Contacts of the helix formed by residues 819 - 835 (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 ASP 819 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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817A HIS 2.3 24.8 + - - +
818A CYS* 1.3 79.8 - - - +
820A ILE* 1.3 65.8 + - + +
822A ASN* 3.0 21.1 + - - +
823A ALA* 3.0 5.8 + - - +
876A ALA* 3.7 19.3 - - - +
877A ARG* 5.1 0.7 + - - +
880A MET* 3.4 23.2 - - - +
908A TYR* 2.6 29.0 + - - -
912A LYS* 6.1 1.3 - - - -
915A TRP* 4.8 7.4 - - + +
916A ARG* 5.3 6.7 + - - +
957A TYR* 3.6 0.8 - - - -
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Residues in contact with ILE 820 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817A HIS* 4.1 30.5 - - + +
819A ASP* 1.3 79.2 - - + +
821A GLY* 1.3 58.0 + - - +
823A ALA* 3.3 6.8 + - - +
824A THR* 2.9 29.8 + - + +
870A ARG* 5.5 6.5 - - - +
871A MET* 3.4 48.5 - - + +
872A ASN* 5.2 6.3 - - - +
876A ALA* 5.5 4.5 - - + -
957A TYR* 4.1 6.0 - - + -
37F A 5.5 16.8 - - - +
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Residues in contact with GLY 821 (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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819A ASP 3.3 0.6 - - - -
820A ILE* 1.3 79.2 - - - +
822A ASN* 1.3 62.8 + - - +
824A THR* 3.1 12.3 - - - +
825A GLU* 2.9 26.0 + - - +
955A THR* 4.4 15.6 + - - +
957A TYR* 3.9 21.2 - - - -
958A LEU* 6.1 0.9 - - - -
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Residues in contact with ASN 822 (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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818A CYS 3.5 5.8 + - - +
819A ASP* 3.0 29.3 + - - +
821A GLY* 1.3 73.6 + - - +
823A ALA* 1.3 56.9 + - - +
825A GLU* 3.3 4.5 + - - +
826A PHE* 2.9 38.7 + - + -
908A TYR* 3.8 29.0 + - + +
915A TRP* 4.8 5.4 - - - -
957A TYR* 4.0 12.4 + - - +
958A LEU* 4.7 10.0 - - + +
961A THR* 3.3 34.8 + - - +
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Residues in contact with ALA 823 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819A ASP* 3.0 16.1 + - - +
820A ILE* 3.8 6.7 - - - +
821A GLY 3.3 0.4 - - - -
822A ASN* 1.3 74.7 - - - +
824A THR* 1.3 60.8 + - - +
826A PHE* 3.2 9.2 + - - +
827A TYR* 2.9 26.2 + - - +
871A MET* 4.4 12.3 - - + -
876A ALA* 4.4 25.4 - - + -
879A LEU* 4.9 10.9 - - + +
880A MET* 4.6 13.7 - - + -
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Residues in contact with THR 824 (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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820A ILE* 2.9 16.5 + - + +
821A GLY* 3.1 22.4 - - - +
823A ALA* 1.3 77.0 - - - +
825A GLU* 1.3 58.6 + - - +
827A TYR* 3.2 12.1 - - - +
828A LYS* 3.0 48.6 + - - +
871A MET* 3.6 31.4 - - + +
955A THR* 6.0 1.3 - - - +
38F G 4.1 9.2 + - - +
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Residues in contact with GLU 825 (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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821A GLY 2.9 18.1 + - - +
822A ASN* 3.8 6.1 - - - +
823A ALA 3.2 0.2 - - - -
824A THR* 1.3 77.5 - - - +
826A PHE* 1.3 62.6 + - + +
828A LYS* 3.1 36.8 + - - +
829A ILE* 2.9 33.7 + - - +
949A ARG* 3.1 32.9 + - - -
950A TYR* 3.6 26.2 - - + +
955A THR* 4.8 12.6 + - - +
958A LEU* 5.9 3.6 - - + -
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Residues in contact with PHE 826 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822A ASN* 2.9 21.5 + - + +
823A ALA* 3.6 9.2 - - - +
825A GLU* 1.3 77.8 - - + +
827A TYR* 1.3 58.8 + - - +
829A ILE* 3.3 16.9 + - + +
830A PHE* 2.9 47.5 + + + -
879A LEU* 6.4 0.4 - - + -
880A MET* 4.9 7.4 - - + -
904A LEU* 4.6 16.8 - - + -
905A MET* 3.7 35.0 - - + -
908A TYR* 3.4 40.8 - + + -
938A PHE* 3.7 21.8 - + - -
942A LEU* 5.6 2.2 - - + -
950A TYR* 5.6 2.5 - - - -
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Residues in contact with TYR 827 (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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823A ALA 2.9 13.4 + - - +
824A THR* 3.2 16.6 - - - +
825A GLU 3.2 0.2 - - - -
826A PHE* 1.3 75.9 - - - +
828A LYS* 1.3 61.9 + - + +
830A PHE* 3.3 7.7 + - - +
831A GLN* 2.9 37.0 + - + +
852A ARG* 3.2 44.1 + - + +
855A LEU* 4.3 16.9 - - + +
856A ASP* 3.6 20.9 + - + +
859A LEU* 6.4 1.8 - - + -
868A VAL* 5.5 6.7 + - + +
871A MET* 5.6 7.2 - - + -
875A TYR* 3.6 26.9 - + - -
879A LEU* 4.2 16.3 - - + +
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Residues in contact with LYS 828 (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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824A THR* 3.0 37.5 + - - +
825A GLU* 3.1 38.4 + - - +
826A PHE 3.4 0.2 - - - -
827A TYR* 1.3 80.5 - - + +
829A ILE* 1.3 57.9 + - - +
831A GLN* 3.3 8.9 + - - +
832A ASP* 2.9 36.6 + - - +
949A ARG* 4.3 15.0 - - - +
955A THR* 5.6 2.4 + - - -
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Residues in contact with ILE 829 (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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825A GLU* 2.9 23.2 + - - +
826A PHE* 3.5 20.9 - - + +
828A LYS* 1.3 75.9 - - - +
830A PHE* 1.3 73.2 + - + +
832A ASP* 3.0 3.3 + - - -
833A GLU* 2.2 52.8 + - + +
901A LEU* 5.7 2.0 - - + -
904A LEU* 4.9 4.5 - - + -
942A LEU* 4.5 7.6 - - + -
946A PHE* 3.9 30.5 - - + -
948A TYR* 4.1 11.0 - - + +
949A ARG* 5.0 5.4 - - - +
950A TYR* 3.4 27.6 - - + +
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Residues in contact with PHE 830 (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 PHE* 2.9 30.0 + + + +
827A TYR* 3.8 5.8 - - - +
829A ILE* 1.3 87.4 - - + +
831A GLN* 1.3 57.7 + - - +
833A GLU* 3.2 6.8 + - + +
834A ILE* 2.9 31.5 + - - +
855A LEU* 3.8 17.7 - - + -
879A LEU* 5.5 7.2 - - + -
884A ALA* 4.9 2.5 - - + -
885A VAL* 3.5 32.3 - - + -
888A VAL* 3.5 41.3 - - + +
901A LEU* 4.0 29.6 - - + -
905A MET* 5.1 6.5 - - + -
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Residues in contact with GLN 831 (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* 2.9 25.0 + - - +
828A LYS* 3.6 9.8 - - - +
829A ILE 3.2 0.2 - - - -
830A PHE* 1.3 76.5 - - - +
832A ASP* 1.3 62.8 + - - +
833A GLU 3.3 0.2 - - - -
834A ILE* 3.7 3.7 + - - +
835A GLY 3.2 18.7 + - - -
848A ARG* 2.3 50.3 + - - +
851A TRP* 3.7 13.3 - - + +
852A ARG* 3.2 56.3 + - - +
855A LEU* 3.9 10.2 - - + +
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Residues in contact with ASP 832 (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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828A LYS* 2.9 19.0 + - - +
829A ILE 3.0 3.8 + - - +
831A GLN* 1.3 80.5 - - - +
833A GLU* 1.3 59.6 + - - +
835A GLY* 2.7 28.3 - - - +
836A GLU* 4.0 0.7 - - - -
837A VAL* 3.8 31.6 + - + +
838A TYR* 5.2 1.0 - - - -
848A ARG* 4.7 14.7 - - - +
851A TRP* 5.0 4.7 - - - -
948A TYR* 4.4 0.8 - - - +
949A ARG* 2.1 47.1 + - - +
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Residues in contact with GLU 833 (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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829A ILE* 2.2 47.5 + - + +
830A PHE* 3.2 10.0 + - + +
832A ASP* 1.3 78.2 - - - +
834A ILE* 1.3 60.4 + - - +
835A GLY 3.0 9.7 - - - +
836A GLU* 3.0 13.1 - - - +
838A TYR* 4.5 8.8 - - + +
888A VAL* 6.3 1.3 - - + -
892A VAL* 3.8 29.9 - - + +
893A PRO* 3.9 2.6 - - - +
897A ARG* 4.1 19.3 + - + +
901A LEU* 4.3 22.9 - - + -
946A PHE* 4.2 9.3 - - + -
948A TYR* 3.2 32.0 + - - -
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Residues in contact with ILE 834 (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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830A PHE 2.9 18.8 + - - +
831A GLN 3.9 4.5 - - - +
833A GLU* 1.3 75.8 - - - +
835A GLY* 1.3 60.5 + - - +
836A GLU* 4.2 3.5 - - - +
851A TRP* 3.5 30.6 + - + +
854A THR* 3.7 13.2 - - + -
855A LEU* 3.6 44.9 - - + +
888A VAL* 5.1 6.7 - - + -
891A LEU* 3.7 31.6 - - + -
892A VAL* 5.2 5.4 - - + +
893A PRO* 4.7 6.9 - - - +
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Residues in contact with GLY 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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831A GLN 3.2 9.1 + - - -
832A ASP 2.7 23.0 - - - +
833A GLU 3.0 4.5 - - - +
834A ILE* 1.3 80.7 - - - +
836A GLU* 1.3 73.3 + - - +
837A VAL 4.0 0.2 - - - -
851A TRP* 3.4 35.4 - - - -
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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