Contacts of the helix formed by residues 780 - 784 (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 VAL 780 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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776C ILE* 3.7 19.5 - - + -
777C SER* 3.3 18.6 + - - +
779C GLU* 1.3 76.5 - - + +
781C LEU* 1.3 57.6 + - - +
782C ALA 3.1 8.8 + - - -
783C ASP* 4.2 7.6 + - - +
784C LEU* 5.1 2.3 - - - +
800C ASP* 5.5 7.2 - - - +
801C ILE* 4.1 34.9 + - + +
478D ARG* 5.3 14.6 - - - +
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Residues in contact with LEU 781 (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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771C ARG* 3.2 55.9 + - - +
772C ASP* 5.4 0.7 - - - -
773C ILE* 4.8 15.3 - - + +
776C ILE* 3.8 27.8 - - + +
777C SER 3.3 19.9 + - - +
778C ASP* 3.9 11.2 + - - +
779C GLU 3.4 0.4 - - - -
780C VAL* 1.3 72.9 - - - +
782C ALA* 1.3 64.2 + - - +
783C ASP 3.2 3.4 - - - -
784C LEU* 3.0 41.6 + - + +
801C ILE* 4.3 14.1 - - + -
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Residues in contact with ALA 782 (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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771C ARG* 4.3 5.9 + - - +
778C ASP 3.3 14.6 + - - +
779C GLU* 3.2 19.5 - - - +
780C VAL 3.1 1.8 - - - -
781C LEU* 1.3 77.1 - - - +
783C ASP* 1.3 63.8 + - - +
784C LEU 3.1 1.4 + - - +
791C ARG* 2.8 24.8 + - - -
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Residues in contact with ASP 783 (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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159A ILE* 3.9 19.9 - - - +
780C VAL 4.2 5.9 + - - +
781C LEU 3.1 1.4 + - - -
782C ALA* 1.3 81.4 - - - +
784C LEU* 1.3 61.8 + - + +
790C VAL* 3.3 27.5 - - + +
791C ARG* 3.3 15.8 + - - +
794C ALA* 4.0 18.1 - - + +
795C GLU 3.9 13.8 + - - +
796C VAL* 6.2 0.7 - - + -
801C ILE 6.0 1.3 - - - +
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Residues in contact with LEU 784 (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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771C ARG* 4.2 23.0 + - + -
773C ILE* 5.8 0.2 - - + -
780C VAL 5.1 2.0 - - - +
781C LEU* 3.0 44.1 + - + +
782C ALA 3.1 1.8 - - - +
783C ASP* 1.3 85.1 - - + +
785C ASP* 1.3 69.8 + - - +
788C GLY* 4.0 13.0 - - - +
789C ILE 3.3 23.3 - - - +
790C VAL* 3.5 7.0 - - + +
791C ARG* 2.9 22.0 + - - -
801C ILE* 4.1 25.1 - - + +
802C LEU 3.8 11.0 - - - +
804C GLY* 5.1 3.8 - - - +
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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