Contacts of the helix formed by residues 780 - 786 (chain B) in PDB entry 6RKU
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 LEU 780 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A GLY 4.5 9.9 - - - +
779B THR* 1.3 77.7 - - - +
781B MET* 1.3 61.2 + - - +
783B ASP* 3.5 23.8 + - + +
784B ALA* 2.9 28.7 + - + +
23G G 3.9 30.3 - - + +
24G G 3.3 30.5 - - - +
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Residues in contact with MET 781 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779B THR* 3.0 16.9 + - + +
780B LEU* 1.3 78.9 - - + +
782B GLY* 1.3 65.7 + - - +
783B ASP 3.1 0.7 - - - -
784B ALA* 3.1 11.6 + - + +
785B VAL* 2.9 37.2 + - + +
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Residues in contact with GLY 782 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776B LEU* 4.1 34.1 + - - -
779B THR* 4.8 5.1 - - - -
780B LEU 4.5 1.0 - - - +
781B MET* 1.3 78.2 - - - +
783B ASP* 1.3 56.5 + - - +
785B VAL* 3.5 11.4 - - - -
786B GLU* 2.8 36.4 + - - +
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Residues in contact with ASP 783 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A TYR* 4.3 15.9 + - - -
176A VAL* 4.7 10.0 - - + +
177A GLY* 4.5 10.7 - - - -
776B LEU 4.0 2.9 + - - +
777B PHE 2.8 28.3 - - - +
778B THR* 4.1 4.9 + - - -
780B LEU* 3.5 34.1 + - + +
781B MET 3.1 0.6 - - - -
782B GLY* 1.3 77.4 - - - +
784B ALA* 1.3 56.3 + - - +
786B GLU* 5.2 1.1 - - - -
787B PRO* 3.1 25.7 - - - +
23G G 3.6 19.8 + - - +
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Residues in contact with ALA 784 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A GLY* 5.2 11.4 - - - +
178A MET* 6.2 3.6 - - - -
780B LEU* 2.9 24.0 + - + +
781B MET* 3.1 14.3 + - + +
783B ASP* 1.3 77.2 - - - +
785B VAL* 1.3 61.2 + - + +
787B PRO* 3.9 8.7 - - - +
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Residues in contact with VAL 785 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776B LEU* 5.4 5.8 - - + -
781B MET* 2.9 33.1 + - + +
782B GLY* 3.4 13.7 - - - +
784B ALA* 1.3 80.2 - - + +
786B GLU* 1.3 73.1 + - + +
787B PRO 3.4 2.5 - - - -
788B ARG* 4.0 14.7 + - - +
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Residues in contact with GLU 786 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LYS* 4.6 18.9 + - + +
22A LEU* 5.4 10.5 - - + +
776B LEU* 4.8 13.8 - - + +
782B GLY 2.8 18.5 + - - +
783B ASP* 5.2 1.1 - - - -
785B VAL* 1.3 81.5 - - + +
787B PRO* 1.3 55.7 - - + +
788B ARG* 2.6 20.6 + - - +
789B ARG* 4.8 14.4 + - - +
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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