Contacts of the helix formed by residues 924 - 945 (chain A) in PDB entry 6DBU
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 924 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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913A PRO* 4.0 16.2 - - - -
914A VAL* 4.8 3.0 - - - -
917A SER* 3.4 16.2 - - - -
920A PRO* 3.3 10.6 + - - +
923A ASP* 1.3 102.4 - - - +
925A PRO* 1.3 63.3 - - - +
926A ASP* 3.1 19.8 + - - +
927A GLN* 3.8 25.1 + - - +
928A LEU* 3.9 11.8 + - - +
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Residues in contact with PRO 925 (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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920A PRO 3.0 15.4 - - - +
921A SER* 4.1 14.1 - - - +
922A ARG* 4.0 8.5 - - - +
923A ASP 3.9 3.8 - - - +
924A CYS* 1.3 87.2 - - - +
926A ASP* 1.3 66.4 + - - +
927A GLN 3.4 0.4 - - - -
928A LEU* 3.1 18.7 + - + +
929A CYS* 3.0 24.4 + - - +
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Residues in contact with ASP 926 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910A GLN* 5.2 1.2 + - - -
924A CYS* 3.1 26.2 - - - +
925A PRO* 1.3 76.0 - - - +
927A GLN* 1.3 78.7 + - - +
929A CYS* 3.2 9.9 + - - +
930A GLN* 3.1 24.1 + - - +
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Residues in contact with GLN 927 (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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909A LEU 3.9 1.0 + - - -
910A GLN* 2.2 78.1 + - - +
913A PRO* 3.5 27.4 - - - +
914A VAL* 3.4 11.9 - - + +
924A CYS* 3.8 21.6 + - - +
925A PRO 3.4 0.2 - - - -
926A ASP* 1.3 89.0 - - - +
928A LEU* 1.3 57.2 + - - +
930A GLN* 3.3 6.0 + - - +
931A TYR* 2.8 29.6 + - - +
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Residues in contact with LEU 928 (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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914A VAL* 3.6 21.9 - - + +
920A PRO* 4.8 11.2 - - + +
921A SER* 5.2 4.7 - - - +
924A CYS 3.9 4.0 + - - +
925A PRO* 3.1 31.1 + - + +
927A GLN* 1.3 75.1 - - - +
929A CYS* 1.3 66.4 + - + +
931A TYR* 3.1 16.9 + - + +
932A SER* 4.4 1.7 + - - -
966A PRO* 5.0 16.4 - - + +
969A VAL* 3.9 32.8 - - + -
970A GLU* 5.7 1.8 - - + +
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Residues in contact with CYS 929 (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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925A PRO 3.0 11.7 + - - +
926A ASP* 3.2 8.9 + - - +
928A LEU* 1.3 79.8 - - + +
930A GLN* 1.3 70.8 + - - +
931A TYR 3.7 0.3 + - - -
932A SER* 4.6 6.2 + - - -
933A TYR* 5.3 0.7 + - - +
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Residues in contact with GLN 930 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910A GLN* 4.6 10.5 - - - +
926A ASP* 3.1 21.1 + - + +
927A GLN* 3.5 9.2 - - - +
928A LEU 3.1 0.6 - - - -
929A CYS* 1.3 85.2 - - - +
931A TYR* 1.3 54.5 + - - +
932A SER 3.3 2.9 - - - -
933A TYR* 3.1 21.0 + - + +
934A ASN* 2.7 36.2 + - + +
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Residues in contact with TYR 931 (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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911A MET* 3.3 55.3 - - + +
914A VAL* 3.7 22.7 - - + -
915A TRP* 3.8 9.0 - + - -
927A GLN 2.8 10.6 + - - +
928A LEU* 3.1 19.9 + - + +
929A CYS 3.3 0.2 - - - -
930A GLN* 1.3 77.9 - - - +
932A SER* 1.3 50.5 + - - +
934A ASN* 4.2 4.7 - - - -
935A SER* 2.5 45.0 + - - -
961A THR 2.6 27.0 + - - -
962A LEU 5.1 1.3 - - - -
965A VAL* 3.4 22.4 - - + +
966A PRO* 3.5 39.0 - - + -
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Residues in contact with SER 932 (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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928A LEU 4.4 2.1 + - - -
929A CYS 4.6 5.1 + - - -
930A GLN 3.3 1.0 - - - -
931A TYR* 1.3 80.1 - - - +
933A TYR* 1.3 57.4 + - - +
935A SER* 2.7 19.0 + - - -
936A GLN* 3.0 19.9 + - - +
966A PRO* 4.0 21.7 - - - +
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Residues in contact with TYR 933 (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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929A CYS 5.3 0.8 + - - +
930A GLN* 3.1 23.4 + - + +
932A SER* 1.3 75.6 - - - +
934A ASN* 1.3 69.5 - - + +
936A GLN* 3.2 8.8 + - + +
937A GLN* 2.3 69.4 + - + +
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Residues in contact with ASN 934 (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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907A LEU* 2.7 58.7 + - - +
910A GLN* 3.3 28.2 - - - +
911A MET* 3.6 18.1 - - + +
930A GLN* 2.7 23.7 + - + +
931A TYR* 3.9 8.1 - - - +
933A TYR* 1.3 79.3 - - + +
935A SER* 1.3 56.7 + - - +
937A GLN* 3.4 5.8 + - - +
938A PHE* 2.9 24.9 + - - +
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Residues in contact with SER 935 (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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764A VAL* 3.8 8.6 - - - +
911A MET* 3.7 24.2 - - - +
931A TYR* 2.5 35.3 + - - -
932A SER* 2.7 17.0 + - - -
934A ASN* 1.3 75.8 - - - +
936A GLN* 1.3 55.9 + - - +
938A PHE* 3.2 4.5 + - - +
939A ALA* 2.9 28.1 + - - +
962A LEU* 4.2 20.0 + - - +
966A PRO* 5.6 1.0 - - - +
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Residues in contact with GLN 936 (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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764A VAL* 2.6 37.0 - - - +
765A LEU* 5.9 4.2 - - - +
932A SER 3.0 17.7 + - - +
933A TYR* 3.2 10.5 + - + +
935A SER* 1.3 73.4 + - - +
937A GLN* 1.3 62.7 + - - +
939A ALA* 3.3 2.5 + - - +
940A ASP* 2.8 47.8 + - - +
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Residues in contact with GLN 937 (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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903A LYS* 3.7 30.6 + - - +
907A LEU* 3.7 27.9 - - + +
933A TYR* 2.3 65.5 + - + +
934A ASN* 3.7 1.3 - - - +
936A GLN* 1.3 77.4 - - - +
938A PHE* 1.3 55.6 + - - +
940A ASP* 3.3 8.7 + - - +
941A LEU* 2.9 30.8 + - - +
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Residues in contact with PHE 938 (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* 3.4 27.6 - + - -
904A LEU* 3.3 47.1 - - + -
907A LEU* 3.8 17.4 - - + +
908A TYR* 3.6 21.8 - + + -
911A MET* 4.3 11.0 - - - -
934A ASN 2.9 15.1 + - - +
935A SER* 3.4 13.0 - - - +
937A GLN* 1.3 76.1 - - - +
939A ALA* 1.3 57.5 + - - +
941A LEU* 3.2 2.8 + - - +
942A LEU* 2.9 51.7 + - + +
958A LEU* 5.2 6.3 - - + -
962A LEU* 4.5 18.8 - - + -
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Residues in contact with ALA 939 (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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763A MET* 4.4 19.0 - - + +
764A VAL* 3.6 31.6 - - + -
935A SER 2.9 16.3 + - - +
936A GLN* 3.3 4.9 + - - +
938A PHE* 1.3 78.8 - - - +
940A ASP* 1.3 60.5 + - - +
942A LEU* 3.3 6.5 + - - +
943A SER* 2.9 34.6 + - - +
962A LEU* 5.2 1.3 - - + +
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Residues in contact with ASP 940 (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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903A LYS* 6.1 1.1 - - - +
936A GLN* 2.8 40.9 + - - +
937A GLN* 3.7 8.2 - - - +
939A ALA* 1.3 73.2 - - - +
941A LEU* 1.3 57.7 + - - +
943A SER* 3.4 5.2 + - - -
944A SER* 2.9 33.4 + - - -
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Residues in contact with LEU 941 (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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900A ALA* 3.2 38.1 - - + +
903A LYS* 3.9 26.0 - - + +
904A LEU* 3.6 34.3 - - + +
907A LEU* 5.3 1.1 - - + -
937A GLN 2.9 18.5 + - - +
938A PHE 3.6 4.3 - - - +
940A ASP* 1.3 77.2 - - - +
942A LEU* 1.3 56.7 + - - +
944A SER* 3.6 7.6 - - - +
945A MET* 2.9 53.7 + - + +
946A PHE* 5.5 1.3 - - + -
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Residues in contact with LEU 942 (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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763A MET* 4.4 13.0 - - + -
826A PHE* 5.9 1.3 - - + -
829A ILE* 4.2 7.9 - - + -
904A LEU* 4.0 15.3 - - + -
938A PHE* 2.9 43.4 + - + +
939A ALA* 3.3 4.9 + - - +
941A LEU* 1.3 78.3 - - - +
943A SER* 1.3 56.8 + - - +
946A PHE* 3.1 33.5 + - + +
947A LYS* 2.9 27.0 + - - -
950A TYR* 3.5 40.5 - - + +
958A LEU* 4.4 15.9 - - + -
962A LEU* 4.9 0.7 - - + -
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Residues in contact with SER 943 (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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760A SER 5.2 0.2 + - - -
761A GLN 3.9 16.0 + - - -
763A MET* 4.7 13.3 - - - +
939A ALA* 2.9 19.3 + - - +
940A ASP* 4.0 5.4 - - - -
942A LEU* 1.3 76.9 - - - +
944A SER* 1.3 58.8 + - - +
947A LYS* 3.2 41.1 - - - +
950A TYR* 6.4 0.2 - - - -
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Residues in contact with SER 944 (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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940A ASP 2.9 22.3 + - - -
941A LEU* 3.4 14.2 + - - +
943A SER* 1.3 78.2 - - - +
945A MET* 1.3 67.1 + - - +
947A LYS* 4.9 0.7 - - - -
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Residues in contact with MET 945 (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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838A TYR* 5.2 2.1 - - - +
896A GLU* 4.1 24.0 - - + +
897A ARG* 3.1 70.0 + - - +
900A ALA* 3.6 31.6 - - + -
941A LEU* 2.9 26.7 + - + +
944A SER* 1.3 84.7 + - - +
946A PHE* 1.3 72.2 + - + +
947A LYS 3.5 1.8 + - - -
948A TYR* 4.3 5.0 + - - +
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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