Contacts of the helix formed by residues 924 - 947 (chain A) in PDB entry 6A5T
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 VAL 924 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903A MET* 3.8 17.7 - - + -
922A GLY 4.3 3.1 - - - +
923A ASP* 1.3 86.8 + - - +
925A GLU* 1.3 66.1 + - + +
926A LEU 3.0 2.2 - - - -
927A GLN* 2.9 9.2 + - + +
928A LYS* 2.9 48.9 + - + +
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Residues in contact with GLU 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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923A ASP* 2.7 19.6 + - - +
924A VAL* 1.3 75.3 - - + +
926A LEU* 1.3 56.2 + - - +
928A LYS* 3.8 21.0 + - - +
929A GLU* 3.6 22.5 + - - +
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Residues in contact with LEU 926 (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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902A LEU* 3.5 31.9 - - + -
920A ILE* 3.9 31.6 - - + -
923A ASP* 3.6 26.7 + - + +
924A VAL 3.0 0.2 - - - -
925A GLU* 1.3 77.2 - - - +
927A GLN* 1.3 64.6 + - - +
928A LYS 3.1 1.9 + - - -
929A GLU* 3.2 14.9 - - + +
930A LEU* 3.1 23.5 + - + +
985A ILE* 4.1 18.6 - - + -
986A PRO* 3.8 31.6 - - + -
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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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899A TYR* 4.2 17.0 + - - -
900A VAL 5.0 1.0 + - - -
901A ASP* 3.6 12.9 + - - +
902A LEU* 3.2 37.0 + - - +
903A MET* 4.7 12.1 - - + +
923A ASP 3.7 13.7 - - - +
924A VAL* 2.9 15.9 + - + +
926A LEU* 1.3 78.6 - - - +
928A LYS* 1.3 58.0 + - - +
930A LEU* 3.2 9.3 + - - +
931A ASN* 2.7 61.9 + - - +
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Residues in contact with LYS 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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924A VAL* 2.9 38.1 + - + +
925A GLU* 4.1 22.7 + - - +
926A LEU 3.1 0.4 - - - -
927A GLN* 1.3 74.4 - - + +
929A GLU* 1.3 65.8 + - - +
930A LEU 3.1 1.1 - - - -
931A ASN* 3.2 12.7 + - - +
932A SER* 3.0 24.6 + - - -
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Residues in contact with GLU 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 GLU 3.6 15.8 + - - +
926A LEU* 3.2 15.7 - - + +
928A LYS* 1.3 75.9 - - - +
930A LEU* 1.3 59.6 + - + +
932A SER* 2.2 28.7 + - - -
933A GLU* 2.9 12.0 + - - +
985A ILE* 5.8 0.4 - - + -
986A PRO* 5.5 6.7 - - + -
989A ILE* 3.4 41.8 - - + +
990A HIS* 3.8 27.1 + - - -
993A ARG* 4.1 14.2 + - - -
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Residues in contact with LEU 930 (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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899A TYR* 6.5 0.4 - - - -
900A VAL* 3.5 50.0 - - + +
902A LEU* 3.8 26.2 - - + -
926A LEU 3.1 9.2 + - - +
927A GLN* 3.2 15.5 + - - +
928A LYS 3.1 0.2 - - - -
929A GLU* 1.3 76.7 - - - +
931A ASN* 1.3 58.4 + - - +
933A GLU* 4.0 8.9 - - + +
934A TYR* 2.9 32.1 + - - +
985A ILE* 4.3 15.7 - - + -
989A ILE* 3.6 26.2 - - + -
1030A THR* 4.5 6.1 - - - +
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Residues in contact with ASN 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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899A TYR* 4.8 9.5 + - - -
927A GLN* 2.7 56.2 + - - +
928A LYS* 3.2 14.3 + - - +
930A LEU* 1.3 75.2 - - - +
932A SER* 1.3 64.6 + - - +
934A TYR* 3.4 4.8 + - - +
935A GLU* 3.0 27.7 + - - +
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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 LYS 3.0 11.6 + - - -
929A GLU* 2.2 31.6 + - - -
931A ASN* 1.3 76.1 - - - +
933A GLU* 1.3 59.6 + - - +
935A GLU* 3.2 6.9 + - - +
936A GLN* 2.9 28.2 + - - +
993A ARG* 3.7 19.5 + - - -
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Residues in contact with GLU 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 GLU 2.9 9.0 + - - +
930A LEU* 4.0 8.9 - - + +
932A SER* 1.3 82.8 + - - +
934A TYR* 1.3 61.4 + - - +
936A GLN* 3.2 12.2 - - + +
937A LEU* 3.0 29.2 + - + +
988A ILE* 4.9 1.2 - - - +
989A ILE* 3.0 49.1 - - + +
992A VAL* 5.2 8.5 - - - +
993A ARG* 5.6 1.8 - - - +
1025A ARG* 5.9 7.2 - - - +
1028A LEU 4.7 3.5 - - - +
1029A ALA* 4.7 8.7 - - + -
1030A THR* 3.5 21.5 + - - -
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Residues in contact with TYR 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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894A PHE* 3.2 38.6 - + - -
895A HIS* 3.8 21.2 - + - +
898A TYR* 4.5 12.3 - - + -
899A TYR* 3.9 48.0 - + + -
900A VAL 6.2 0.2 - - - +
930A LEU 2.9 18.3 + - - +
931A ASN* 3.9 5.4 - - - +
933A GLU* 1.3 75.4 - - - +
935A GLU* 1.3 71.4 + - + +
937A LEU* 3.1 11.1 + - + +
938A VAL* 2.9 42.2 + - + +
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Residues in contact with GLU 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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931A ASN 3.0 19.5 + - - +
932A SER* 3.8 4.5 - - - +
934A TYR* 1.3 80.6 - - + +
936A GLN* 1.3 63.2 + - - +
938A VAL* 2.9 26.1 + - + +
939A SER* 2.9 18.4 + - - +
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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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932A SER 2.9 14.0 + - - +
933A GLU* 3.2 17.0 - - + +
934A TYR 3.1 0.2 - - - -
935A GLU* 1.3 77.5 - - - +
937A LEU* 1.3 64.8 + - + +
939A SER* 3.2 9.3 + - - -
940A ASP* 3.0 31.1 + - - +
1025A ARG* 4.1 34.6 - - - +
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Residues in contact with LEU 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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886A THR* 4.6 15.3 + - + -
894A PHE* 4.2 15.2 - - + -
898A TYR* 3.5 44.2 - - + +
933A GLU* 3.0 17.8 + - + +
934A TYR* 3.1 12.3 + - + +
936A GLN* 1.3 77.7 - - + +
938A VAL* 1.3 64.2 + - - +
940A ASP* 3.3 15.9 + - + +
941A ARG* 2.9 24.3 + - - +
1022A CYS 5.8 0.4 - - - +
1025A ARG* 4.1 26.9 - - + +
1026A ALA 4.9 0.2 - - - +
1029A ALA* 4.5 10.1 - - + -
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Residues in contact with VAL 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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894A PHE* 5.1 5.2 - - + -
934A TYR* 2.9 47.4 + - + +
935A GLU* 2.9 22.7 + - + +
937A LEU* 1.3 76.2 - - - +
939A SER* 1.3 66.2 + - - +
941A ARG* 3.1 7.4 + - - +
942A LYS* 3.0 25.5 + - + +
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Residues in contact with SER 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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935A GLU* 2.9 13.9 + - - +
936A GLN* 3.7 15.2 - - - -
938A VAL* 1.3 77.7 - - - +
940A ASP* 1.3 60.4 + - - +
942A LYS* 3.2 8.5 + - - +
943A PHE* 2.8 32.3 + - - +
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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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886A THR* 4.8 8.1 - - + +
936A GLN* 3.0 22.4 + - - +
937A LEU* 3.3 18.9 + - + +
939A SER* 1.3 77.3 - - - +
941A ARG* 1.3 57.9 + - - +
943A PHE* 3.4 8.7 - - - +
944A LEU* 2.9 34.5 + - + +
1022A CYS* 3.1 35.0 - - + +
1025A ARG* 3.3 32.3 + - - +
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Residues in contact with ARG 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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886A THR* 3.3 25.7 + - - +
887A ILE* 5.3 0.4 - - - -
888A PRO 3.1 7.7 + - - -
889A GLY 2.2 34.6 + - - -
890A SER 4.1 1.2 + - - -
891A ASP* 3.3 16.5 + - - +
894A PHE* 3.0 55.0 - - + +
937A LEU 2.9 13.6 + - - +
938A VAL* 3.6 8.1 - - - +
940A ASP* 1.3 78.6 - - - +
942A LYS* 1.3 60.1 + - - +
944A LEU* 3.7 2.4 - - - +
945A ARG* 2.8 77.7 + - - +
1299A GLY 3.8 0.4 + - - -
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Residues in contact with LYS 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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938A VAL* 3.0 19.0 + - + +
939A SER* 3.7 7.9 - - - +
941A ARG* 1.3 75.6 - - - +
943A PHE* 1.3 57.7 + - - +
945A ARG* 4.3 4.7 - - - +
946A GLU* 2.5 75.8 + - - +
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Residues in contact with PHE 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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939A SER 2.8 17.9 + - - +
940A ASP* 3.4 7.2 - - - +
942A LYS* 1.3 75.2 - - - +
944A LEU* 1.3 85.9 + - + +
945A ARG 2.8 9.7 + - - -
947A ILE* 3.1 49.2 + - + +
948A VAL* 3.7 20.6 + - + -
1018A SER* 4.2 28.5 - - - -
1019A LEU* 5.2 0.7 - - + -
1022A CYS* 4.2 14.4 - - - -
205E GLY* 4.5 14.1 - - - -
206E ARG* 3.5 29.6 - - + -
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Residues in contact with LEU 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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884A ILE* 3.7 19.3 - - + -
886A THR* 4.6 7.2 - - - +
887A ILE* 3.5 40.0 - - + +
940A ASP* 2.9 21.5 + - + +
941A ARG* 4.3 2.7 - - - +
943A PHE* 1.3 94.5 - - + +
945A ARG* 1.3 59.1 + - - +
948A VAL* 4.7 13.9 - - + -
949A PHE* 3.5 32.1 + - + +
1019A LEU* 3.6 30.3 - - + -
1022A CYS* 4.3 13.0 - - + -
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Residues in contact with ARG 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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887A ILE* 2.1 35.5 + - + +
888A PRO 3.7 1.0 + - - -
891A ASP* 4.1 7.5 + - - -
941A ARG* 2.8 71.8 + - - +
942A LYS* 3.8 4.7 - - - +
943A PHE 2.9 0.2 - - - -
944A LEU* 1.3 82.0 - - - +
946A GLU* 1.3 67.1 + - + +
949A PHE 4.4 2.9 - - - +
950A VAL* 4.2 16.8 - - - +
1295A PRO* 5.0 11.4 - - + -
1299A GLY* 3.5 21.8 + - - -
1301A TYR* 2.7 31.2 + - + +
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Residues in contact with GLU 946 (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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942A LYS* 2.5 60.0 + - + +
945A ARG* 1.3 88.5 - - + +
947A ILE* 1.3 67.9 + - + +
950A VAL* 4.4 11.8 - - - +
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Residues in contact with ILE 947 (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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943A PHE* 3.1 40.3 + - + +
946A GLU* 1.3 83.0 - - + +
948A VAL* 1.3 80.2 + - + +
950A VAL* 3.9 6.9 - - - +
200E ARG* 3.8 20.7 - - + +
205E GLY 5.6 1.1 - - - +
206E ARG* 3.9 14.4 - - - +
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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
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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