Contacts of the helix formed by residues 1031 - 1037 (chain W) in PDB entry 5O9G
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 ILE1031 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1025W PHE* 4.5 24.9 - - + +
1027W ASN 4.7 12.1 - - - +
1028W LEU* 4.6 0.8 - - - -
1030W GLU* 1.3 84.5 - - + +
1032W LEU* 1.3 63.5 + - - +
1033W ASP* 3.2 3.6 - - - +
1034W GLU* 3.1 28.1 + - + +
1035W LEU* 3.1 25.5 + - + +
1144W LYS* 6.0 7.0 - - - +
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Residues in contact with LEU1032 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028W LEU* 3.3 38.4 + - + +
1029W LYS* 5.1 4.5 - - - -
1030W GLU 3.5 3.2 + - - +
1031W ILE* 1.3 77.7 - - - +
1033W ASP* 1.3 58.1 + - - +
1035W LEU* 3.0 6.4 + - + +
1036W ILE* 2.9 45.6 + - + +
1041W LEU* 3.9 27.1 - - + -
1046W PHE* 3.6 35.9 - - + +
1049W TYR* 4.0 22.2 - - + -
1050W GLY 5.6 0.2 - - - +
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Residues in contact with ASP1033 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350W TYR* 5.3 1.0 + - - -
1031W ILE* 3.2 1.2 - - - +
1032W LEU* 1.3 77.0 - - - +
1034W GLU* 1.3 67.0 + - + +
1036W ILE* 4.3 4.2 - - - +
1037W ALA* 3.5 24.8 + - - +
1046W PHE* 3.2 31.3 - - - -
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Residues in contact with GLU1034 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031W ILE* 3.1 24.5 + - + +
1033W ASP* 1.3 81.4 - - + +
1035W LEU* 1.3 66.9 + - + +
1036W ILE 3.4 0.8 + - - -
1037W ALA* 4.3 5.8 + - - +
1038W ASP* 4.0 17.5 + - - +
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Residues in contact with LEU1035 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021W ALA* 5.1 6.5 - - + +
1025W PHE* 3.6 61.9 - - + -
1028W LEU* 3.7 33.9 - - + -
1031W ILE* 3.3 24.9 - - + +
1032W LEU* 3.0 16.3 + - + +
1034W GLU* 1.3 81.9 - - + +
1036W ILE* 1.3 58.1 + - - +
1038W ASP* 2.8 23.8 - - - +
1040W THR* 4.9 0.5 - - - -
1041W LEU* 3.5 19.7 + - + +
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Residues in contact with ILE1036 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350W TYR* 4.4 15.0 - - + +
1032W LEU* 2.9 27.6 + - + +
1033W ASP* 4.3 3.6 - - - +
1034W GLU 3.4 0.2 - - - -
1035W LEU* 1.3 77.4 - - - +
1037W ALA* 1.3 62.1 + - - +
1038W ASP* 3.1 10.0 + - - +
1039W GLY* 3.5 6.4 + - - -
1041W LEU* 3.4 45.7 - - + +
1042W PRO 4.1 9.2 - - - +
1043W VAL* 5.1 5.6 - - + -
1044W LYS 5.2 3.8 - - - +
1046W PHE* 3.6 33.7 - - + -
1049W TYR* 4.0 19.7 - - + -
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Residues in contact with ALA1037 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345W LYS* 4.1 20.7 - - - +
350W TYR* 3.5 47.0 + - + +
1033W ASP 3.5 16.8 + - - +
1034W GLU* 4.3 6.0 + - - +
1036W ILE* 1.3 75.7 - - - +
1038W ASP* 1.3 61.6 + - - +
1039W GLY* 3.2 1.4 + - - -
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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