Contacts of the helix formed by residues 963 - 969 (chain A) in PDB entry 1OY9
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 963 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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949A ALA* 3.5 27.7 - - - +
952A LEU* 4.0 14.3 - - + +
953A MET* 4.4 1.1 - - + -
957A GLY 4.0 9.6 - - - +
958A LYS 3.9 6.7 - - - +
959A GLY* 3.2 25.6 + - - +
962A GLU* 1.3 78.4 - - - +
964A THR* 1.3 64.8 + - - +
965A LEU 3.4 0.4 - - - -
966A ASP* 3.5 6.4 - - - +
967A ALA* 3.1 18.9 + - - +
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Residues in contact with THR 964 (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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535A LEU* 4.6 9.6 - - - +
945A ILE 5.5 0.2 - - - +
949A ALA* 3.9 6.5 - - + +
950A LYS* 4.0 20.4 - - - +
953A MET* 4.6 9.2 - - + -
959A GLY 4.2 0.4 + - - -
960A LEU 4.3 4.9 + - - +
961A ILE* 3.2 22.9 + - - +
963A ALA* 1.3 80.5 - - - +
965A LEU* 1.3 66.6 + - - +
967A ALA 3.3 6.6 + - - -
968A VAL 3.6 2.1 + - - -
971A ARG* 3.7 2.3 + - - -
1025A PHE* 3.0 48.8 - - + +
1028A VAL* 4.5 16.6 - - + -
1029A VAL* 5.0 4.6 - - + +
1033A PHE* 5.9 0.7 - - + -
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Residues in contact with LEU 965 (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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528A THR* 3.6 24.0 - - + +
531A VAL* 3.8 25.4 - - + -
532A GLY* 3.9 21.1 - - - -
535A LEU* 4.1 8.7 - - + +
961A ILE* 3.6 17.2 + - + +
962A GLU* 4.6 4.3 - - - +
963A ALA 3.4 0.4 - - - -
964A THR* 1.3 81.3 + - - +
966A ASP* 1.3 66.5 + - - +
967A ALA 3.2 0.2 + - - -
968A VAL* 3.5 8.8 + - - +
969A ARG* 3.1 23.6 + - + +
1025A PHE* 4.2 2.4 - - - -
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Residues in contact with ASP 966 (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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952A LEU* 3.5 29.5 - - - +
962A GLU 3.1 22.0 + - - +
963A ALA* 3.4 8.4 + - - +
964A THR 3.3 0.2 - - - -
965A LEU* 1.3 81.9 - - - +
967A ALA* 1.3 57.6 + - - +
969A ARG* 3.2 37.2 + - - +
970A MET* 3.1 21.5 - - - +
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Residues in contact with ALA 967 (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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948A PHE* 4.3 3.8 - - + -
949A ALA* 3.8 10.3 - - + +
952A LEU* 3.8 17.7 - - + -
963A ALA 3.1 16.7 + - - +
964A THR 3.8 0.7 - - - +
965A LEU 3.2 0.8 - - - -
966A ASP* 1.3 77.3 - - - +
968A VAL* 1.3 50.6 + - - +
970A MET* 2.8 13.3 - - - +
971A ARG* 2.7 65.6 + - - +
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Residues in contact with VAL 968 (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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523A SER* 5.0 1.9 + - - -
527A TYR* 3.2 41.3 - - + +
528A THR* 4.4 5.5 + - + -
531A VAL* 4.3 9.6 - - + -
945A ILE* 4.9 0.2 - - + -
964A THR 3.6 0.4 + - - -
965A LEU 3.5 8.9 + - - +
967A ALA* 1.3 71.1 - - - +
969A ARG* 1.3 63.1 + - - +
970A MET 3.0 6.0 + - - -
971A ARG* 3.2 16.2 - - - +
972A LEU* 3.2 24.3 + - + +
1019A ILE* 3.7 21.8 - - + -
1025A PHE* 3.4 33.7 - - + -
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Residues in contact with ARG 969 (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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422A GLU* 4.1 16.2 + - - +
523A SER* 4.8 7.6 + - - -
524A THR* 4.8 22.9 + - + +
528A THR* 3.9 27.8 - - + +
965A LEU* 3.1 18.2 + - + +
966A ASP* 3.2 34.6 + - - +
968A VAL* 1.3 76.9 - - - +
970A MET* 1.3 76.2 + - - +
972A LEU 5.3 0.2 - - - -
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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