Contacts of the helix formed by residues 898 - 905 (chain A) in PDB entry 3LZB
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 GLU 898 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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894A ILE* 3.9 11.7 - - + +
895A PRO* 2.9 38.2 + - + +
897A SER* 1.3 85.4 + - - +
899A ILE* 1.3 60.9 + - - +
900A SER 3.4 2.2 - - - -
901A SER* 3.3 16.3 + - - +
902A ILE* 2.8 32.2 - - + +
911C GLN* 3.4 30.7 + - - +
917C ILE* 5.8 3.3 - - + +
920C TYR* 4.4 13.0 - - - -
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Residues in contact with ILE 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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854A ILE* 3.9 21.8 - - + +
855A LYS* 4.0 11.2 - - + -
862A ILE* 4.6 2.5 - - + -
891A TYR* 3.4 51.6 - - + -
894A ILE* 4.0 12.6 - - + -
895A PRO 3.7 13.9 - - - +
896A ALA* 2.9 20.0 + - - +
898A GLU* 1.3 75.8 - - - +
900A SER* 1.3 63.8 + - - +
902A ILE* 3.5 8.1 + - + +
903A LEU* 3.1 42.7 + - + +
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Residues in contact with SER 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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854A ILE* 5.8 0.2 - - - +
859A LEU* 4.1 20.1 - - - +
862A ILE* 4.6 14.1 - - - +
863A LEU* 4.4 15.0 - - - -
896A ALA 4.5 1.6 + - - -
897A SER 4.0 10.4 + - - -
899A ILE* 1.3 75.5 - - - +
901A SER* 1.3 60.5 + - - +
903A LEU* 3.4 4.2 - - - +
904A GLU* 2.5 50.0 + - - +
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Residues in contact with SER 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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897A SER 4.4 1.6 + - - -
898A GLU* 3.3 20.7 + - - +
900A SER* 1.3 79.9 + - - +
902A ILE* 1.3 61.4 + - - +
903A LEU 3.2 1.3 - - - -
904A GLU* 3.6 9.4 - - - +
905A LYS* 2.9 30.5 + - - +
917C ILE* 3.9 27.2 - - - +
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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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891A TYR* 4.0 20.9 - - + -
894A ILE* 3.9 24.5 - - + -
898A GLU* 2.8 27.8 - - + +
899A ILE* 3.5 15.9 - - + +
901A SER* 1.3 74.3 - - - +
903A LEU* 1.3 72.6 + - + +
905A LYS* 3.6 5.8 + - - +
906A GLY 3.3 3.1 + - - -
907A GLU* 2.8 62.7 + - + +
917C ILE* 4.5 14.6 - - + -
920C TYR* 6.2 2.5 - - + -
921C MET* 4.4 9.4 - - + -
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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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857A MET 4.7 2.9 - - - +
859A LEU* 4.3 18.8 - - + -
862A ILE* 4.0 19.5 - - + -
874A TRP* 4.0 28.5 - - + +
891A TYR* 3.8 25.4 - - + +
899A ILE* 3.1 32.2 + - + +
900A SER 3.4 4.3 - - - +
902A ILE* 1.3 86.0 - - + +
904A GLU* 1.3 58.1 + - - +
906A GLY* 2.6 24.3 + - - -
907A GLU 3.7 14.1 - - - +
908A ARG* 2.8 25.5 + - - +
929A ILE* 4.6 1.4 - - - +
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Residues in contact with GLU 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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859A LEU* 3.8 18.4 - - + -
863A LEU* 3.7 26.6 - - + +
900A SER* 2.5 41.1 + - - +
901A SER* 3.5 9.3 + - - +
903A LEU* 1.3 76.7 - - - +
905A LYS* 1.3 58.2 + - - +
906A GLY* 2.9 6.8 + - - -
929A ILE* 4.9 5.3 - - + +
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Residues in contact with LYS 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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901A SER 2.9 18.2 + - - +
902A ILE 4.1 2.9 - - - +
903A LEU 3.1 0.4 - - - -
904A GLU* 1.3 75.0 - - - +
906A GLY* 1.3 59.2 + - - +
907A GLU* 3.5 3.1 + - - +
917C ILE* 4.3 12.1 - - + -
918C ASP* 6.3 0.4 - - - -
921C MET* 3.9 30.2 - - + +
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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