Contacts of the helix formed by residues 854 - 865 (chain B) in PDB entry 1GKU
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 THR 854 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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828B TYR* 3.6 31.4 - - + +
853B LEU* 1.3 78.4 - - - +
855B ARG* 1.3 65.4 + - - +
856B ASP* 3.5 8.2 + - - +
857B ASP* 3.3 28.6 + - - +
858B VAL* 3.1 18.4 + - - +
880B TYR* 4.0 2.9 - - - -
884B PHE* 3.6 26.5 - - + -
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Residues in contact with ARG 855 (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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378B ASN* 3.6 23.1 + - - +
854B THR* 1.3 72.1 - - - +
856B ASP* 1.3 88.3 + - - +
858B VAL* 3.1 13.1 + - - +
859B GLN* 3.1 30.3 + - - +
877B PHE* 3.2 35.2 - - + +
878B ALA* 4.6 3.7 - - - +
880B TYR* 4.2 12.1 - - + -
881B ASP* 2.7 49.9 + - + +
884B PHE* 5.3 1.8 - - - -
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Residues in contact with ASP 856 (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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377B ARG* 4.8 3.4 - - - +
378B ASN* 3.4 40.9 + - - +
379B VAL* 5.6 1.4 + - - +
854B THR* 3.5 7.3 + - - +
855B ARG* 1.3 93.4 + - - +
857B ASP* 1.3 65.8 + - - +
859B GLN* 3.3 3.4 + - - +
860B ARG* 3.0 24.7 + - - +
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Residues in contact with ASP 857 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B GLN 4.5 10.6 - - - +
411B ALA* 5.3 2.3 - - - -
828B TYR* 5.8 1.0 - - - -
852B PRO 4.4 2.3 - - - +
853B LEU* 3.7 25.3 - - + +
854B THR* 3.3 37.0 + - - +
855B ARG 3.2 0.8 - - - -
856B ASP* 1.3 77.7 - - - +
858B VAL* 1.3 64.3 + - - +
860B ARG* 3.2 24.5 + - - +
861B LEU* 3.0 33.2 + - + +
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Residues in contact with VAL 858 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806B LEU* 4.4 24.9 - - + -
853B LEU* 3.9 20.2 - - + +
854B THR 3.1 12.0 + - - +
855B ARG* 3.1 8.8 + - - +
857B ASP* 1.3 78.7 - - - +
859B GLN* 1.3 62.5 + - - +
861B LEU* 4.8 0.7 - - - -
862B ILE* 3.1 39.8 + - + +
867B LEU* 4.0 13.9 - - + +
877B PHE* 4.2 15.9 - - + -
880B TYR* 3.9 25.4 - - + +
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Residues in contact with GLN 859 (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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378B ASN* 3.0 28.6 + - - +
379B VAL* 3.5 26.4 - - + +
380B ASP* 3.4 21.2 + - - +
855B ARG* 3.1 21.4 + - - +
856B ASP* 3.9 5.2 - - - +
858B VAL* 1.3 77.3 - - - +
860B ARG* 1.3 60.3 + - - +
862B ILE* 3.6 7.3 + - - +
863B GLN* 3.0 32.1 + - + +
877B PHE* 3.4 50.2 - - + +
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Residues in contact with ARG 860 (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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371B LEU* 5.4 6.0 - - + +
374B TYR* 4.1 16.8 - - + -
375B LEU* 3.9 42.0 - - - +
379B VAL* 4.3 9.5 - - + +
410B GLN 5.2 0.8 + - - -
411B ALA* 4.2 9.6 - - - +
413B ASP* 2.6 42.4 + - - -
414B VAL* 3.9 11.9 - - - +
423B PHE* 5.2 0.4 - - - -
465B ARG* 4.1 0.2 - - - +
856B ASP 3.0 17.4 + - - +
857B ASP* 3.2 22.9 + - - +
859B GLN* 1.3 74.9 - - - +
861B LEU* 1.3 73.6 + - - +
863B GLN* 3.1 6.8 + - - +
864B GLU* 2.9 44.8 + - - +
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Residues in contact with LEU 861 (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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413B ASP* 4.1 19.7 - - - +
465B ARG* 4.5 7.0 - - - +
468B LEU* 4.3 24.7 - - + -
853B LEU* 3.9 35.4 - - + -
857B ASP* 3.0 20.5 + - + +
858B VAL 4.0 1.3 - - - +
860B ARG* 1.3 89.3 - - - +
862B ILE* 1.3 63.8 + - - +
864B GLU* 2.9 14.5 + - - +
865B GLY 3.0 9.9 + - - -
866B VAL* 3.2 18.8 + - + -
867B LEU* 4.0 23.6 - - + +
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Residues in contact with ILE 862 (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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858B VAL* 3.1 34.1 + - + +
859B GLN* 3.9 5.6 - - - +
860B ARG 3.3 0.2 - - - -
861B LEU* 1.3 76.5 - - - +
863B GLN* 1.3 69.8 + - - +
865B GLY* 3.4 10.7 + - - -
867B LEU* 3.8 32.9 - - + +
869B VAL* 3.7 31.2 - - + -
872B LEU* 4.6 1.3 - - + -
877B PHE* 3.9 23.3 - - + -
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Residues in contact with GLN 863 (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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371B LEU* 5.8 1.7 - - - +
374B TYR* 3.8 28.3 + - + -
379B VAL* 3.6 28.2 - - + +
383B GLU* 4.4 5.2 - - - +
859B GLN* 3.0 20.3 + - + +
860B ARG 3.1 9.3 + - - +
862B ILE* 1.3 86.4 - - - +
864B GLU* 1.3 61.4 + - - +
865B GLY 3.6 0.3 + - - -
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Residues in contact with GLU 864 (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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371B LEU* 4.4 21.9 - - + +
423B PHE* 3.6 26.6 - - + +
465B ARG* 2.5 47.2 + - - -
860B ARG* 2.9 22.5 + - - +
861B LEU* 2.9 11.5 + - - +
863B GLN* 1.3 80.0 - - - +
865B GLY* 1.3 58.2 + - - +
866B VAL* 3.5 10.2 - - + +
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Residues in contact with GLY 865 (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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427B ARG* 4.6 12.7 + - - -
861B LEU 3.0 3.0 + - - -
862B ILE 3.4 8.4 + - - -
863B GLN 3.3 3.2 - - - -
864B GLU* 1.3 79.8 - - - +
866B VAL* 1.3 63.9 + - - +
867B LEU 3.6 4.7 - - - +
868B VAL* 4.5 10.4 - - - +
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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