Contacts of the helix formed by residues 793 - 809 (chain B) in PDB entry 5TKD
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 THR 793 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726B GLU* 4.6 23.4 + - - +
729B ASN* 3.9 23.7 + - - +
730B LEU 3.3 42.4 - - - +
731B VAL* 3.7 8.5 - - + +
792B SER* 1.4 70.4 + - - +
794B ALA* 1.4 64.4 + - - +
795B MET 3.2 0.2 - - - -
796B ASP* 3.1 24.6 + - - +
797B LYS* 3.8 14.1 - - - +
859B PHE* 4.9 1.7 - - - -
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Residues in contact with ALA 794 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782B GLU* 4.6 0.4 - - - +
792B SER* 3.1 15.9 + - - +
793B THR* 1.4 80.3 + - - +
795B MET* 1.4 60.8 + - - +
797B LYS* 3.2 29.1 + - + +
798B TRP 3.7 0.2 + - - -
853B PRO* 3.9 38.8 - - + +
854B THR* 5.8 0.2 - - - -
856B ARG* 3.0 15.4 + - - -
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Residues in contact with MET 795 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731B VAL* 3.7 26.7 - - + -
733B GLY* 3.7 11.7 - - - -
764B LEU* 3.7 28.5 - - + -
778B TRP 5.0 0.5 - - - +
780B ALA* 3.8 27.8 + - + +
782B GLU* 4.0 5.4 + - + +
783B CYS* 3.7 19.5 - - - -
792B SER* 3.1 32.7 + - - +
794B ALA* 1.4 77.7 - - - +
796B ASP* 1.3 64.6 + - - +
798B TRP* 3.3 6.4 + - - +
799B GLY* 3.1 21.3 + - - -
856B ARG* 4.1 0.4 - - - +
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Residues in contact with ASP 796 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722B LEU* 4.4 13.3 - - + +
725B LEU* 5.7 0.7 - - - +
730B LEU 4.5 2.4 - - - +
731B VAL* 3.6 10.7 - - - +
732B HIS* 2.8 30.4 + - - +
733B GLY* 2.8 30.4 + - - -
735B VAL* 3.8 15.6 + - + +
793B THR* 3.1 14.9 + - - +
795B MET* 1.3 77.4 - - - +
797B LYS* 1.4 57.9 + - - +
799B GLY* 3.7 3.1 - - - +
800B PHE* 2.8 29.6 + - - +
859B PHE* 3.7 9.0 - - + -
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Residues in contact with LYS 797 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726B GLU* 3.3 28.3 - - - -
793B THR* 3.8 10.5 - - - +
794B ALA* 3.2 30.5 + - + +
796B ASP* 1.4 74.6 - - - +
798B TRP* 1.3 65.9 + - - +
800B PHE* 3.5 2.5 + - - +
801B GLY 3.0 17.8 + - - -
848B CYS* 3.3 18.7 - - - +
853B PRO 5.7 0.2 - - - +
856B ARG* 3.8 24.2 - - + +
857B PRO 3.4 28.0 - - - +
858B SER* 4.0 4.5 - - - +
859B PHE* 3.7 24.2 - - + -
862B ILE* 4.2 3.8 - - + -
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Residues in contact with TRP 798 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777B PRO 2.8 21.0 + - - -
778B TRP 3.4 19.5 - - - -
779B LEU 3.3 9.5 + - - -
780B ALA* 3.7 13.7 - - + -
781B PRO* 3.5 33.9 - - + -
794B ALA 3.7 2.4 + - - -
795B MET 3.3 9.7 + - - +
797B LYS* 1.3 76.0 - - - +
799B GLY* 1.3 65.1 + - - +
801B GLY 3.0 2.3 + - - -
802B ALA 2.9 20.1 + - - -
827B TYR* 3.6 18.6 - + - -
831B HIS 5.5 0.4 - - - -
832B ARG* 6.1 0.2 - - - -
833B LEU* 4.0 20.6 - - + -
848B CYS 3.7 8.3 - - - -
849B LEU* 3.4 49.0 - - + +
850B THR 3.5 23.6 - - - -
851B TYR* 3.9 16.4 - + - -
856B ARG* 3.7 9.9 - - - +
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Residues in contact with GLY 799 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735B VAL* 3.7 22.2 - - - +
778B TRP 3.5 19.5 + - - -
795B MET 3.1 13.5 + - - -
796B ASP* 3.4 3.6 + - - -
797B LYS 3.4 0.2 - - - -
798B TRP* 1.3 75.4 - - - +
800B PHE* 1.3 53.3 + - - +
802B ALA* 3.4 2.8 + - - +
803B THR* 2.8 38.2 + - - -
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Residues in contact with PHE 800 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715B ALA 3.7 24.5 - - - -
718B LEU* 3.6 23.3 - - + -
719B ALA* 3.8 13.9 - - + -
722B LEU* 3.8 13.0 - - + -
735B VAL* 3.9 8.1 - - - +
796B ASP 2.8 22.6 + - - +
797B LYS 3.5 4.0 - - - +
799B GLY* 1.3 73.2 - - - +
801B GLY* 1.3 58.8 + - - +
803B THR* 3.2 4.3 + - - -
804B LEU* 2.9 61.8 + - + +
844B LEU* 4.3 3.4 - - + -
848B CYS* 4.2 13.7 - - - -
859B PHE* 3.6 18.2 - + + -
862B ILE* 3.5 31.0 - - + -
866B LEU* 4.1 4.7 - - + -
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Residues in contact with GLY 801 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B LYS 3.0 14.8 + - - -
798B TRP 3.0 3.8 + - - -
800B PHE* 1.3 78.6 - - - +
802B ALA* 1.4 61.2 + - - +
804B LEU* 3.2 11.9 + - - +
805B LEU* 3.1 23.6 + - - +
845B THR* 3.8 7.1 - - - +
848B CYS* 3.9 17.3 - - - -
849B LEU* 3.9 12.1 - - - -
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Residues in contact with ALA 802 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777B PRO* 3.4 30.2 - - + +
778B TRP* 3.9 19.9 + - + +
798B TRP 2.9 14.3 + - - +
799B GLY 3.8 4.0 - - - +
801B GLY* 1.4 74.4 - - - +
803B THR* 1.4 56.8 + - - +
805B LEU* 3.3 9.6 + - - +
806B GLU* 3.0 26.9 + - - +
813B ALA* 5.4 0.7 - - - +
814B PRO* 5.2 2.8 - - - +
833B LEU* 4.6 4.3 - - + -
849B LEU* 3.5 13.2 - - + +
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Residues in contact with THR 803 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718B LEU* 4.0 6.3 - - + -
735B VAL* 3.3 7.1 + - - +
736B CYS* 3.2 22.6 + - - -
737B GLY* 3.9 13.0 - - - +
740B ILE* 3.5 33.0 - - + -
778B TRP* 3.7 1.3 - - - -
799B GLY 2.8 21.0 + - - -
800B PHE* 3.2 5.8 + - - -
802B ALA* 1.4 73.2 - - - +
804B LEU* 1.3 59.2 + - - +
806B GLU* 3.2 9.7 + - - +
807B ILE* 2.8 46.4 + - + +
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Residues in contact with LEU 804 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715B ALA* 3.8 30.5 - - + -
718B LEU* 5.5 1.6 - - + -
800B PHE* 2.9 50.7 + - + +
801B GLY* 3.4 10.3 - - - +
803B THR* 1.3 76.4 - - - +
805B LEU* 1.4 56.8 + - - +
807B ILE* 3.3 13.0 + - + +
808B CYS* 2.9 38.4 + - - -
841B LEU* 4.9 9.0 - - + -
844B LEU* 3.9 22.4 - - + -
845B THR* 3.8 20.6 - - + -
848B CYS* 6.0 0.2 - - - -
866B LEU* 5.2 2.0 - - + -
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Residues in contact with LEU 805 (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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801B GLY 3.1 16.2 + - - +
802B ALA* 3.3 8.7 + - - +
804B LEU* 1.4 74.8 - - - +
806B GLU* 1.3 58.0 + - - +
808B CYS* 3.2 5.0 + - - +
809B PHE* 2.8 46.9 + - + -
814B PRO* 4.0 18.2 - - + -
833B LEU* 3.7 27.6 - - + -
834B PRO 3.4 27.4 - - - +
835B GLU 4.3 0.2 - - - -
836B PRO* 3.7 33.4 - - + -
845B THR* 3.9 11.0 - - + -
849B LEU* 3.7 13.0 - - + -
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Residues in contact with GLU 806 (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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696B ASP* 3.5 25.7 - - + +
699B LEU* 4.8 2.0 - - + -
700B ARG* 4.7 2.1 + - - -
736B CYS 3.8 0.2 - - - -
737B GLY* 2.8 34.3 + - - -
738B ARG 4.3 0.7 + - - -
778B TRP* 2.9 31.1 + - - +
802B ALA 3.0 12.4 + - - +
803B THR* 3.2 11.0 + - - +
805B LEU* 1.3 74.0 - - - +
807B ILE* 1.4 58.6 + - + +
809B PHE 3.4 6.1 + - - -
811B GLY* 2.8 46.8 + - - +
812B GLU 3.8 1.0 + - - -
813B ALA* 4.2 25.1 - - + +
814B PRO* 4.9 0.6 - - - +
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Residues in contact with ILE 807 (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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695B LEU* 3.7 31.6 - - + -
699B LEU* 3.7 15.1 - - + +
710B TRP* 5.6 1.6 - - + -
711B LYS* 3.2 50.7 + - + +
714B VAL* 3.9 17.7 - - + -
715B ALA 5.2 2.9 - - - +
718B LEU* 5.1 3.4 - - + -
737B GLY* 5.9 0.2 - - - -
740B ILE* 4.8 1.1 - - + -
803B THR* 2.8 38.7 + - + +
804B LEU* 3.7 17.0 - - + +
806B GLU* 1.4 75.0 - - + +
808B CYS* 1.3 67.0 + - - +
810B ASP* 3.0 13.0 + - - -
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Residues in contact with CYS 808 (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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708B MET* 4.6 19.1 - - - -
711B LYS* 3.1 23.0 + - - +
804B LEU* 2.9 28.1 + - - +
805B LEU* 3.5 4.9 - - - +
807B ILE* 1.3 76.1 - - - +
809B PHE* 1.4 62.8 + - + +
810B ASP* 3.2 2.6 + - - +
836B PRO* 3.9 28.5 - - + -
837B SER* 4.7 15.3 - - - +
841B LEU* 4.4 15.7 - - - -
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Residues in contact with PHE 809 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805B LEU* 2.8 32.4 + - + +
806B GLU 4.1 0.9 - - - +
807B ILE 3.2 0.4 - - - -
808B CYS* 1.4 78.7 - - + +
810B ASP* 1.4 68.2 + - - +
811B GLY 3.3 2.0 - - - -
812B GLU* 3.2 41.3 + - + +
814B PRO* 3.9 25.1 - - + -
834B PRO* 4.4 12.1 - - + -
835B GLU 3.5 21.8 - - - -
836B PRO* 4.1 5.8 - - + -
837B SER* 3.8 30.7 - - - -
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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
------------------------------------------------------------
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