Contacts of the helix formed by residues 834 - 854 (chain A) in PDB entry 1TXD
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 ASN 834 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833A SER* 1.3 80.9 + - - +
835A LEU* 1.3 64.4 + - - +
836A GLU* 3.2 4.5 - - - +
837A ASP* 3.0 31.3 + - - +
838A ILE* 3.2 11.0 + - - +
883A ALA* 2.9 38.6 + - - +
886A THR* 3.6 19.8 - - + +
887A PHE* 3.1 31.2 + - - +
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Residues in contact with LEU 835 (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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806A LEU* 4.4 11.2 - - + +
809A LEU* 3.8 43.1 - - + -
810A ASP* 3.9 23.6 - - + +
814A TYR* 4.0 21.1 - - + -
832A PHE* 2.8 30.8 + - + +
833A SER 3.3 1.2 - - - +
834A ASN* 1.3 75.1 + - - +
836A GLU* 1.3 64.2 + - - +
838A ILE* 3.3 23.9 + - + +
839A LEU* 2.9 26.9 + - + +
887A PHE* 4.0 8.6 - - + -
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Residues in contact with GLU 836 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810A ASP* 5.9 2.2 - - - -
814A TYR* 5.0 13.6 + - + -
833A SER 4.8 2.3 + - - +
834A ASN* 3.2 2.6 - - - -
835A LEU* 1.3 78.6 - - - +
837A ASP* 1.3 69.8 + - - +
839A LEU* 3.5 9.4 - - + +
840A GLN* 3.0 35.7 + - + +
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Residues in contact with ASP 837 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834A ASN* 3.0 29.7 + - + +
836A GLU* 1.3 88.9 - - - +
838A ILE* 1.3 67.5 + - - +
840A GLN* 4.2 5.1 - - - +
841A LEU* 3.0 25.8 + - - +
879A LYS* 5.7 3.0 - - - +
883A ALA* 4.9 9.1 - - + +
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Residues in contact with ILE 838 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806A LEU* 3.8 10.5 - - + +
834A ASN* 3.2 12.3 + - - +
835A LEU* 3.4 24.0 - - + +
837A ASP* 1.3 77.4 - - - +
839A LEU* 1.3 64.6 + - - +
841A LEU* 4.2 5.8 - - + -
842A HIS* 3.1 31.3 + - + +
880A LEU* 6.2 0.7 - - + -
883A ALA* 3.8 36.3 - - + +
884A ALA* 4.1 1.1 - - - +
887A PHE* 3.7 41.5 - - + -
933A GLN* 3.6 37.0 - - - +
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Residues in contact with LEU 839 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A VAL* 4.5 3.1 - - + +
806A LEU* 4.0 26.4 - - + +
807A LYS* 4.0 24.5 - - + +
810A ASP* 3.8 33.9 - - + +
835A LEU* 2.9 21.7 + - + +
836A GLU* 3.5 8.5 - - + +
838A ILE* 1.3 80.6 - - - +
840A GLN* 1.3 69.1 + - - +
842A HIS* 3.9 1.0 - - - +
843A ILE* 3.0 50.6 + - + +
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Residues in contact with GLN 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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836A GLU* 3.0 26.3 + - + +
837A ASP* 3.5 4.9 + - - +
839A LEU* 1.3 84.3 - - - +
841A LEU* 1.3 62.6 + - - +
843A ILE* 3.8 28.4 - - - +
844A GLY* 2.9 21.5 + - - -
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Residues in contact with LEU 841 (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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837A ASP 3.0 18.3 + - - +
838A ILE* 3.6 6.1 - - + +
840A GLN* 1.3 76.3 - - - +
842A HIS* 1.3 77.3 + - + +
844A GLY* 3.2 2.4 + - - -
845A LEU* 2.9 35.5 + - + +
879A LYS* 3.8 38.2 - - + +
880A LEU* 3.6 46.7 - - + +
883A ALA* 4.2 11.9 - - + -
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Residues in contact with HIS 842 (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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799A GLU* 2.7 23.4 + - - +
802A HIS* 3.5 21.8 - + + -
803A VAL* 3.3 15.1 - - + +
806A LEU* 3.8 5.8 - - + -
838A ILE* 3.1 25.5 + - + +
839A LEU 4.0 2.2 - - - +
841A LEU* 1.3 93.2 - - + +
843A ILE* 1.3 60.2 + - - +
845A LEU* 3.7 3.3 - - + +
846A ASN* 2.9 31.0 + - - +
880A LEU* 4.4 5.5 - - + +
933A GLN* 2.8 40.9 + - - -
936A ARG* 4.4 2.2 - - + -
937A LEU* 5.0 0.2 - - + -
940A TYR* 3.2 28.0 + + - -
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Residues in contact with ILE 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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803A VAL* 3.8 26.0 - - + +
807A LYS* 4.0 18.6 - - - +
839A LEU* 3.0 43.9 + - + +
840A GLN* 3.8 26.0 - - - +
842A HIS* 1.3 76.0 - - - +
844A GLY* 1.3 58.0 + - - +
846A ASN* 3.3 4.3 + - - +
847A GLU* 2.8 43.8 + - + +
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Residues in contact with GLY 844 (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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840A GLN 2.9 18.1 + - - -
841A LEU* 3.7 3.4 - - - -
843A ILE* 1.3 73.9 - - - +
845A LEU* 1.3 61.2 + - - +
847A GLU* 3.2 7.8 + - - +
848A GLN* 3.1 32.0 + - - +
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Residues in contact with LEU 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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799A GLU* 3.6 23.3 - - - +
841A LEU* 2.9 25.6 + - + +
842A HIS* 3.7 9.4 - - + +
843A ILE 3.3 0.2 - - - -
844A GLY* 1.3 75.2 - - - +
846A ASN* 1.3 58.1 + - - +
848A GLN* 3.2 12.0 + - - +
849A MET* 3.0 34.1 + - + +
871A TRP* 3.6 46.4 - - + +
872A PHE* 4.3 19.5 - - + -
880A LEU* 5.4 2.0 - - + -
940A TYR* 3.8 14.6 - - + +
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Residues in contact with ASN 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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796A PHE* 4.2 4.2 + - - +
799A GLU* 4.0 11.8 - - + +
800A ARG* 3.7 40.0 - - - +
803A VAL* 3.9 15.1 - - + +
842A HIS 2.9 19.1 + - - +
843A ILE* 3.5 6.1 - - - +
845A LEU* 1.3 76.9 - - - +
847A GLU* 1.3 59.9 + - - +
849A MET* 3.3 7.2 + - - +
850A LYS* 2.9 57.0 + - - +
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Residues in contact with GLU 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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843A ILE* 2.8 34.5 + - + +
844A GLY* 3.2 8.5 + - - +
846A ASN* 1.3 80.5 - - - +
848A GLN* 1.3 57.8 + - + +
850A LYS* 3.3 27.1 + - - +
851A ALA* 3.0 27.2 + - - +
854A LYS* 5.1 3.5 + - - -
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Residues in contact with GLN 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 GLY 3.1 12.0 + - - +
845A LEU* 3.2 22.1 + - - +
847A GLU* 1.3 74.1 - - + +
849A MET* 1.3 64.9 + - - +
851A ALA* 3.4 7.2 + - - +
852A VAL* 3.1 27.2 + - - +
870A THR* 4.9 10.1 - - - +
871A TRP* 3.4 38.7 - - - +
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Residues in contact with MET 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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795A LEU* 3.5 40.2 - - + -
796A PHE* 3.4 44.1 - - + +
799A GLU* 3.6 40.6 - - + +
845A LEU* 3.0 30.3 + - + +
846A ASN* 3.6 9.9 - - - +
847A GLU 3.2 0.2 - - - -
848A GLN* 1.3 74.7 - - - +
850A LYS* 1.3 66.3 + - - +
852A VAL* 3.1 9.9 + - - +
853A ARG* 3.4 7.6 + - - +
871A TRP* 3.5 26.9 - - + -
872A PHE* 5.1 2.0 - - + -
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Residues in contact with LYS 850 (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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796A PHE* 5.7 0.2 - - - -
800A ARG* 3.7 37.5 - - - +
846A ASN* 2.9 41.0 + - - +
847A GLU* 3.5 29.8 + - - +
849A MET* 1.3 76.9 - - - +
851A ALA* 1.3 59.7 + - - +
853A ARG* 3.2 16.8 + - - +
854A LYS* 3.2 30.4 + - - +
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Residues in contact with ALA 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 GLU 3.0 15.7 + - - +
848A GLN* 3.7 8.5 - - - +
849A MET 3.2 0.2 - - - -
850A LYS* 1.3 73.3 - - - +
852A VAL* 1.3 65.6 + - - +
853A ARG 3.1 0.4 - - - -
854A LYS* 3.2 30.9 + - + +
855A ARG* 3.3 16.6 + - - +
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Residues in contact with VAL 852 (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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796A PHE* 4.2 14.1 - - + -
848A GLN 3.1 16.0 + - - +
849A MET 3.1 8.2 + - - +
851A ALA* 1.3 77.2 - - + +
853A ARG* 1.3 59.2 + - - +
855A ARG* 3.3 46.4 + - - +
856A ASN* 5.4 0.9 - - - +
861A ILE* 4.1 27.8 - - + +
864A ILE* 4.4 3.1 - - + -
867A ASP* 3.8 27.8 - - - +
871A TRP* 3.9 13.7 - - + -
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Residues in contact with ARG 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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766A PRO 5.5 2.0 + - - -
772A LEU* 4.3 24.1 - - - +
793A ASN* 2.5 39.1 + - - +
796A PHE* 3.3 41.1 - - + +
797A TYR* 5.4 0.8 - - - +
800A ARG* 3.2 25.5 - - - +
849A MET 3.4 11.0 + - - +
850A LYS* 3.2 15.4 + - - +
851A ALA 3.1 0.4 - - - -
852A VAL* 1.3 74.5 - - - +
854A LYS* 1.3 56.1 + - - +
855A ARG 3.0 10.6 + - - -
856A ASN* 3.3 22.6 + - - +
859A SER* 4.9 10.2 - - - +
861A ILE* 4.0 22.9 - - + +
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Residues in contact with LYS 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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847A GLU* 5.1 2.8 + - - -
850A LYS* 3.2 13.4 + - - +
851A ALA* 3.2 34.4 + - + +
853A ARG* 1.3 77.4 - - - +
855A ARG* 1.3 63.0 + - - +
856A ASN* 3.3 4.9 + - - -
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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