Contacts of the helix formed by residues 892 - 901 (chain A) in PDB entry 2EYQ
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 892 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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891A PHE* 1.3 73.9 - - - +
893A LEU* 1.3 68.7 + - - -
894A ALA* 2.9 5.4 - - - -
895A GLN* 2.5 32.8 + - - -
896A LEU* 2.9 10.6 + - - -
929A ARG* 3.6 10.8 - - - -
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Residues in contact with LEU 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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537A GLU* 6.1 4.7 - - + -
538A GLU* 6.0 6.3 - - + +
892A GLY* 1.3 69.2 - - - -
894A ALA* 1.3 69.8 + - - +
896A LEU* 4.2 7.9 - - - -
897A HIS* 3.0 41.6 + - + +
929A ARG* 3.6 41.2 - - + +
932A ALA* 4.9 6.1 - - + -
933A ILE* 3.7 21.1 - - + -
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Residues in contact with ALA 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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892A GLY* 4.2 2.0 - - - -
893A LEU* 1.3 81.6 - - - +
895A GLN* 1.3 74.1 + - + +
897A HIS* 3.8 4.1 - - - +
898A GLN* 3.3 16.2 + - - +
946A ALA* 4.8 8.3 - - - +
950A LEU* 4.9 13.1 - - + +
953A ARG* 4.0 33.2 - - - +
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Residues in contact with GLN 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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870A ILE* 3.1 30.4 - - + +
890A HIS 5.4 0.8 + - - -
891A PHE* 3.7 20.1 - - + +
892A GLY* 2.5 45.7 + - - +
894A ALA* 1.3 81.3 - - + +
896A LEU* 1.3 72.0 + - - +
898A GLN* 2.7 11.8 + - + +
899A LEU* 2.7 21.7 + - - +
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Residues in contact with LEU 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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888A ALA* 4.1 12.3 - - + +
891A PHE* 3.5 28.7 - - + +
892A GLY 2.9 17.4 + - - +
893A LEU* 3.8 13.9 - - - +
895A GLN* 1.3 69.6 - - - +
897A HIS* 1.3 52.5 + - - +
899A LEU* 2.4 42.6 + - + +
900A ARG* 2.6 19.4 + - - -
914A LEU* 4.2 24.2 - - + -
929A ARG* 4.3 8.5 - - + +
930A LEU* 4.1 19.7 - - + -
933A ILE* 3.4 31.9 - - + -
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Residues in contact with HIS 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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893A LEU* 3.0 36.8 + - + +
894A ALA 3.8 3.1 - - - +
896A LEU* 1.3 77.9 - - - +
898A GLN* 1.3 62.5 + - - +
900A ARG* 3.3 21.5 + - - +
901A GLY 3.1 19.1 + - - -
933A ILE* 4.1 16.3 - - + +
936A LEU* 3.6 19.3 - - + -
942A GLY* 4.2 14.5 + - - -
943A PHE* 3.3 18.7 + - + -
946A ALA* 4.0 25.4 - - + -
1151A EPE 3.4 19.4 + - - -
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Residues in contact with GLN 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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870A ILE* 4.2 20.6 - - + +
894A ALA 3.3 12.1 + - - +
895A GLN* 2.7 22.1 + - + +
897A HIS* 1.3 76.9 - - - +
899A LEU* 1.3 56.9 - - - +
901A GLY* 3.8 4.0 + - - -
902A ARG* 3.2 36.8 + - - +
943A PHE* 4.3 15.3 - - - -
947A THR* 4.9 4.9 + - - -
950A LEU* 3.4 33.4 - - + +
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Residues in contact with LEU 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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815A LEU* 4.0 15.5 - - + -
870A ILE* 3.9 30.5 - - + -
873A THR* 4.4 10.5 - - - +
883A ILE* 3.8 26.4 - - + +
885A ILE* 3.4 24.2 - - + -
891A PHE* 4.2 15.5 - - + -
895A GLN 2.7 12.1 + - - +
896A LEU* 2.4 45.3 + - + +
898A GLN* 1.3 63.8 - - - +
900A ARG* 1.3 65.5 + - - +
901A GLY 3.0 2.0 - - - -
902A ARG* 2.5 35.4 + - - +
903A VAL 4.3 0.9 + - - -
914A LEU* 5.9 0.2 - - + -
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Residues in contact with ARG 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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786A VAL* 4.1 19.0 + - + +
788A THR* 2.9 34.7 + - + +
883A ILE* 4.9 2.2 - - - +
885A ILE* 6.1 0.4 - - - -
896A LEU* 2.6 13.8 + - - +
897A HIS* 3.3 20.4 + - - +
899A LEU* 1.3 74.9 - - - +
901A GLY* 1.3 62.2 + - - +
902A ARG 3.4 0.2 + - - -
903A VAL* 3.8 12.8 + - - +
912A ALA* 4.6 10.5 - - + -
914A LEU* 5.2 6.5 - - + +
933A ILE* 3.3 25.0 - - - +
936A LEU* 3.3 25.1 + - - +
938A ASP 3.5 10.7 + - - -
939A LEU* 3.3 24.9 - - + +
943A PHE* 4.4 1.8 - - - +
1151A EPE 2.6 41.2 + - - +
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Residues in contact with GLY 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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784A LEU* 6.0 0.5 - - - +
897A HIS 3.1 10.9 + - - -
898A GLN 4.3 1.3 - - - -
899A LEU 3.0 1.2 - - - -
900A ARG* 1.3 77.0 - - - +
902A ARG* 1.3 55.2 + - - +
903A VAL 2.9 21.4 + - - +
939A LEU* 3.7 28.0 - - - +
943A PHE* 4.1 15.5 - - - -
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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