Contacts of the helix formed by residues 739 - 744 (chain C) in PDB entry 5UH8
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 ASN 739 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A TYR* 5.2 4.9 - - - -
738C SER* 1.3 73.3 + - - +
740C ARG* 1.3 54.1 + - - +
742C VAL* 2.8 36.5 + - - +
743C GLU* 2.9 42.5 + - - +
898C ILE* 3.8 17.1 - - - +
899C LEU 3.0 22.9 + - - +
900C PRO* 4.1 14.3 - - - +
901C VAL* 3.7 12.9 - - - +
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Residues in contact with ARG 740 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718C ASN 5.3 2.0 + - - -
719C LEU* 5.0 2.4 - - - +
738C SER* 3.6 14.6 + - - +
739C ASN* 1.3 77.0 - - - +
741C LEU* 1.3 74.6 + - - +
743C GLU* 4.4 9.5 - - - +
744C GLU* 2.9 69.2 + - + +
746C VAL* 3.7 17.6 - - - +
901C VAL* 4.7 15.5 - - + +
912C PRO* 5.7 7.4 - - - -
914C ASP* 2.9 44.6 + - - -
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Residues in contact with LEU 741 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719C LEU* 4.3 11.2 - - + -
737C LEU* 3.7 29.4 - - + -
738C SER* 2.8 22.2 + - - +
740C ARG* 1.3 106.5 - - - +
742C VAL* 1.3 60.6 + - + +
745C ASP* 3.8 2.1 + - - -
746C VAL* 3.3 42.9 + - + -
747C LEU* 3.6 36.4 + - + -
748C THR* 4.6 1.4 + - - -
879C ILE* 4.4 6.8 - - + +
914C ASP* 3.9 18.8 - - + +
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Residues in contact with VAL 742 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A TYR* 4.0 15.3 - - + +
148A PRO* 6.3 0.2 - - + -
738C SER 5.0 0.4 - - - +
739C ASN* 2.8 24.4 + - - +
741C LEU* 1.3 80.2 - - + +
743C GLU* 1.3 61.1 + - - +
744C GLU 3.2 4.7 + - - -
745C ASP* 3.4 8.0 + - - +
748C THR* 5.5 0.4 - - - -
878C LYS* 3.2 44.4 - - + +
879C ILE* 3.9 25.6 - - + +
898C ILE* 4.1 20.9 - - + -
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Residues in contact with GLU 743 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A LYS* 5.8 3.1 - - - +
146A TYR* 3.5 58.8 - - + +
165A ASP* 5.5 4.3 - - - +
167A ILE* 3.3 33.9 - - + +
739C ASN* 2.9 47.5 + - - +
740C ARG* 4.2 6.6 - - - +
742C VAL* 1.3 76.3 - - + +
744C GLU* 1.3 60.5 + - + +
745C ASP* 5.8 0.4 - - - -
901C VAL* 5.2 11.3 + - - +
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Residues in contact with GLU 744 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ILE* 4.7 10.5 - - + +
740C ARG* 2.9 55.1 + - + +
743C GLU* 1.3 83.7 - - + +
745C ASP* 1.3 63.7 + - - +
746C VAL* 2.8 20.7 + - + +
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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