Contacts of the helix formed by residues 839 - 858 (chain A) in PDB entry 1TBF
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 CYS 839 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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559A PHE* 4.2 12.6 - - - -
628A ALA* 4.4 4.5 - - - -
632A GLY* 3.8 18.8 - - - -
634A ILE* 3.8 29.6 - - - -
832A LEU* 3.9 32.0 - - + +
833A THR* 3.8 9.6 + - - +
836A SER* 2.9 15.7 + - - +
838A ASP* 1.3 74.8 - - - +
840A PHE* 1.3 63.4 + - - +
841A PRO* 3.2 5.2 - - - -
842A LEU* 3.1 22.7 + - + +
843A LEU 3.9 0.2 + - - -
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Residues in contact with PHE 840 (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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833A THR* 3.6 19.5 + - + -
837A GLU 3.1 17.7 + - - +
839A CYS* 1.3 75.6 - - - +
841A PRO* 1.3 72.1 - - + +
843A LEU* 3.0 27.3 + - + -
844A ASP* 2.9 47.7 + - + -
847A ARG* 3.5 31.2 - - - -
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Residues in contact with PRO 841 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A PHE* 3.7 31.9 - - + -
769A THR* 4.8 1.7 - - - +
838A ASP 3.4 13.5 - - - +
839A CYS 3.2 5.8 - - - -
840A PHE* 1.3 96.9 - - + +
842A LEU* 1.3 56.8 + - - +
844A ASP* 3.7 9.2 - - + +
845A GLY* 3.0 25.1 + - - -
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Residues in contact with LEU 842 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A PHE* 3.7 45.3 - - + +
624A CYS* 4.0 23.1 - - - -
628A ALA* 5.3 2.9 - - + -
762A ALA* 5.5 1.6 - - + -
766A SER* 4.5 2.0 - - - -
769A THR* 3.2 39.8 - - + +
829A TYR* 3.7 22.9 - - + -
832A LEU* 3.9 26.5 - - + -
839A CYS* 3.1 13.8 + - + +
841A PRO* 1.3 74.2 - - - +
843A LEU* 1.3 66.4 + - - +
845A GLY 3.4 0.2 + - - -
846A CYS* 3.1 19.4 + - - +
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Residues in contact with LEU 843 (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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826A LEU* 3.9 23.1 - - + +
829A TYR* 3.8 14.1 - - + +
830A GLU* 3.8 46.4 - - + +
833A THR* 3.9 18.1 + - + +
839A CYS 3.9 0.8 + - - -
840A PHE* 3.0 27.4 + - + +
842A LEU* 1.3 76.4 - - - +
844A ASP* 1.3 64.5 + - - +
846A CYS* 3.2 2.6 + - + +
847A ARG* 3.0 44.3 + - - +
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Residues in contact with ASP 844 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840A PHE* 2.9 42.1 + - + +
841A PRO* 3.7 9.2 - - + +
843A LEU* 1.3 77.3 - - - +
845A GLY* 1.3 63.0 + - - +
847A ARG* 3.3 19.4 + - - +
848A LYS* 3.0 55.6 + - - +
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Residues in contact with GLY 845 (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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769A THR* 3.3 24.7 - - - -
770A LYS 4.8 0.8 - - - +
841A PRO 3.0 14.4 + - - -
842A LEU 3.9 0.2 - - - -
844A ASP* 1.3 78.1 - - - +
846A CYS* 1.3 61.9 + - - +
848A LYS* 3.3 10.7 + - - +
849A ASN* 3.0 29.1 + - - -
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Residues in contact with CYS 846 (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 ILE* 3.6 16.8 - - - +
769A THR* 3.8 3.2 - - + +
821A ILE* 3.8 29.9 - - - +
825A CYS* 3.9 22.7 - - - -
826A LEU* 4.1 12.8 - - + -
829A TYR* 4.2 15.7 - - + -
842A LEU 3.1 13.5 + - - +
843A LEU* 3.2 9.4 + - - +
845A GLY* 1.3 76.1 - - - +
847A ARG* 1.3 57.0 + - - +
849A ASN* 3.3 3.3 + - - +
850A ARG* 2.9 26.9 + - - +
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Residues in contact with ARG 847 (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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826A LEU* 3.8 20.4 - - + -
830A GLU* 5.8 1.3 - - - -
840A PHE* 3.5 33.4 - - - -
843A LEU* 3.0 43.1 + - + +
844A ASP* 3.7 12.8 + - - +
846A CYS* 1.3 75.2 - - - +
848A LYS* 1.3 63.3 + - + +
850A ARG* 3.2 9.9 + - - +
851A GLN* 3.2 20.3 + - - +
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Residues in contact with LYS 848 (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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844A ASP* 3.0 52.4 + - - +
845A GLY* 3.7 9.2 - - - +
847A ARG* 1.3 75.5 - - + +
849A ASN* 1.3 65.7 + - - +
851A GLN* 3.3 9.5 + - - +
852A LYS* 3.1 27.6 + - + +
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Residues in contact with ASN 849 (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 ILE 2.9 29.1 + - - +
770A LYS 2.8 29.7 + - - +
772A TRP* 3.5 27.3 + - + +
775A GLN* 3.5 23.3 - - + +
821A ILE* 4.2 3.8 - - + -
845A GLY 3.0 16.6 + - - +
846A CYS 3.8 1.3 - - - +
848A LYS* 1.3 74.7 - - - +
850A ARG* 1.3 66.3 + - - +
852A LYS* 3.7 4.2 - - - +
853A TRP* 2.9 35.1 + - + -
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Residues in contact with ARG 850 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818A VAL* 3.6 25.4 - - + +
821A ILE* 3.7 29.3 - - + +
822A ASP* 2.8 41.6 + - - -
826A LEU* 4.6 10.0 - - - +
846A CYS 2.9 13.9 + - - +
847A ARG* 3.2 13.0 + - - +
849A ASN* 1.3 77.4 - - - +
851A GLN* 1.3 57.0 + - - +
853A TRP* 3.8 1.9 - - - -
854A GLN* 2.9 53.4 + - - +
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Residues in contact with GLN 851 (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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847A ARG 3.2 9.1 + - - +
848A LYS* 3.6 9.9 - - - +
849A ASN 3.2 0.4 - - - -
850A ARG* 1.3 79.1 - - - +
852A LYS* 1.3 89.3 + - - +
854A GLN* 3.5 5.5 + - - +
855A ALA* 3.0 33.5 + - - +
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Residues in contact with LYS 852 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772A TRP* 3.5 65.4 - - + +
848A LYS* 3.1 21.7 + - + +
849A ASN 3.2 3.6 + - - +
851A GLN* 1.3 92.9 + - - +
853A TRP* 1.4 62.0 + - - +
855A ALA* 3.4 6.8 + - - +
856A LEU* 3.3 23.9 + - - +
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Residues in contact with TRP 853 (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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772A TRP* 3.5 31.1 - + - -
775A GLN* 2.9 31.6 + - - +
776A GLN* 4.2 17.9 - - + -
779A ALA* 3.5 21.5 - - + -
813A ILE* 4.1 15.3 - - + -
814A PRO* 3.5 39.7 - - + +
817A GLN* 3.6 23.7 - - + +
818A VAL* 3.8 18.4 - - + -
821A ILE* 4.4 9.6 - - + -
849A ASN* 2.9 29.0 + - + +
852A LYS* 1.4 71.1 - - - +
854A GLN* 1.3 65.9 + - - +
856A LEU* 3.0 15.8 + - + +
857A ALA* 3.0 18.0 + - - +
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Residues in contact with GLN 854 (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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815A SER* 5.9 0.2 - - - -
818A VAL* 3.6 27.0 - - + +
850A ARG* 2.9 35.8 + - - +
851A GLN* 3.9 5.6 - - - +
853A TRP* 1.3 76.7 - - - +
855A ALA* 1.3 62.1 + - - +
857A ALA* 3.1 19.7 + - - +
858A GLU* 3.0 59.2 + - - +
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Residues in contact with ALA 855 (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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851A GLN* 3.0 30.3 + - - +
852A LYS* 3.7 6.3 - - - +
853A TRP 3.2 0.4 - - - -
854A GLN* 1.3 78.5 - - - +
856A LEU* 1.3 61.4 + - + +
857A ALA 3.6 0.2 + - - -
858A GLU* 3.7 19.3 + - - +
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Residues in contact with LEU 856 (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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772A TRP* 3.8 34.8 - - + -
776A GLN* 5.3 4.7 - - - +
814A PRO* 3.9 18.2 - - + +
852A LYS 3.3 7.3 + - - +
853A TRP* 3.0 23.3 + - + +
855A ALA* 1.3 76.9 - - + +
857A ALA* 1.3 60.9 + - - +
858A GLU 3.3 6.9 + - - +
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Residues in contact with ALA 857 (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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811A ASN 6.2 0.2 - - - -
814A PRO* 3.9 14.4 - - + +
815A SER* 4.0 21.8 - - - +
853A TRP 3.0 11.2 + - - +
854A GLN* 3.1 24.2 + - - +
856A LEU* 1.3 75.6 - - - +
858A GLU* 1.3 63.0 - - - +
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Residues in contact with GLU 858 (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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854A GLN* 3.0 49.0 + - - +
855A ALA* 3.7 12.3 + - - +
856A LEU 3.3 8.6 - - - +
857A ALA* 1.3 82.7 - - - +
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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
------------------------------------------------------------
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