Contacts of the helix formed by residues 768 - 782 (chain B) in PDB entry 1KT8
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 768 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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599B ARG* 3.6 2.5 - - - -
742B ASN* 3.2 22.0 - - - +
766B LEU* 2.8 12.5 + - - -
767B PRO* 1.3 73.1 - - - +
769B VAL* 1.3 60.1 + - - -
770B VAL 3.3 2.0 - - - -
771B ARG* 3.3 7.1 + - - +
772B GLN* 3.0 28.1 + - - +
900B ILP 3.4 17.3 - - - -
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Residues in contact with VAL 769 (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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591B PHE* 4.1 15.7 - - + -
592B ARG* 4.0 22.2 + - + +
595B LEU* 3.9 34.8 - - + -
596B ASN* 3.7 30.1 - - - +
599B ARG* 4.0 8.3 - - - +
767B PRO 4.5 2.0 - - - +
768B GLY* 1.3 69.2 - - - -
770B VAL* 1.3 68.1 + - + +
772B GLN* 3.3 6.6 + - - +
773B SER* 3.0 24.8 + - - -
813B THR* 5.3 3.1 - - - +
900B ILP 2.9 18.0 + - - +
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Residues in contact with VAL 770 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591B PHE* 4.9 10.5 - - + -
769B VAL* 1.3 76.6 - - + +
771B ARG* 1.3 57.0 + - - +
773B SER* 3.1 8.1 + - - -
774B LEU* 2.9 41.8 + - + +
811B SER* 3.9 6.5 - - - -
812B GLY 3.5 34.3 - - - +
813B THR* 3.8 9.6 - - - +
816B GLN* 3.4 39.9 - - - +
849B LEU* 4.5 9.4 - - + -
900B ILP 2.9 11.7 + - - +
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Residues in contact with ARG 771 (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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742B ASN* 3.5 36.3 - - - +
744B PHE* 3.6 24.8 - - + -
758B THR* 3.9 7.0 + - - +
759B PRO 3.0 28.3 + - - -
761B LEU* 3.6 34.3 - - - +
765B ILE* 3.9 7.3 - - - +
766B LEU 4.4 2.2 - - - -
767B PRO* 5.2 2.0 - - - +
768B GLY 3.3 15.5 + - - +
770B VAL* 1.3 79.5 - - - +
772B GLN* 1.3 74.5 + - - +
774B LEU 3.4 1.2 + - - -
775B LEU* 3.1 37.2 + - + +
788B GLU* 3.0 29.9 + - - +
811B SER* 3.7 13.7 + - - +
900B ILP 4.3 0.8 + - - -
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Residues in contact with GLN 772 (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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592B ARG* 4.3 7.6 - - - +
595B LEU* 4.7 11.7 - - + -
761B LEU* 5.1 6.7 - - - +
768B GLY 3.0 15.8 + - - +
769B VAL* 3.7 6.7 - - - +
770B VAL 3.3 0.2 - - - -
771B ARG* 1.3 95.5 - - - +
773B SER* 1.3 57.1 + - - +
775B LEU* 3.4 13.1 + - - +
776B ASP* 2.9 61.3 + - - +
788B GLU* 5.7 2.0 + - - -
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Residues in contact with SER 773 (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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591B PHE* 3.3 16.7 - - - -
592B ARG* 3.0 35.7 + - - +
769B VAL 3.0 13.3 + - - -
770B VAL* 3.1 10.3 + - - -
772B GLN* 1.3 77.8 - - - +
774B LEU* 1.3 59.4 + - - +
776B ASP 3.4 0.3 + - - -
777B MET* 2.9 32.6 + - - +
849B LEU* 4.8 6.3 - - - -
861B TRP* 3.5 19.3 - - - -
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Residues in contact with LEU 774 (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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744B PHE* 4.0 12.1 - - + -
756B LEU* 5.2 0.4 - - - -
770B VAL* 2.9 24.4 + - + +
771B ARG 3.9 4.0 - - - +
773B SER* 1.3 74.1 - - - +
775B LEU* 1.3 67.6 + - - +
777B MET* 3.7 2.7 - - + +
778B ALA* 2.9 27.8 + - - +
809B PHE* 3.7 30.5 - - + -
811B SER* 3.9 21.3 - - - -
817B VAL* 4.5 6.7 - - + -
845B PHE* 3.7 41.4 - - + -
849B LEU* 4.0 28.0 - - + -
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Residues in contact with LEU 775 (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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744B PHE* 3.6 25.8 - - + -
756B LEU* 5.0 3.8 - - + +
758B THR* 3.9 12.8 - - + -
771B ARG* 3.1 48.0 + - - +
772B GLN* 3.6 18.2 - - - +
774B LEU* 1.3 76.6 - - - +
776B ASP* 1.3 56.6 + - - +
778B ALA* 3.8 1.0 - - - +
779B GLN* 2.9 42.8 + - - +
786B VAL* 3.9 24.0 - - + +
787B VAL 5.2 2.9 - - - +
788B GLU* 4.0 25.1 - - + +
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Residues in contact with ASP 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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592B ARG* 3.0 33.8 + - - -
772B GLN* 2.9 39.7 + - - +
773B SER 3.6 4.9 - - - +
775B LEU* 1.3 74.5 - - - +
777B MET* 1.3 57.9 + - - +
779B GLN* 3.6 8.9 + - - +
780B THR* 2.8 32.9 + - - -
861B TRP* 3.8 7.5 + - + -
1002B ACY 3.3 15.7 - - + +
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Residues in contact with MET 777 (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 SER 2.9 20.1 + - - +
774B LEU* 3.7 4.5 - - + +
776B ASP* 1.3 73.8 - - - +
778B ALA* 1.3 64.7 + - - +
780B THR* 3.3 5.2 + - - -
781B TRP* 3.2 33.7 + - + +
845B PHE* 3.8 24.7 - - + +
848B GLU* 3.2 47.6 - - + +
849B LEU* 3.6 22.9 - - + -
852B ILE* 4.3 6.3 - - + -
861B TRP* 3.6 28.5 - - + -
1002B ACY 3.3 12.8 + - - +
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Residues in contact with ALA 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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756B LEU* 3.9 19.1 - - + -
774B LEU 2.9 18.9 + - - +
775B LEU 3.9 1.6 - - - +
777B MET* 1.3 73.6 - - - +
779B GLN* 1.3 68.6 + - - +
781B TRP* 3.3 22.2 + - + +
782B GLY* 3.4 8.7 + - - -
783B GLU 4.8 1.2 + - - -
784B PHE* 4.2 11.6 - - + +
786B VAL* 3.7 24.6 - - + +
845B PHE* 4.1 7.6 - - + -
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Residues in contact with GLN 779 (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 LEU* 2.9 29.7 + - - +
776B ASP* 3.6 8.7 + - - +
778B ALA* 1.3 76.4 - - - +
780B THR* 1.3 65.5 + - - +
782B GLY* 3.0 16.2 + - - -
786B VAL* 3.5 37.5 - - + +
788B GLU* 5.8 1.8 + - - -
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Residues in contact with THR 780 (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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776B ASP 2.8 17.4 + - - -
777B MET* 3.4 10.5 - - - +
779B GLN* 1.3 78.3 - - - +
781B TRP* 1.3 70.3 + - + +
782B GLY* 3.3 0.9 + - - -
1002B ACY 3.1 25.8 + - + +
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Residues in contact with TRP 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 MET* 3.2 22.0 + - + +
778B ALA* 3.7 13.9 - - - +
779B GLN 3.3 0.4 - - - -
780B THR* 1.3 83.9 - - + +
782B GLY* 1.3 63.8 + - - +
783B GLU* 3.2 25.2 + - + +
784B PHE* 4.2 13.9 - + + -
841B LEU* 3.6 25.1 - - + -
844B ARG* 3.2 61.5 - - + +
845B PHE* 3.5 24.2 - + - -
848B GLU* 2.8 34.9 + - + -
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Residues in contact with GLY 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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778B ALA 3.4 4.5 + - - -
779B GLN* 3.0 15.7 + - - -
780B THR 4.2 0.7 - - - -
781B TRP* 1.3 80.0 - - - +
783B GLU* 1.3 63.1 + - - +
784B PHE 3.5 6.7 - - - -
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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