Contacts of the helix formed by residues 936 - 941 (chain A) in PDB entry 1HU3
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 ILE 936 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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900A PHE* 3.9 24.5 - - + -
901A LYS* 4.1 12.6 - - + -
910A MSE 3.0 41.3 - - + -
932A LEU* 2.9 33.7 + - + +
933A LEU* 4.6 1.6 - - - -
935A THR* 1.3 90.1 - - + +
937A GLY* 1.3 69.0 + - - +
938A LYS* 3.4 2.9 - - - -
939A ASP* 3.0 23.4 + - - +
940A LEU* 3.1 38.1 + - + +
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Residues in contact with GLY 937 (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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933A LEU* 2.7 38.0 + - - -
934A THR 4.4 1.0 + - - -
935A THR 3.6 0.8 - - - -
936A ILE* 1.3 78.2 - - - +
938A LYS* 1.3 57.7 + - - +
940A LEU* 3.2 4.9 + - - +
941A ASP* 2.9 26.3 + - - +
949A MSE 4.8 2.1 - - - +
984A TRP* 3.6 20.8 - - - -
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Residues in contact with LYS 938 (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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934A THR 5.8 0.2 + - - -
936A ILE 3.4 0.9 - - - -
937A GLY* 1.3 72.3 - - - +
939A ASP* 1.3 79.6 + - - +
941A ASP* 3.1 26.0 + - - +
983A ASN 5.4 0.9 - - - +
984A TRP* 3.3 52.4 + - + +
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Residues in contact with ASP 939 (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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900A PHE* 4.7 18.5 - - + -
907A GLU* 3.1 18.1 - - - +
935A THR 4.5 3.6 - - - +
936A ILE* 3.0 23.3 + - - +
938A LYS* 1.3 90.4 - - - +
940A LEU* 1.3 62.5 + - - +
942A PHE* 4.3 6.8 + - - +
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Residues in contact with LEU 940 (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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900A PHE* 4.1 9.9 - - + -
907A GLU* 3.6 31.7 - - + +
910A MSE 3.6 30.1 - - + -
911A HIS* 4.2 8.7 + - + +
914A VAL* 4.6 17.3 - - + -
933A LEU* 4.6 9.4 - - + -
936A ILE* 3.1 38.8 + - + +
937A GLY* 3.6 5.6 - - - +
939A ASP* 1.3 77.8 - - - +
941A ASP* 1.3 57.1 + - - +
942A PHE* 2.8 11.2 + - - +
945A ALA* 3.4 10.7 - - - +
949A MSE 2.9 30.5 - - + +
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Residues in contact with ASP 941 (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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937A GLY 2.9 15.0 + - - +
938A LYS* 3.1 15.2 + - - +
940A LEU* 1.3 73.4 - - - +
942A PHE* 1.3 58.5 + - - +
945A ALA* 5.1 0.2 - - - -
946A LYS* 2.8 37.8 + - - +
949A MSE 3.1 33.2 - - - +
980A ARG* 3.5 15.5 + - - +
984A TRP* 2.5 33.8 + - + +
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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