Contacts of the helix formed by residues 839 - 854 (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 PRO 839 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679B VAL* 5.6 2.2 - - + -
807B GLU* 3.4 15.3 - - - +
819B PRO* 4.6 2.7 - - + -
834B THR* 3.0 31.4 - - + +
835B MET* 3.2 41.1 - - + +
837B ASN 3.0 1.4 - - - -
838B GLY* 1.3 85.9 - - - +
840B GLU* 1.3 56.6 + - - +
841B LEU 3.4 1.8 - - - -
842B ILE* 3.5 23.6 - - + -
843B LEU* 2.5 41.1 + - + +
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Residues in contact with GLU 840 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746B TYR* 6.0 1.6 - - + -
806B ARG* 3.9 20.5 + - - +
807B GLU* 3.4 5.6 + - - +
837B ASN 3.1 13.3 + - - +
838B GLY 2.7 9.2 + - - +
839B PRO* 1.3 72.5 - - - +
841B LEU* 1.3 54.1 + - - +
843B LEU* 3.5 4.8 - - - +
844B ARG* 2.8 35.3 + - + +
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Residues in contact with LEU 841 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746B TYR* 3.7 43.5 - - + +
756B LEU* 3.9 20.0 - - + -
781B TRP* 3.6 31.4 - - + -
784B PHE* 4.2 13.0 - - + -
807B GLU* 3.0 20.0 + - - +
809B PHE* 4.4 4.9 - - + -
840B GLU* 1.3 73.2 - - - +
842B ILE* 1.3 67.3 + - - +
844B ARG* 3.2 7.0 + - + +
845B PHE* 2.9 41.8 + - + +
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Residues in contact with ILE 842 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B VAL* 4.6 2.2 - - + -
807B GLU* 3.0 17.9 + - - +
809B PHE* 3.7 39.3 - - + -
817B VAL* 3.8 18.1 - - + +
819B PRO* 3.9 17.7 - - + -
834B THR* 3.4 32.5 - - + -
839B PRO* 3.5 19.5 - - + -
841B LEU* 1.3 75.7 - - - +
843B LEU* 1.3 60.3 + - + +
845B PHE* 3.4 3.5 + - - +
846B GLN* 3.0 47.7 + - - +
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Residues in contact with LEU 843 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B VAL* 5.0 9.4 - - + -
838B GLY* 3.0 27.1 - - - +
839B PRO* 2.5 25.1 + - + +
840B GLU* 3.5 6.3 - - - +
842B ILE* 1.3 75.6 - - + +
844B ARG* 1.3 60.9 + - - +
846B GLN* 3.4 20.1 + - + +
847B LYS* 3.0 24.0 + - - +
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Residues in contact with ARG 844 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781B TRP* 3.2 58.9 - - + +
783B GLU* 2.8 41.4 + - - +
784B PHE* 5.1 4.0 - - - -
840B GLU* 2.8 18.6 + - + +
841B LEU* 3.7 8.9 - - - +
843B LEU* 1.3 73.9 - - - +
845B PHE* 1.3 64.8 + - - +
847B LYS* 3.2 6.9 + - - +
848B GLU* 3.0 30.3 + - + +
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Residues in contact with PHE 845 (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* 3.8 17.0 - - + -
774B LEU* 3.7 50.3 - - + -
777B MET* 3.8 18.4 - - + -
778B ALA* 4.1 4.9 - - + -
781B TRP* 3.5 26.0 - + - -
809B PHE* 3.9 26.0 - + - -
817B VAL* 4.0 14.4 - - + -
841B LEU* 2.9 43.7 + - + +
842B ILE 3.6 4.5 - - - +
844B ARG* 1.3 76.8 - - - +
846B GLN* 1.3 63.2 + - - +
848B GLU* 3.3 4.0 + - - +
849B LEU* 3.0 29.3 + - - +
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Residues in contact with GLN 846 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674B PHE* 4.0 7.5 - - - -
679B VAL* 3.1 40.8 - - - +
816B GLN* 5.8 2.7 - - + +
817B VAL* 3.1 41.8 + - + +
842B ILE* 3.0 27.3 + - - +
843B LEU* 3.7 14.7 - - + +
845B PHE* 1.3 77.1 - - - +
847B LYS* 1.3 63.1 + - - +
849B LEU* 3.3 4.5 + - - +
850B LYS* 2.9 25.4 + - - +
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Residues in contact with LYS 847 (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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843B LEU 3.0 17.2 + - - +
844B ARG* 3.2 6.7 + - - +
846B GLN* 1.3 76.3 - - - +
848B GLU* 1.3 64.3 + - + +
850B LYS* 3.2 9.9 + - + +
851B GLU* 3.0 51.0 + - + +
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Residues in contact with GLU 848 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777B MET* 3.2 29.9 - - + +
781B TRP* 2.8 43.3 + - + -
844B ARG* 3.0 26.1 + - + +
845B PHE 3.8 0.4 - - - +
847B LYS* 1.3 77.3 - - + +
849B LEU* 1.3 63.4 + - - +
851B GLU* 3.4 12.4 + - - +
852B ILE* 3.0 31.5 + - + +
857B ARG* 3.0 34.5 + - - +
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Residues in contact with LEU 849 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591B PHE* 4.2 28.3 - - + -
770B VAL* 4.5 6.5 - - + -
773B SER* 4.8 4.9 - - - -
774B LEU* 4.0 20.9 - - + -
777B MET* 3.6 24.9 - - + -
816B GLN* 3.3 32.1 - - + +
817B VAL* 4.2 14.6 - - + -
845B PHE 3.0 20.6 + - - +
846B GLN* 3.8 4.3 - - - +
848B GLU* 1.3 75.7 - - - +
850B LYS* 1.3 56.1 + - - +
852B ILE* 3.2 2.8 + - + +
853B GLN* 2.7 43.0 + - - +
861B TRP* 4.4 4.9 - - + -
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Residues in contact with LYS 850 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636B ALA* 6.0 4.5 - - - +
846B GLN 2.9 17.4 + - - +
847B LYS* 3.6 9.0 - - + +
849B LEU* 1.3 76.1 - - - +
851B GLU* 1.3 61.5 + - + +
853B GLN* 4.5 1.8 + - - -
854B TYR* 2.8 63.7 + - + +
856B ILE* 5.6 7.9 - - + -
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Residues in contact with GLU 851 (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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847B LYS* 3.0 46.7 + - + +
848B GLU* 3.7 12.5 - - - +
850B LYS* 1.3 80.3 - - + +
852B ILE* 1.3 61.0 + - - +
856B ILE* 2.9 55.8 + - + +
857B ARG* 3.1 33.5 + - - -
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Residues in contact with ILE 852 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591B PHE* 4.7 4.5 - - + -
777B MET* 4.3 8.3 - - + -
848B GLU* 3.0 26.0 + - - +
849B LEU* 3.7 5.2 - - - +
851B GLU* 1.3 75.9 - - - +
853B GLN* 1.3 65.8 + - + +
855B GLY* 3.4 10.4 + - - -
857B ARG* 4.0 31.3 - - + +
859B HIS* 3.6 46.7 - - + +
861B TRP* 4.1 28.5 - - + -
862B MET* 3.2 29.1 - - + +
1002B ACY 5.6 0.7 - - - +
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Residues in contact with GLN 853 (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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581B PHE* 3.4 53.9 - - + +
589B ARG* 4.6 5.9 + - - +
591B PHE* 3.4 48.5 - - + -
816B GLN* 2.8 41.2 + - - +
849B LEU* 2.7 30.1 + - - +
850B LYS* 4.1 3.0 + - - +
852B ILE* 1.3 74.3 - - + +
854B TYR* 1.3 61.5 + - + +
855B GLY 3.3 2.6 + - - -
862B MET* 3.6 15.8 - - - +
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Residues in contact with TYR 854 (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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581B PHE* 3.4 36.6 - + + -
582B LYS 4.0 21.3 - - - -
583B GLY* 3.4 22.5 - - - -
584B LYS 3.9 2.9 + - - -
589B ARG* 3.8 6.7 + - - +
633B PRO 6.1 0.2 - - - -
634B ASP* 5.8 2.9 - - - -
635B ALA 4.9 4.7 - - - -
636B ALA* 5.9 0.9 - - - -
637B GLY* 3.5 19.7 - - - -
638B THR 2.9 35.9 + - - -
850B LYS* 2.8 57.5 + - + +
853B GLN* 1.3 74.6 - - + +
855B GLY* 1.3 60.4 + - - +
856B ILE* 3.3 20.3 + - + +
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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
------------------------------------------------------------
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