Contacts of the helix formed by residues 818 - 830 (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 SER 818 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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816B ARG* 5.5 2.7 - - - +
817B VAL* 1.3 77.6 - - - +
819B ASP* 1.3 60.8 + - - +
820B VAL* 3.0 11.5 + - - +
821B GLY 2.9 7.4 + - - -
822B GLN* 2.8 24.6 + - - +
837B GLU* 5.7 1.8 - - - -
845B GLU* 2.5 22.3 + - - +
848B ARG* 3.1 21.3 + - - -
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Residues in contact with ASP 819 (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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817B VAL 4.0 0.2 + - - -
818B SER* 1.3 73.9 - - - +
820B VAL* 1.3 63.9 + - - +
822B GLN* 3.5 17.5 + - + +
823B ARG* 2.8 73.7 + - + +
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Residues in contact with VAL 820 (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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660B GLU* 5.1 3.6 - - - +
664B ARG* 5.1 22.4 - - + +
668B GLU* 4.7 15.3 - - - +
818B SER* 3.0 10.5 - - - +
819B ASP* 1.3 81.3 - - - +
821B GLY* 1.3 59.7 + - - +
823B ARG* 3.1 27.5 + - - +
824B ILE* 2.9 36.2 + - + +
848B ARG* 3.8 16.8 - - - +
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Residues in contact with GLY 821 (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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817B VAL* 3.9 6.3 - - - -
818B SER* 2.9 11.5 + - - -
820B VAL* 1.3 82.1 - - - +
822B GLN* 1.3 59.9 + - - +
824B ILE* 3.4 5.5 + - - +
825B ALA* 3.2 11.6 + - - +
848B ARG* 3.5 29.6 - - - +
887B PHE* 3.1 24.3 - - - -
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Residues in contact with GLN 822 (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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817B VAL* 3.4 24.8 - - + +
818B SER 2.8 11.2 + - - +
819B ASP* 3.6 17.0 + - + +
820B VAL 3.1 0.4 - - - -
821B GLY* 1.3 77.7 - - - +
823B ARG* 1.3 58.1 + - + +
825B ALA* 3.3 1.8 + - - -
826B LYS* 2.9 22.9 + - - +
833B PHE* 3.5 16.7 - - + -
835B GLY* 3.5 28.5 - - - +
836B ARG 3.8 12.3 - - - +
837B GLU* 4.2 9.2 - - - +
891B GLN* 3.6 22.0 - - - +
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Residues in contact with ARG 823 (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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664B ARG* 5.9 3.0 - - - +
819B ASP* 2.8 46.7 + - + +
820B VAL* 3.1 27.3 + - - +
822B GLN* 1.3 75.9 - - + +
824B ILE* 1.3 60.9 + - - +
826B LYS* 3.8 10.5 - - + +
827B GLU* 3.0 31.4 + - - +
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Residues in contact with ILE 824 (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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664B ARG* 6.0 3.1 - - - +
820B VAL* 2.9 24.0 + - + +
821B GLY* 3.6 8.1 - - - +
822B GLN 3.2 0.2 - - - -
823B ARG* 1.3 77.9 - - - +
825B ALA* 1.3 62.3 - - - +
827B GLU* 3.3 1.9 + - - -
828B TYR* 3.3 16.1 + - - +
848B ARG* 4.1 19.7 - - + +
849B PRO* 3.6 15.3 - - + +
850B THR 2.8 33.9 - - - +
851B ARG 4.0 3.4 - - - -
852B PRO* 3.4 42.1 - - + +
887B PHE* 4.6 4.7 - - + -
888B MET* 4.4 10.1 - - + -
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Residues in contact with ALA 825 (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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821B GLY 3.2 8.7 + - - +
822B GLN 3.5 8.1 - - - +
824B ILE* 1.3 77.9 - - - +
826B LYS* 1.3 55.0 + - - +
828B TYR* 2.9 2.8 + - - -
829B LEU* 2.6 38.4 + - + +
833B PHE* 3.8 5.6 - - + -
887B PHE* 4.0 6.5 - - + -
888B MET* 3.9 14.8 - - - -
891B GLN* 3.5 39.3 - - + -
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Residues in contact with LYS 826 (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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822B GLN 2.9 16.7 + - - +
823B ARG* 3.8 11.2 - - + +
825B ALA* 1.3 77.1 - - - +
827B GLU* 1.3 62.6 + - - +
830B GLY* 3.0 26.7 + - - +
831B ASP 6.2 0.9 - - - +
833B PHE* 3.6 42.8 - - + -
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Residues in contact with GLU 827 (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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464B GLU* 4.6 6.6 - - - +
467B LYS* 3.7 36.1 + - - +
823B ARG 3.0 14.7 + - - +
824B ILE* 3.4 10.5 - - - +
826B LYS* 1.3 77.2 - - - +
828B TYR* 1.3 58.6 + - - +
830B GLY* 5.0 0.9 + - - -
852B PRO* 4.0 18.4 - - + +
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Residues in contact with TYR 828 (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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824B ILE 3.3 3.0 + - - +
825B ALA 2.9 4.0 + - - +
827B GLU* 1.3 80.3 - - - +
829B LEU* 1.3 67.9 + - + +
830B GLY 3.6 0.4 - - - -
852B PRO* 4.0 19.5 - - + -
854B THR* 3.6 26.1 - - + +
857B ASP* 5.8 0.7 - - - -
884B PHE* 3.7 21.0 - + - -
888B MET* 3.6 44.0 - - + -
922B ARG* 3.7 32.3 + - - -
926B LEU* 4.3 13.2 - - + +
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Residues in contact with LEU 829 (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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825B ALA* 2.6 21.2 + - + +
828B TYR* 1.3 91.4 - - + +
830B GLY* 1.3 70.6 + - - +
831B ASP 3.7 0.2 - - - -
832B ASP* 3.3 18.1 + - + +
833B PHE* 3.6 22.0 - - + +
888B MET* 3.6 15.5 - - + +
891B GLN* 3.1 45.8 - - + +
892B CYS* 3.6 14.4 - - - +
922B ARG* 4.8 7.9 + - + +
926B LEU* 4.1 22.7 - - + -
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Residues in contact with GLY 830 (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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826B LYS* 3.0 22.0 + - - -
827B GLU 4.8 0.8 + - - -
828B TYR 3.6 1.0 - - - -
829B LEU* 1.3 82.0 - - - +
831B ASP* 1.3 75.7 + - - +
832B ASP* 3.3 1.7 + - - +
833B PHE* 4.1 3.0 - - - +
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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