Contacts of the helix formed by residues 894 - 900 (chain A) in PDB entry 1Y5I
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 ALA 894 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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891A ASP* 3.0 34.9 + - + +
893A PRO* 1.3 78.0 - - - +
895A THR* 1.3 63.0 + - - +
896A TYR 3.2 3.4 - - - -
897A GLU* 3.1 9.4 + - + +
898A ARG* 2.9 33.8 + - + +
938A PRO* 4.2 26.2 - - + -
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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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205A TYR* 4.1 20.6 - - + -
208A LEU* 3.7 21.7 + - + +
209A ILE* 4.0 23.0 - - + +
830A ALA* 4.4 6.7 - - + -
833A PHE* 3.8 12.1 - - + -
834A SER* 3.5 8.7 - - - +
891A ASP 3.5 3.4 + - - -
892A TYR* 2.9 25.5 + - - -
893A PRO 3.3 1.0 - - - -
894A ALA* 1.3 77.1 - - - +
896A TYR* 1.3 59.8 + - - +
898A ARG* 3.3 7.0 + - - +
899A PHE* 2.8 27.5 + - - +
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Residues in contact with TYR 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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827A LYS* 3.7 31.9 - - + +
830A ALA* 3.7 12.6 - - + +
831A LYS* 3.6 54.9 + - + -
834A SER* 2.9 24.0 + - - +
894A ALA 3.2 0.2 - - - -
895A THR* 1.3 70.2 - - - +
897A GLU* 1.3 88.1 + - + +
899A PHE* 3.5 6.1 - - - +
900A THR* 2.8 56.2 + - + +
934A LYS* 4.9 2.0 - - - -
946A ASN* 4.9 5.2 + - - -
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Residues in contact with GLU 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 PRO 5.5 0.6 + - - +
894A ALA* 3.1 11.3 + - - +
896A TYR* 1.3 99.0 - - + +
898A ARG* 1.3 59.6 + - - +
900A THR* 3.6 4.3 + - - -
901A SER* 2.8 26.5 + - - -
934A LYS* 2.9 35.1 + - - +
936A GLU 4.5 7.1 - - - +
937A GLY* 5.6 1.1 - - - -
938A PRO* 4.1 36.0 - - + +
939A ALA* 4.0 7.4 + - - +
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Residues in contact with ARG 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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204A ARG* 3.0 8.6 + - - -
208A LEU* 3.9 15.7 - - + -
598A TRP* 3.1 57.8 + - + +
599A GLN* 3.0 38.6 + - - +
889A GLU 4.5 6.3 + - - -
891A ASP* 3.7 35.6 + - - +
894A ALA* 2.9 29.0 + - + +
895A THR* 3.6 4.9 - - - +
897A GLU* 1.3 75.7 - - + +
899A PHE* 1.3 67.2 + - - +
900A THR 3.1 1.8 - - - -
901A SER 2.9 21.5 - - - +
938A PRO* 5.9 2.3 - - + +
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Residues in contact with PHE 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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201A SER* 3.2 28.3 - - - -
204A ARG* 2.9 34.3 + - + +
205A TYR* 3.7 29.2 - - + -
208A LEU* 3.7 8.0 - - + +
823A TRP* 3.6 44.5 - + - -
826A TYR* 4.3 4.7 - - + -
827A LYS* 4.0 27.8 - - + -
830A ALA* 4.2 11.0 - - + -
895A THR 2.8 17.5 + - - +
896A TYR* 3.5 9.6 - + - +
898A ARG* 1.3 77.5 - - - +
900A THR* 1.3 72.5 + - + +
901A SER 3.4 2.6 + - - -
945A LEU* 3.6 8.0 - - - +
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Residues in contact with THR 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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827A LYS* 3.8 19.5 - - + -
896A TYR* 2.8 52.0 + - + +
897A GLU* 3.6 2.0 + - - -
898A ARG 3.1 0.2 - - - -
899A PHE* 1.3 81.6 - - + +
901A SER* 1.3 57.6 + - - +
934A LYS* 2.8 37.4 + - - -
944A MET* 3.6 2.3 - - - +
945A LEU 2.8 38.8 + - - +
946A ASN* 4.0 9.5 - - - +
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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