Contacts of the helix formed by residues 1162 - 1167 (chain O) in PDB entry 5X0X
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 SER1162 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13J T 5.0 1.6 - - - -
1110O PHE* 2.9 24.0 + - - +
1111O GLN* 2.8 28.4 + - - -
1113O THR* 5.1 3.6 - - - -
1116O MET* 4.6 12.3 - - - -
1133O LEU 4.1 7.2 + - - -
1134O ASP* 6.1 0.9 - - - -
1161O LEU* 1.3 75.7 - - - +
1163O THR* 1.3 68.8 + - - +
1164O ARG* 3.6 0.4 - - - +
1165O ALA* 2.9 33.0 + - - +
1166O GLY* 3.3 5.5 + - - -
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Residues in contact with THR1163 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109O PHE* 3.5 40.2 - - + -
1110O PHE 2.8 10.2 + - - +
1111O GLN* 2.2 39.0 + - - +
1161O LEU* 4.1 3.4 - - - +
1162O SER* 1.3 73.8 - - - +
1164O ARG* 1.3 67.4 + - - +
1167O GLY* 2.9 28.0 + - - -
1180O ILE* 6.0 1.1 - - + -
1184O ASP* 5.0 4.5 - - - +
1189O GLN* 4.2 20.4 - - - +
1190O ASP* 5.0 6.7 - - - +
1192O GLN* 6.0 2.2 - - - -
1193O ALA* 4.2 12.8 - - + +
1196O ARG* 6.0 0.2 - - - -
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Residues in contact with ARG1164 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137I A 4.6 11.7 + - - -
138I T 4.0 18.5 + - - -
12J A 5.5 15.7 + - + -
13J T 3.8 15.6 - - - +
14J A 4.5 0.7 + - - +
1111O GLN* 2.3 53.3 + - - +
1162O SER* 5.5 0.2 - - - +
1163O THR* 1.3 87.0 + - - +
1165O ALA* 1.3 67.8 + - + +
1166O GLY 3.4 0.6 + - - -
1167O GLY* 3.5 7.7 + - - +
1168O LEU 4.9 1.9 + - - -
1184O ASP 4.5 0.8 - - - -
1185O TRP* 3.1 45.7 + - - +
1189O GLN* 3.3 43.9 + - - +
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Residues in contact with ALA1165 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12J A 3.9 2.5 - - + +
13J T 2.7 70.1 - - - +
14J A 2.7 11.3 + - - -
1134O ASP 5.0 0.9 - - - -
1135O GLY* 4.1 6.9 - - - +
1162O SER* 2.9 32.1 + - - +
1164O ARG* 1.3 82.7 - - + +
1166O GLY* 1.3 52.9 + - - +
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Residues in contact with GLY1166 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J A 3.6 10.3 + - - -
1133O LEU* 3.8 28.2 + - - +
1134O ASP 4.6 0.6 + - - -
1142O ARG* 4.2 11.9 + - - -
1161O LEU* 5.5 2.5 - - - -
1162O SER 3.3 6.6 + - - -
1163O THR 3.9 0.2 - - - -
1165O ALA* 1.3 78.6 - - - +
1167O GLY* 1.3 67.1 + - - +
1168O LEU* 3.5 6.7 + - - +
1170O LEU* 4.1 11.6 - - - +
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Residues in contact with GLY1167 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1161O LEU* 6.0 2.0 - - - -
1163O THR 2.9 20.2 + - - -
1164O ARG* 3.5 7.8 + - - -
1166O GLY* 1.3 80.8 - - - +
1168O LEU* 1.3 71.2 + - - +
1170O LEU* 3.3 22.7 - - - +
1196O ARG* 3.2 22.4 + - - -
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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