Contacts of the helix formed by residues 921 - 927 (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 GLY 921 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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893B ARG* 6.4 0.4 - - - -
894B PRO 5.7 0.4 - - - -
895B PHE* 4.1 11.2 - - - -
920B GLU* 1.3 81.2 - - - +
922B ARG* 1.3 60.0 + - - -
923B ALA 3.2 2.2 - - - -
924B TYR* 3.3 5.6 + - - +
925B GLU* 2.9 28.7 + - - +
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Residues in contact with ARG 922 (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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828B TYR* 3.7 38.4 + - - -
829B LEU* 4.8 5.5 + - + +
832B ASP* 3.6 32.8 + - + +
892B CYS* 3.3 25.4 - - - -
893B ARG* 5.2 6.9 + - + +
921B GLY* 1.3 72.3 - - - -
923B ALA* 1.3 58.1 + - - +
925B GLU* 3.1 35.3 + - - +
926B LEU* 2.9 63.7 + - + +
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Residues in contact with ALA 923 (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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770B PRO* 3.7 31.9 - - + -
889B ALA* 4.1 7.3 - - + +
892B CYS* 3.6 15.9 - - + -
893B ARG 3.9 13.4 + - - +
895B PHE* 4.5 10.8 - - + -
922B ARG* 1.3 80.5 - - - +
924B TYR* 1.3 56.3 + - - +
926B LEU* 3.1 6.9 + - - +
927B TYR* 2.8 32.4 + - - +
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Residues in contact with TYR 924 (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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895B PHE* 3.9 23.3 - + + +
919B ALA* 3.8 37.2 - - + -
920B GLU* 4.6 1.8 - - - -
921B GLY* 3.3 14.5 + - - +
923B ALA* 1.3 79.5 - - - +
925B GLU* 1.3 65.3 + - - +
927B TYR 3.6 11.0 - - - -
928B ARG* 3.4 67.1 + - - +
929B ALA* 4.4 2.7 - - - -
930B VAL* 3.9 31.3 + - + -
932B VAL* 3.9 15.1 - - + +
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Residues in contact with GLU 925 (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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885B ARG* 3.7 9.2 + - - -
921B GLY 2.9 13.0 + - - +
922B ARG* 3.1 45.8 + - - +
924B TYR* 1.3 85.2 - - - +
926B LEU* 1.3 61.0 + - + +
928B ARG* 4.8 6.6 + - - +
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Residues in contact with LEU 926 (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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828B TYR* 4.3 18.2 - - + +
829B LEU* 4.1 11.2 - - + -
884B PHE* 4.9 7.6 - - + -
885B ARG* 2.7 57.4 + - + +
888B MET* 3.9 25.4 - - + -
889B ALA* 4.3 9.0 - - + +
892B CYS* 4.6 1.3 - - - -
922B ARG* 2.9 56.1 + - + +
923B ALA* 3.6 4.7 - - - +
925B GLU* 1.3 77.7 - - + +
927B TYR* 1.3 58.4 + - - +
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Residues in contact with TYR 927 (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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771B LEU* 4.3 13.3 - - + +
774B TYR* 3.8 9.2 - - - -
782B ASP* 2.4 35.3 + - - -
785B ARG* 3.4 10.9 + - - -
786B ILE* 5.9 3.8 - - + -
882B LEU* 5.0 8.3 - - + -
885B ARG* 4.0 11.7 - - + +
886B ARG* 3.7 49.3 + - + -
889B ALA* 3.8 22.2 - - + +
923B ALA 2.8 18.9 + - - +
924B TYR* 3.6 9.7 - - - +
925B GLU 3.5 0.6 - - - -
926B LEU* 1.3 75.4 - - - +
928B ARG* 1.3 65.3 + - - +
929B ALA* 2.8 34.4 + - + +
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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