Contacts of the helix formed by residues 775 - 786 (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 775 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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774B TYR* 1.3 71.3 - - - +
776B THR* 1.3 67.2 + - - +
777B GLU* 3.3 18.8 + - - +
778B THR* 2.8 26.5 + - - +
779B MET* 3.1 21.7 + - - +
812B THR 3.7 8.5 - - - -
813B ASP* 3.8 18.4 - - - +
814B SER 3.6 13.9 - - - +
815B THR* 3.6 30.7 - - + -
847B ILE* 3.7 7.6 - - - -
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Residues in contact with THR 776 (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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775B THR* 1.3 71.8 - - - +
777B GLU* 1.3 56.6 + - - +
779B MET* 4.0 2.8 - - + +
780B LEU* 2.9 44.2 + - + +
795B MET* 3.7 26.7 - - + -
810B HIS 2.6 19.0 + - - +
811B ARG* 3.2 2.4 - - - -
812B THR 2.8 32.9 + - - -
847B ILE* 3.8 9.4 - - - +
973B PRO* 3.4 33.9 - - + +
976B TYR* 4.1 2.2 - - + -
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Residues in contact with GLU 777 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775B THR* 3.0 15.5 + - - +
776B THR* 1.3 75.9 - - - +
778B THR* 1.3 78.1 + - - +
780B LEU* 3.1 6.3 + - - +
781B SER* 3.0 25.1 + - - +
962B ILE* 3.7 23.7 - - + +
963B GLN* 4.6 10.7 - - + +
966B LYS* 3.2 52.3 - - + +
967B GLU* 6.1 0.2 - - - +
976B TYR* 4.4 14.6 - - + +
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Residues in contact with THR 778 (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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773B PRO 4.2 2.1 + - - -
774B TYR* 3.5 15.8 - - - -
775B THR* 2.8 34.3 + - - +
777B GLU* 1.3 92.1 - - - +
779B MET* 1.3 55.9 + - - +
781B SER* 3.7 6.8 - - - -
782B ASP* 2.9 31.5 + - - +
886B ARG* 3.7 26.7 - - - +
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Residues in contact with MET 779 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774B TYR* 3.5 32.3 - - + -
775B THR 3.1 16.9 + - - +
776B THR* 4.2 12.6 - - - +
778B THR* 1.3 75.7 + - - +
780B LEU* 1.3 69.0 + - + +
782B ASP* 4.0 0.5 - - - +
783B ALA* 2.9 33.6 + - - +
794B THR* 3.9 21.5 - - + -
795B MET* 4.5 9.2 - - - -
798B ALA* 4.2 22.7 - - + -
810B HIS 4.6 1.8 - - - +
847B ILE* 4.0 21.3 - - + -
879B LEU* 4.3 15.7 - - + -
882B LEU* 5.6 0.4 - - + +
883B ILE* 4.0 23.1 - - + -
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Residues in contact with LEU 780 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776B THR* 2.9 41.4 + - + +
777B GLU* 3.5 4.3 - - - +
779B MET* 1.3 77.3 - - + +
781B SER* 1.3 62.9 - - - +
783B ALA* 3.6 1.9 + - - +
784B ASN* 3.3 22.9 + - - +
791B VAL* 3.8 27.0 - - + +
794B THR* 3.7 29.8 + - + -
795B MET* 3.5 25.6 - - + -
959B SER* 5.0 1.0 - - - -
962B ILE* 4.1 19.3 - - + -
976B TYR* 3.9 27.6 - - + -
977B ALA 4.8 1.6 - - - +
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Residues in contact with SER 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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777B GLU* 3.0 16.5 + - - +
778B THR* 3.7 8.3 - - - -
779B MET 3.2 0.2 - - - -
780B LEU* 1.3 77.0 - - - +
782B ASP* 1.3 63.0 - - - +
784B ASN* 3.1 2.9 + - - +
785B ARG* 3.0 21.1 + - - +
959B SER* 3.3 42.2 + - - +
962B ILE* 3.5 11.0 - - - +
963B GLN* 3.7 15.2 - - - +
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Residues in contact with ASP 782 (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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774B TYR* 2.7 38.0 + - + +
778B THR 2.9 14.8 + - - +
779B MET 4.0 1.1 - - - +
781B SER* 1.3 75.1 - - - +
783B ALA* 1.3 58.8 + - - +
784B ASN 3.0 0.7 + - - -
785B ARG* 2.6 37.7 + - - +
786B ILE* 2.7 46.4 + - + +
882B LEU* 4.5 2.7 - - + -
886B ARG* 3.9 6.1 + - - -
927B TYR* 2.4 22.9 + - - -
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Residues in contact with ALA 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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779B MET 2.9 19.6 + - - +
780B LEU 3.9 2.0 - - - +
782B ASP* 1.3 76.9 - - - +
784B ASN* 1.3 49.9 - - - +
787B LEU* 2.2 37.6 - - - +
789B PHE* 3.3 11.7 + - + +
794B THR* 3.5 30.7 - - + +
879B LEU* 3.9 16.2 - - + -
882B LEU* 4.0 12.3 - - + +
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Residues in contact with ASN 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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780B LEU 3.3 16.7 + - - +
781B SER 3.1 4.6 + - - +
782B ASP 3.0 0.6 - - - -
783B ALA* 1.3 75.1 - - - +
785B ARG* 1.3 58.6 + - - +
787B LEU 2.6 18.8 - - - +
788B LYS* 3.8 16.1 + - - +
789B PHE 2.6 26.8 - - - +
790B SER 5.8 0.9 - - - -
791B VAL* 5.9 1.8 - - + +
957B THR* 4.0 7.3 - - - -
958B GLN* 3.3 27.2 - - + +
959B SER* 2.6 39.6 - - - +
991B GLU* 5.4 0.7 + - - +
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Residues in contact with ARG 785 (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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781B SER 3.0 15.3 + - - +
782B ASP* 2.6 29.6 + - - +
784B ASN* 1.3 78.2 - - - +
786B ILE* 1.3 85.5 + - + +
788B LYS* 3.8 15.8 + - - +
927B TYR* 3.4 15.4 + - - -
928B ARG 5.0 9.7 + - - -
959B SER* 4.5 10.5 - - - +
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Residues in contact with ILE 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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782B ASP* 2.7 34.9 + - + +
785B ARG* 1.3 111.2 - - + +
787B LEU* 1.3 76.7 + - + +
788B LYS* 4.1 8.3 - - - +
882B LEU* 4.3 21.1 - - + -
927B TYR* 5.6 4.0 - - + +
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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