Contacts of the strand formed by residues 753 - 768 (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 GLU 753 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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751B GLU* 3.5 15.2 - - - +
752B GLU* 1.3 84.5 - - + +
754B PHE* 1.3 65.9 + - - +
943B VAL 3.4 9.2 - - - +
944B LYS* 4.3 26.3 - - + -
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Residues in contact with PHE 754 (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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738B ALA* 4.7 0.7 - - + -
740B VAL* 3.8 22.4 - - + -
747B LEU* 4.1 11.7 - - + -
749B HIS* 3.8 28.7 - + + -
751B GLU* 3.8 28.3 - - + +
752B GLU 4.0 4.0 - - - -
753B GLU* 1.3 84.6 - - - +
755B ASP* 1.3 69.1 + - - +
756B LEU* 4.1 19.7 - - + -
906B PHE* 4.2 17.9 - - + -
907B ASP* 5.2 4.3 - - + -
942B ARG* 4.0 0.6 - - - -
943B VAL* 3.1 41.4 + - + +
945B ALA* 3.7 24.2 - - + -
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Residues in contact with ASP 755 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754B PHE* 1.3 80.4 - - - +
756B LEU* 1.3 61.4 + - - +
905B GLU 3.9 0.3 - - - +
906B PHE* 3.9 14.0 - - - +
907B ASP 4.1 5.5 + - - -
940B THR* 4.2 13.0 - - + -
941B PHE 3.1 14.6 - - - +
942B ARG* 3.8 13.7 - - - +
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Residues in contact with LEU 756 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740B VAL* 4.0 22.4 - - + -
743B PHE* 4.1 12.1 - - + -
745B LEU* 4.3 15.5 - - + -
747B LEU* 4.6 4.9 - - + -
754B PHE* 4.1 7.4 - - + -
755B ASP* 1.3 75.2 - - - +
757B THR* 1.3 59.7 + - - +
758B ILE* 3.5 26.7 - - + -
904B ILE* 4.3 6.3 - - + -
905B GLU 2.8 14.1 - - - +
906B PHE* 3.9 9.0 - - + -
939B GLY 3.4 0.7 - - - +
940B THR* 3.0 23.9 - - - -
941B PHE* 3.3 11.1 + - + +
943B VAL* 3.8 30.1 - - + -
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Residues in contact with THR 757 (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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756B LEU* 1.3 70.8 - - - +
758B ILE* 1.3 64.3 + - - +
759B LYS* 3.8 23.9 + - + +
903B SER 3.4 2.4 - - - +
904B ILE* 3.1 6.1 - - - -
905B GLU* 2.6 52.8 + - + +
939B GLY* 3.6 6.1 - - - +
940B THR* 2.7 22.9 + - - +
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Residues in contact with ILE 758 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743B PHE* 3.5 28.9 - - + -
745B LEU* 4.6 11.0 - - + -
756B LEU* 3.5 29.2 - - + -
757B THR* 1.3 79.2 - - - +
759B LYS* 1.3 70.7 + - - +
902B TYR* 3.8 10.8 - - + -
903B SER 3.6 1.6 - - - -
904B ILE* 3.9 23.6 - - + -
936B LEU* 3.7 27.4 - - + -
937B PRO 3.4 15.0 - - - +
938B THR* 3.2 2.1 - - - -
939B GLY* 2.6 36.2 + - - +
941B PHE* 4.6 1.1 - - + -
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Residues in contact with LYS 759 (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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757B THR* 3.8 15.2 - - + +
758B ILE* 1.3 81.5 - - - +
760B LEU* 1.3 84.0 + - + +
902B TYR* 3.4 10.8 - - - -
903B SER* 3.0 52.9 + - - +
905B GLU* 3.0 44.1 + - - +
938B THR* 3.7 19.3 - - + -
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Residues in contact with LEU 760 (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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759B LYS* 1.3 93.2 - - + +
761B VAL* 1.3 74.1 + - - +
762B GLU* 4.5 7.4 - - - +
763B GLU* 5.6 9.9 - - + +
901B LYS 3.9 6.5 - - - -
902B TYR* 4.3 7.2 - - + -
938B THR* 4.4 8.4 + - + +
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Residues in contact with VAL 761 (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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760B LEU* 1.3 90.4 - - - +
762B GLU* 1.3 67.0 + - - +
901B LYS* 3.4 29.5 + - + +
902B TYR 3.6 6.5 - - - +
903B SER* 3.2 38.6 - - - +
912B GLU* 4.2 11.7 - - - +
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Residues in contact with GLU 762 (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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760B LEU* 4.5 6.0 - - - +
761B VAL* 1.3 86.4 + - - +
763B GLU* 1.3 73.0 + - - +
764B ARG* 3.3 33.4 + - + +
899B VAL 4.7 0.4 - - - -
900B LYS* 3.9 1.4 - - - +
901B LYS* 3.3 40.2 + - + +
914B GLU* 4.5 4.2 - - - +
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Residues in contact with GLU 763 (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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760B LEU* 5.6 9.8 - - + +
762B GLU* 1.3 82.4 - - - +
764B ARG* 1.3 70.0 + - - +
898B VAL* 5.9 0.9 - - + -
899B VAL 3.4 7.9 - - - -
900B LYS* 3.6 34.7 + - + -
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Residues in contact with ARG 764 (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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762B GLU* 3.3 36.6 + - + +
763B GLU* 1.3 79.1 - - - +
765B GLU* 1.3 63.3 + - - +
766B GLU* 2.9 31.3 + - - +
898B VAL* 3.5 8.8 - - - +
899B VAL* 2.8 53.9 + - + +
901B LYS* 5.4 1.4 - - - +
914B GLU* 2.7 33.7 + - - -
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Residues in contact with GLU 765 (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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764B ARG* 1.3 80.3 - - - +
766B GLU* 1.3 74.4 + - - +
896B LYS* 3.6 45.5 + - + +
897B VAL 3.3 9.6 - - - +
898B VAL* 4.5 13.3 - - + +
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Residues in contact with GLU 766 (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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764B ARG* 2.9 40.8 + - + +
765B GLU* 1.3 85.0 - - - +
767B LEU* 1.3 64.6 + - - +
768B ARG* 3.7 25.4 + - + +
895B PHE 3.6 0.3 - - - +
896B LYS* 3.0 7.6 - - - -
897B VAL* 2.7 50.7 + - + +
899B VAL* 4.2 11.0 - - + +
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Residues in contact with LEU 767 (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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766B GLU* 1.3 72.6 - - - +
768B ARG* 1.3 62.7 + - - +
769B THR 4.3 0.2 + - - -
894B PRO* 4.1 27.1 - - + +
895B PHE 3.2 7.0 - - - +
896B LYS* 3.4 36.3 - - + -
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Residues in contact with ARG 768 (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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766B GLU* 3.9 29.9 + - + +
767B LEU* 1.3 78.5 - - - +
769B THR* 1.3 62.5 + - - +
894B PRO* 3.2 7.2 - - - +
895B PHE* 2.6 70.6 + - + +
897B VAL* 4.2 12.9 - - + +
899B VAL* 5.0 5.3 - - - +
916B ILE* 4.0 20.2 - - - +
930B VAL* 3.3 24.9 - - - +
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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