A GLU* 1.3 58.4 + - - +
906A ASN 3.5 0.2 - - - -
908A THR* 3.3 13.0 + - - -
914A LEU* 4.3 0.9 - - - +
916A VAL* 3.7 17.3 - - + -
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Residues in contact with GLU 905 (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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3A ZN 2.1 34.6 - - - -
901A HIS* 3.2 28.6 + - + +
904A MET* 1.3 77.7 - - - +
906A ASN* 1.3 76.4 + - - +
908A THR 5.3 0.9 - - - -
909A ARG 5.2 3.5 - - - +
910A LEU* 5.5 1.9 - - - +
914A LEU* 4.2 35.2 - - + +
915A LEU* 3.5 9.1 - - - +
916A VAL* 2.9 37.6 + - + -
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Residues in contact with ASN 906 (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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901A HIS* 5.4 1.0 - - - -
902A GLN* 3.0 42.8 + - + +
904A MET 3.5 0.2 - - - -
905A GLU* 1.3 103.5 + - - +
907A CYS* 1.3 67.4 + - - +
908A THR 3.5 3.4 + - - +
909A ARG 5.9 0.4 - - - -
910A LEU* 3.7 26.3 - - + +
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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