Contacts of the helix formed by residues 846 - 863 (chain A) in PDB entry 6DBT
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 GLU 846 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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844A SER* 3.1 2.4 - - - -
845A ARG* 1.3 90.7 - - + +
847A GLU* 1.3 65.9 + - - +
848A ARG 3.3 1.6 - - - -
849A ARG* 3.7 34.6 + - - +
850A ARG* 3.0 30.2 + - - +
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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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840A LYS* 3.1 25.4 - - - +
842A ASN 4.6 0.2 - - - +
843A PRO* 3.2 8.5 - - + +
844A SER* 2.3 53.9 + - - +
846A GLU* 1.3 77.5 - - - +
848A ARG* 1.3 63.7 + - - +
850A ARG* 3.0 32.4 + - - +
851A TRP* 2.9 43.8 + - + -
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Residues in contact with ARG 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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831A GLN* 2.3 37.7 + - - +
832A ASP* 4.7 11.4 - - - +
843A PRO* 3.4 31.5 + - + +
844A SER 2.1 38.4 + - - -
845A ARG* 3.1 47.9 + - - +
846A GLU 3.3 0.6 - - - -
847A GLU* 1.3 77.7 - - - +
849A ARG* 1.3 60.2 + - + +
851A TRP* 3.3 18.1 + - + +
852A ARG* 2.9 17.6 + - - +
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Residues in contact with ARG 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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831A GLN* 4.5 0.4 - - - +
845A ARG* 3.3 31.3 + - - +
846A GLU* 3.3 34.4 + - - +
847A GLU 3.2 0.6 - - - -
848A ARG* 1.3 78.0 - - + +
850A ARG* 1.3 60.3 - - - +
852A ARG* 3.4 25.8 + - - +
853A SER* 2.9 28.3 + - - -
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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
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846A GLU* 3.0 13.7 + - - +
847A GLU* 3.0 47.6 + - - +
849A ARG* 1.3 76.5 - - - +
851A TRP* 1.3 95.1 + - + +
853A SER* 3.2 7.3 + - - -
854A THR* 2.9 33.9 + - + +
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Residues in contact with TRP 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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831A GLN* 3.7 20.4 - - + +
832A ASP* 5.0 5.4 - - - -
834A ILE* 3.5 27.2 + - + +
835A GLY* 3.4 31.2 - - - -
836A GLU 4.2 7.9 - - - -
840A LYS* 3.0 39.5 - - - -
843A PRO* 4.1 14.6 - - + -
847A GLU* 2.9 30.4 + - + +
848A ARG* 3.6 20.0 - - + +
849A ARG 3.3 0.2 - - - -
850A ARG* 1.3 100.0 - - + +
852A ARG* 1.3 59.9 + - - +
854A THR* 3.1 8.4 - - + +
855A LEU* 2.9 31.2 + - - +
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Residues in contact with ARG 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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827A TYR* 3.2 36.9 + - + +
831A GLN* 3.2 40.6 + - + +
848A ARG* 2.9 11.1 + - - +
849A ARG* 3.7 28.7 - - - +
851A TRP* 1.3 76.4 - - - +
853A SER* 1.3 57.7 + - - +
855A LEU* 3.7 5.2 - - + +
856A ASP* 2.9 33.2 + - + +
39F A 5.4 6.7 + - - -
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Residues in contact with SER 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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849A ARG 2.9 17.6 + - - -
850A ARG* 3.6 7.6 - - - -
851A TRP 3.2 0.2 - - - -
852A ARG* 1.3 77.3 - - - +
854A THR* 1.3 62.1 + - - +
856A ASP* 3.3 4.5 + - - +
857A LYS* 3.0 45.5 + - - +
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Residues in contact with THR 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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834A ILE* 3.7 17.7 - - + -
850A ARG* 2.9 17.3 + - + +
851A TRP* 3.1 26.5 - - + +
853A SER* 1.3 75.8 - - - +
855A LEU* 1.3 57.6 + - - +
857A LYS* 3.9 3.5 - - - +
858A GLN* 2.9 31.5 + - - +
891A LEU* 3.4 17.5 - - - +
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Residues in contact with LEU 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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827A TYR* 4.3 22.4 - - + +
830A PHE* 3.8 28.0 - - + +
831A GLN* 3.9 18.6 - - + +
834A ILE* 3.6 13.9 - - + -
851A TRP 2.9 17.5 + - - +
852A ARG* 3.7 6.1 - - - +
854A THR* 1.3 79.0 - - - +
856A ASP* 1.3 57.8 + - - +
858A GLN* 3.3 8.7 + - + +
859A LEU* 2.9 40.5 + - + +
888A VAL* 3.6 30.7 - - + -
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Residues in contact with ASP 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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827A TYR* 3.6 21.8 + - - +
852A ARG* 2.9 19.9 + - + +
853A SER* 3.3 6.2 + - - +
855A LEU* 1.3 77.1 - - - +
857A LYS* 1.3 60.7 + - + +
859A LEU* 3.4 7.7 + - - +
860A ARG* 2.9 25.0 + - - +
865A LEU 3.5 8.8 - - - +
867A PRO* 3.0 50.3 - - - +
868A VAL 4.5 1.2 + - - +
875A TYR* 5.3 3.0 + - - -
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Residues in contact with LYS 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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853A SER* 3.0 35.1 + - - +
854A THR* 4.5 3.4 - - - +
856A ASP* 1.3 75.5 - - + +
858A GLN* 1.3 59.0 + - - +
860A ARG* 3.3 26.7 + - - +
861A LYS* 2.9 27.0 + - - +
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Residues in contact with GLN 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 THR 2.9 21.1 + - - +
855A LEU* 3.4 12.8 - - + +
856A ASP 3.2 0.2 - - - -
857A LYS* 1.3 72.5 - - - +
859A LEU* 1.3 65.2 + - + +
861A LYS* 3.1 10.8 + - - +
862A LYS* 2.1 47.7 + - - +
887A ALA 2.8 21.7 + - - +
888A VAL* 4.4 2.4 - - + +
890A GLU* 2.5 38.7 + - - +
891A LEU* 3.4 36.2 - - + +
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Residues in contact with LEU 859 (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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827A TYR* 6.4 2.0 - - + -
855A LEU* 2.9 26.3 + - + +
856A ASP* 3.6 10.1 - - - +
858A GLN* 1.3 77.5 - - + +
860A ARG* 1.3 52.8 + - - +
862A LYS* 4.3 0.9 - - - +
863A MET* 2.7 61.5 + - + +
864A LYS 2.8 13.0 + - - -
865A LEU* 4.2 20.4 - - + +
875A TYR* 5.3 3.6 - - - +
879A LEU* 3.7 30.7 - - + -
884A ALA* 4.4 14.6 - - + +
887A ALA* 4.6 11.7 - - + -
888A VAL* 5.7 2.5 - - + +
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Residues in contact with ARG 860 (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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856A ASP* 2.9 15.8 + - - +
857A LYS* 3.3 27.8 - - - +
858A GLN 3.2 0.2 - - - -
859A LEU* 1.3 74.8 - - - +
861A LYS* 1.3 63.2 + - - +
864A LYS* 3.3 31.0 - - + +
865A LEU 3.8 18.1 + - - +
866A LYS* 3.6 17.2 - - - +
867A PRO* 3.5 28.1 - - - +
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Residues in contact with LYS 861 (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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857A LYS 2.9 12.9 + - - +
858A GLN* 3.1 13.7 + - - +
860A ARG* 1.3 81.0 - - - +
862A LYS* 1.3 98.3 + - - +
864A LYS* 4.4 8.1 - - - +
890A GLU* 3.9 18.4 + - - -
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Residues in contact with LYS 862 (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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858A GLN* 2.1 68.7 + - - +
859A LEU* 4.4 1.3 - - - +
861A LYS* 1.3 100.8 - - - +
863A MET* 1.3 69.1 + - + +
864A LYS* 3.7 4.5 + - - +
887A ALA* 3.4 36.6 - - + -
890A GLU* 3.2 23.1 - - + +
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Residues in contact with MET 863 (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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859A LEU* 2.7 37.2 + - + +
862A LYS* 1.3 80.0 - - + +
864A LYS* 1.3 68.0 + - - +
865A LEU* 3.6 15.9 + - + +
878A ARG* 4.1 26.7 + - - +
881A THR* 4.6 6.7 - - - -
883A GLU* 4.8 13.9 - - + -
884A ALA* 4.0 29.8 - - + -
887A ALA* 4.9 4.7 - - + -
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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