Contacts of the helix formed by residues 888 - 896 (chain A) in PDB entry 4EZJ
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 ILE 888 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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887A THR* 1.4 68.6 - - - +
889A ALA* 1.3 57.7 + - - +
891A ILE* 2.8 28.9 + - + +
892A GLN* 3.2 13.3 + - - +
907A LEU* 4.2 13.5 - - + -
949A ASN* 3.2 30.7 + - + +
952A ILE* 2.7 38.2 + - + +
953A MET 4.7 0.2 - - - -
954A ILE* 3.7 34.5 - - + -
960A LEU* 4.1 4.5 - - + -
988A THR* 5.8 0.4 - - - +
990A ASP* 3.6 23.1 - - - +
991A PHE* 3.9 24.5 - - + -
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Residues in contact with ALA 889 (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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888A ILE* 1.3 75.0 - - - +
890A LYS* 1.4 56.6 + - - +
892A GLN* 2.9 23.4 + - - +
893A GLN* 2.9 25.4 + - - +
902A PHE* 6.4 0.2 - - - -
948A HIS* 4.6 3.6 - - + +
949A ASN* 3.2 29.1 + - - +
950A ASP* 3.4 35.4 - - + +
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Residues in contact with LYS 890 (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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886A THR* 3.4 30.3 - - - +
887A THR* 3.3 19.6 + - - +
888A ILE 3.2 1.0 - - - -
889A ALA* 1.4 77.0 - - - +
891A ILE* 1.4 51.7 + - - +
893A GLN* 3.4 28.0 + - + +
894A SER* 2.6 46.9 + - - +
950A ASP* 4.5 0.6 + - - +
1201A 0SC 4.5 21.8 - - + -
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Residues in contact with ILE 891 (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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886A THR* 3.8 15.0 - - + -
887A THR 3.5 13.4 + - - +
888A ILE* 2.8 14.4 + - + +
890A LYS* 1.4 74.6 - - - +
892A GLN* 1.4 64.0 + - - +
894A SER* 3.4 20.4 - - - +
895A THR* 3.9 4.3 + - - -
906A VAL* 3.8 39.2 - - + +
907A LEU* 3.9 14.8 - - + +
910A TRP* 3.7 36.3 - - + -
954A ILE* 3.6 32.1 - - + -
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Residues in contact with GLN 892 (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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888A ILE* 3.2 15.1 + - - +
889A ALA* 2.9 13.5 + - - +
891A ILE* 1.4 81.8 - - - +
893A GLN* 1.4 56.4 + - - +
894A SER 3.3 0.4 + - - -
895A THR* 4.3 0.7 - - - -
896A VAL* 3.1 37.5 + - + +
897A GLY 4.9 0.9 - - - -
899A THR 5.2 3.1 - - - +
902A PHE* 3.7 29.4 - - + +
903A LYS 3.4 28.6 + - - +
906A VAL* 3.4 25.6 - - - +
907A LEU* 5.1 0.8 - - - +
949A ASN* 4.6 9.0 - - - +
990A ASP* 3.2 26.9 + - - +
1080A TRP* 3.9 9.0 - - - -
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Residues in contact with GLN 893 (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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889A ALA* 2.9 26.4 + - - +
890A LYS* 3.5 36.4 + - + +
892A GLN* 1.4 71.3 - - - +
894A SER* 1.4 55.4 + - - +
896A VAL 2.1 29.1 - - - +
897A GLY* 3.3 25.8 + - - +
898A ASN* 6.3 0.4 - - - -
950A ASP* 5.2 3.4 + - - +
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Residues in contact with SER 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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890A LYS* 2.6 33.5 + - - +
891A ILE* 3.4 16.0 - - - +
892A GLN 3.3 0.6 - - - -
893A GLN* 1.4 78.5 - - - +
895A THR* 1.3 63.0 + - - +
910A TRP* 5.4 8.0 + - - -
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Residues in contact with THR 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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891A ILE 3.9 2.2 + - - -
892A GLN 3.7 2.3 + - - -
894A SER* 1.3 78.9 - - - +
896A VAL* 1.3 67.4 + - + +
903A LYS* 5.2 7.0 - - + +
906A VAL* 3.4 36.4 - - + +
909A HIS* 5.2 5.8 + - - +
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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
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892A GLN* 3.1 20.9 + - + +
893A GLN* 2.1 38.2 - - - +
894A SER 3.7 0.2 - - - -
895A THR* 1.3 82.3 - - + +
897A GLY* 1.3 60.9 + - - +
899A THR* 3.0 30.3 - - + +
901A ALA* 3.7 15.9 - - + +
902A PHE* 5.6 0.7 - - - -
903A LYS* 3.7 37.5 - - + +
906A VAL* 5.5 0.9 - - + -
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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