Contacts of the helix formed by residues 770 - 782 (chain A) in PDB entry 1KEK
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 GLN 770 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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681A VAL* 3.9 15.9 - - + +
682A PRO 4.6 0.9 - - - +
683A GLN* 3.0 50.7 + - - +
742A THR* 4.0 18.2 - - + -
765A GLN* 3.6 11.6 - - + +
766A PRO 3.6 12.3 - - - +
767A LEU 2.8 7.7 + - - +
769A THR* 1.3 108.7 + - - +
771A ARG* 1.3 59.6 + - - +
772A ASP 3.4 2.2 - - - -
773A ALA* 3.4 6.8 + - - +
774A GLN* 2.9 41.4 + - + +
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Residues in contact with ARG 771 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676A GLY* 5.2 2.8 + - - -
742A THR* 4.0 13.9 - - - +
743A LEU* 3.7 26.5 - - + +
767A LEU* 2.9 38.9 + - + +
768A ASP* 4.0 23.1 - - - +
769A THR 3.9 0.2 - - - -
770A GLN* 1.3 77.5 - - - +
772A ASP* 1.3 72.4 + - - +
775A VAL* 2.9 45.5 + - + +
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Residues in contact with ASP 772 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768A ASP 4.9 6.3 + - - +
770A GLN 3.4 0.8 - - - -
771A ARG* 1.3 87.8 + - - +
773A ALA* 1.3 61.3 + - - +
775A VAL* 5.4 0.2 - - - -
776A PRO* 3.3 18.7 - - - +
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Residues in contact with ALA 773 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720A ASN* 4.2 23.2 + - + +
769A THR 5.9 0.7 - - - +
770A GLN* 3.4 7.5 + - - +
771A ARG 3.2 0.2 - - - -
772A ASP* 1.3 79.1 - - - +
774A GLN* 1.3 74.4 + - - +
776A PRO* 2.9 21.3 - - - +
777A ASN* 3.5 14.7 + - - -
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Residues in contact with GLN 774 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720A ASN* 5.2 1.0 + - - +
737A ARG* 3.2 24.8 + - - +
739A GLN* 2.9 25.3 + - - +
740A ILE* 4.0 13.5 - - + +
742A THR* 3.6 27.8 - - + +
770A GLN* 2.9 33.2 + - + +
773A ALA* 1.3 88.1 - - + +
775A VAL* 1.3 58.9 + - - +
777A ASN* 3.4 9.5 + - - +
778A LEU* 2.8 31.5 + - - +
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Residues in contact with VAL 775 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742A THR* 3.8 16.6 - - - +
743A LEU* 4.0 31.4 - - + -
771A ARG* 2.9 32.3 + - + +
772A ASP* 5.4 0.2 - - - -
774A GLN* 1.3 72.8 - - - +
776A PRO* 1.3 67.4 - - + +
778A LEU* 3.5 5.6 - - - +
779A GLU* 3.0 39.8 + - + +
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Residues in contact with PRO 776 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718A PRO* 4.8 9.9 - - + +
772A ASP 3.3 18.8 - - - +
773A ALA* 2.9 18.2 - - - +
775A VAL* 1.3 97.1 - - + +
777A ASN* 1.3 61.5 + - - +
779A GLU* 3.2 8.8 + - + +
780A TYR* 2.9 29.0 + - - +
783A ARG* 5.0 0.9 + - - -
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Residues in contact with ASN 777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718A PRO* 3.3 25.1 - - - +
720A ASN* 2.7 35.3 + - - +
721A PHE* 3.5 16.8 - - + -
737A ARG* 3.4 18.0 + - - -
739A GLN* 3.2 19.3 - - - +
773A ALA 3.5 8.5 + - - +
774A GLN* 3.4 15.2 + - - +
775A VAL 3.3 0.4 - - - -
776A PRO* 1.3 76.0 - - - +
778A LEU* 1.3 55.3 + - - +
780A TYR* 3.2 2.5 + - - -
781A ALA* 2.7 36.9 + - - +
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Residues in contact with LEU 778 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674A LYS* 4.5 8.5 - - - -
705A LEU* 4.4 18.2 - - + -
739A GLN* 3.7 26.6 + - + +
740A ILE 4.3 1.8 - - - +
741A ASN* 3.8 50.3 - - + +
742A THR 5.6 0.7 - - - +
774A GLN 2.8 17.7 + - - +
775A VAL* 3.5 6.3 - - - +
777A ASN* 1.3 76.9 - - - +
779A GLU* 1.3 77.4 + - - +
781A ALA 3.3 0.2 + - - -
782A ALA* 2.8 38.5 + - + +
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Residues in contact with GLU 779 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674A LYS* 4.3 12.4 - - - +
775A VAL* 3.0 24.8 + - + +
776A PRO* 3.2 10.1 + - + +
778A LEU* 1.3 102.7 - - - +
780A TYR* 1.3 59.2 + - - +
782A ALA* 3.6 12.0 + - - +
783A ARG* 3.4 28.5 + - - +
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Residues in contact with TYR 780 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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713A GLU 2.6 30.6 + - - -
714A LEU* 3.8 2.4 - - + -
716A GLY* 3.1 44.0 + - - -
717A ALA* 3.4 26.1 + - + -
718A PRO* 4.2 13.9 - - + -
721A PHE* 4.3 7.2 - + + -
776A PRO 2.9 15.6 + - - +
777A ASN* 3.7 4.3 - - - +
779A GLU* 1.3 71.5 - - - +
781A ALA* 1.3 64.0 + - - +
782A ALA 3.1 1.6 - - - -
783A ARG* 2.9 49.8 + - - +
784A ILE* 3.6 24.9 + - + +
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Residues in contact with ALA 781 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705A LEU* 4.0 14.1 - - + +
707A VAL* 3.9 20.5 - - + +
721A PHE* 3.9 6.3 - - + -
739A GLN* 3.8 21.8 - - + -
777A ASN 2.7 22.2 + - - +
778A LEU 3.7 3.4 - - - +
780A TYR* 1.3 73.2 - - - +
782A ALA* 1.3 57.1 + - - +
784A ILE* 3.0 38.6 + - - +
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Residues in contact with ALA 782 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705A LEU* 4.3 11.4 - - + +
778A LEU* 2.8 24.6 + - + +
779A GLU* 3.8 11.4 - - - +
780A TYR 3.1 0.6 - - - -
781A ALA* 1.3 76.6 - - - +
783A ARG* 1.3 60.0 + - + +
784A ILE 3.3 4.7 + - - +
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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