Contacts of the helix formed by residues 894 - 905 (chain F) in PDB entry 2X36
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 GLY 894 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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770F TRP* 3.7 29.5 - - - -
893F GLY* 1.3 72.2 - - - -
895F ILE* 1.3 65.5 + - - +
897F GLU* 3.4 20.1 + - - +
898F LYS* 2.9 29.0 + - - +
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Residues in contact with ILE 895 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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880F THR* 5.6 0.9 - - + -
892F VAL* 3.5 23.3 - - + +
893F GLY* 4.2 2.0 - - - +
894F GLY* 1.3 73.7 - - - +
896F LYS* 1.3 57.5 + - - +
897F GLU* 4.1 0.2 + - - -
898F LYS* 2.9 8.1 + - + +
899F THR* 2.7 48.1 + - - +
912F LEU* 4.6 13.7 - - + -
916F ASN* 3.2 36.8 - - + +
919F ASP* 3.3 31.0 - - + +
920F PHE* 3.9 32.5 - - + -
923F LEU* 4.3 1.3 - - + -
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Residues in contact with LYS 896 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895F ILE* 1.3 76.9 - - - +
897F GLU* 1.3 79.8 + - + +
899F THR* 2.9 13.3 + - - -
900F ILE* 2.9 40.1 + - + +
923F LEU* 3.0 38.6 - - + +
927F ILE* 4.7 10.5 - - + -
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Residues in contact with GLU 897 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770F TRP* 4.2 15.1 + - + +
774F GLY* 3.9 38.6 - - - +
775F GLY* 4.1 6.3 + - - +
894F GLY* 3.4 24.3 - - - +
895F ILE 4.1 0.2 + - - -
896F LYS* 1.3 89.3 - - + +
898F LYS* 1.3 57.8 + - + +
900F ILE* 3.6 8.4 - - + +
901F ALA* 3.0 29.6 + - - +
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Residues in contact with LYS 898 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768F LEU* 3.4 49.1 - - + +
769F ALA 4.0 11.9 - - - +
770F TRP* 3.5 18.4 - - + +
852F ASP* 3.0 25.2 + - - -
855F SER* 3.8 1.2 + - - -
880F THR* 3.3 20.5 + - + +
892F VAL* 3.1 21.8 - - + +
893F GLY 2.6 28.0 + - - +
894F GLY 2.9 15.3 + - - +
895F ILE* 3.5 6.5 - - + +
897F GLU* 1.3 77.4 - - - +
899F THR* 1.3 62.6 + - - +
901F ALA* 3.5 3.8 + - - -
902F ALA* 3.1 20.6 + - - +
910F ILE* 5.4 0.7 - - + -
912F LEU* 5.8 3.8 - - + -
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Residues in contact with THR 899 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895F ILE* 2.7 26.0 + - - +
896F LYS 3.6 3.8 - - - -
898F LYS* 1.3 73.2 - - - +
900F ILE* 1.3 59.8 + - - +
902F ALA* 3.4 7.6 - - - +
903F LYS* 3.3 22.1 + - - +
910F ILE* 4.3 7.9 - - + +
912F LEU* 4.9 1.9 - - - +
920F PHE* 3.4 40.7 - - + -
923F LEU* 3.8 9.9 - - + -
927F ILE* 3.9 19.5 - - + -
928F THR* 5.0 0.4 - - - +
931F LEU* 3.4 19.3 - - + -
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Residues in contact with ILE 900 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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896F LYS* 2.9 46.3 + - + +
897F GLU* 3.6 7.9 - - + +
899F THR* 1.3 75.1 - - - +
901F ALA* 1.3 61.2 + - - +
903F LYS* 3.1 10.1 + - + +
904F ARG* 2.9 36.8 + - - +
927F ILE* 4.2 24.0 - - + -
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Residues in contact with ALA 901 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768F LEU* 4.7 1.3 - - + -
775F GLY 3.7 7.9 - - - +
776F SER* 3.6 31.2 - - - +
777F THR* 3.0 26.6 + - - +
897F GLU 3.0 15.5 + - - +
898F LYS* 3.5 5.1 + - - +
900F ILE* 1.3 73.6 - - - +
902F ALA* 1.3 67.5 + - - +
904F ARG* 3.2 13.9 - - - +
905F ALA* 3.2 14.7 + - - +
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Residues in contact with ALA 902 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768F LEU* 3.9 14.1 - - + +
777F THR* 4.5 0.7 - - - -
898F LYS 3.1 14.2 + - - +
899F THR* 3.4 13.7 - - - +
901F ALA* 1.3 75.3 - - - +
903F LYS* 1.3 63.2 + - + +
905F ALA 3.1 8.5 + - - -
907F VAL* 2.5 50.4 + - + +
910F ILE* 4.6 13.5 - - + -
931F LEU* 5.3 4.7 - - + -
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Residues in contact with LYS 903 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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899F THR 3.3 12.9 + - - +
900F ILE* 3.1 11.3 + - + +
902F ALA* 1.3 78.3 - - - +
904F ARG* 1.3 63.3 + - - +
906F GLY* 3.0 13.8 + - - +
907F VAL 4.8 5.6 - - - +
926F PHE* 3.8 7.3 + - - -
927F ILE* 2.8 37.8 + - + +
929F GLU 3.7 16.4 + - - -
930F GLY 5.3 0.9 - - - -
931F LEU* 3.5 32.1 - - + +
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Residues in contact with ARG 904 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777F THR* 5.3 0.7 - - - +
900F ILE* 2.9 22.3 + - - +
901F ALA* 3.2 17.3 - - - +
903F LYS* 1.3 76.7 - - - +
905F ALA* 1.3 56.5 + - + +
906F GLY 3.3 3.3 + - - -
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Residues in contact with ALA 905 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766F MET* 3.8 28.6 - - + +
777F THR* 4.1 10.5 - - + +
901F ALA 3.2 7.4 + - - +
902F ALA 3.1 8.2 + - - +
904F ARG* 1.3 78.6 - - + +
906F GLY* 1.3 64.0 + - - +
907F VAL* 3.2 5.2 + - + +
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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