Contacts of the helix formed by residues 940 - 971 (chain E) in PDB entry 6MZL
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 940 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938E SER 3.2 4.7 + - - +
939E ASP* 1.3 80.3 - - - +
941E ARG* 1.3 57.8 + - - +
942E ALA 3.1 0.7 - - - -
943E GLN* 3.0 6.1 + - - +
944E LEU* 2.4 35.7 + - - +
574G THR* 5.5 2.2 - - + -
576G THR* 5.2 14.4 - - + -
578G LEU* 6.0 1.6 - - - +
84K ALA 5.8 0.2 - - - +
85K ARG* 3.6 24.9 - - + -
86K THR* 5.6 2.9 - - + +
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Residues in contact with ARG 941 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
940E VAL* 1.3 74.7 - - - +
942E ALA* 1.3 60.8 + - - +
944E LEU* 3.5 10.2 - - - +
945E LYS* 2.9 26.3 + - - +
84K ALA* 5.5 7.9 - - + -
85K ARG* 3.8 31.7 - - + +
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Residues in contact with ALA 942 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938E SER* 5.2 3.6 - - - -
939E ASP* 3.7 24.8 - - - +
940E VAL 3.7 0.6 - - - +
941E ARG* 1.3 77.1 - - - +
943E GLN* 1.3 57.5 + - - +
945E LYS* 3.1 9.9 + - - +
946E PHE* 2.9 25.2 + - - +
85K ARG* 5.2 1.2 - - - +
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Residues in contact with GLN 943 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
939E ASP* 3.2 31.9 + - - +
940E VAL* 3.0 8.7 + - - +
942E ALA* 1.3 75.6 - - - +
944E LEU* 1.3 61.3 + - - +
946E PHE* 3.2 10.2 + - + +
947E PHE* 2.9 27.7 + - - +
573G GLN* 4.4 5.9 + - - +
574G THR* 4.1 19.7 - - + +
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Residues in contact with LEU 944 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
940E VAL 2.4 29.1 + - - +
941E ARG* 3.5 12.1 - - - +
942E ALA 3.2 0.2 - - - -
943E GLN* 1.3 70.1 - - - +
945E LYS* 1.3 57.0 + - - +
947E PHE* 3.3 8.1 + - - +
948E GLU* 2.8 26.6 + - - +
578G LEU* 5.7 9.4 - - + -
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Residues in contact with LYS 945 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941E ARG 2.9 15.3 + - - +
942E ALA* 3.4 11.9 - - - +
944E LEU* 1.3 75.9 - - - +
946E PHE* 1.3 57.7 + - - +
948E GLU* 3.3 9.8 + - - +
949E GLN* 2.8 26.3 + - - +
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Residues in contact with PHE 946 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942E ALA 2.9 12.9 + - - +
943E GLN* 3.2 13.4 + - + +
945E LYS* 1.3 75.2 - - - +
947E PHE* 1.3 60.9 + - - +
949E GLN* 3.1 9.4 + - - +
950E LEU* 2.9 27.0 + - - +
573G GLN* 5.2 1.8 - - - +
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Residues in contact with PHE 947 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
943E GLN 2.9 10.4 + - - +
944E LEU* 3.6 10.1 - - - +
946E PHE* 1.3 73.9 - - - +
948E GLU* 1.3 59.2 + - - +
950E LEU* 3.4 8.0 + - - +
951E ASP* 2.8 30.5 + - - +
573G GLN* 3.4 27.7 - - - +
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Residues in contact with GLU 948 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
944E LEU 2.8 14.7 + - - +
945E LYS* 3.3 14.6 - - + +
946E PHE 3.2 0.2 - - - -
947E PHE* 1.3 76.2 - - - +
949E GLN* 1.3 57.7 + - - +
951E ASP* 3.7 6.4 - - - +
952E GLN* 2.8 30.2 + - - +
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Residues in contact with GLN 949 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
945E LYS 2.8 13.1 + - - +
946E PHE* 3.1 12.7 + - - +
948E GLU* 1.3 74.2 - - - +
950E LEU* 1.3 59.9 + - - +
952E GLN* 3.2 7.6 + - - +
953E ILE* 2.9 28.4 + - - +
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Residues in contact with LEU 950 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946E PHE 2.9 14.0 + - - +
947E PHE* 3.6 11.2 - - - +
949E GLN* 1.3 77.0 - - - +
951E ASP* 1.3 57.5 + - - +
953E ILE* 3.3 8.1 + - - +
954E GLU* 2.9 27.6 + - - +
573G GLN* 6.1 0.7 - - - +
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Residues in contact with ASP 951 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
947E PHE 2.8 17.7 + - - +
948E GLU* 3.8 7.4 - - - +
950E LEU* 1.3 73.0 - - - +
952E GLN* 1.3 60.1 + - - +
954E GLU* 3.7 6.4 - - - +
955E LYS* 2.8 31.0 + - - +
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Residues in contact with GLN 952 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948E GLU 2.8 19.0 + - - +
949E GLN* 3.2 8.7 + - - +
951E ASP* 1.3 73.6 - - - +
953E ILE* 1.3 60.3 + - - +
955E LYS* 3.9 5.6 - - - +
956E GLN* 2.9 31.4 + - - +
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Residues in contact with ILE 953 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
949E GLN 2.9 14.0 + - - +
950E LEU* 3.3 10.5 + - - +
952E GLN* 1.3 77.6 - - - +
954E GLU* 1.3 57.4 + - - +
956E GLN* 3.4 6.1 + - - +
957E ARG* 2.9 28.6 + - - +
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Residues in contact with GLU 954 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
950E LEU 2.9 15.9 + - - +
951E ASP* 3.9 7.2 - - - +
952E GLN 3.3 0.2 - - - -
953E ILE* 1.3 76.7 - - - +
955E LYS* 1.3 57.7 + - - +
957E ARG* 3.3 9.5 + - - +
958E LYS* 2.8 27.4 + - - +
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Residues in contact with LYS 955 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951E ASP 2.8 22.4 + - - +
952E GLN* 3.9 5.4 - - - +
954E GLU* 1.3 70.9 - - - +
956E GLN* 1.3 60.6 + - - +
958E LYS* 3.2 8.0 + - - +
959E ASP* 2.9 28.8 + - - +
109M PRO* 5.6 11.2 - - + -
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Residues in contact with GLN 956 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
952E GLN 2.9 18.7 + - - +
953E ILE* 3.7 6.1 - - - +
955E LYS* 1.3 75.2 - - - +
957E ARG* 1.3 59.4 + - - +
959E ASP* 3.5 6.5 + - - +
960E GLU* 2.8 29.7 + - - +
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Residues in contact with ARG 957 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953E ILE 2.9 18.1 + - - +
954E GLU* 3.4 9.6 - - - +
955E LYS 3.2 0.2 - - - -
956E GLN* 1.3 78.1 - - - +
958E LYS* 1.3 56.1 + - - +
960E GLU* 3.4 7.9 + - - +
961E GLN* 2.8 28.1 + - - +
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Residues in contact with LYS 958 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
954E GLU 2.8 16.7 + - - +
955E LYS* 3.2 9.6 + - - +
957E ARG* 1.3 75.2 - - - +
959E ASP* 1.3 60.0 + - - +
961E GLN* 3.2 8.7 + - - +
962E GLU* 2.9 26.7 + - - +
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Residues in contact with ASP 959 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
955E LYS 2.9 16.1 + - - +
956E GLN* 3.9 6.5 - - - +
958E LYS* 1.3 73.5 - - - +
960E GLU* 1.3 59.4 + - - +
962E GLU* 3.3 9.2 + - - +
963E ARG* 2.9 28.1 + - - +
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Residues in contact with GLU 960 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956E GLN 2.8 19.4 + - - +
957E ARG* 3.6 8.5 - - - +
958E LYS 3.3 0.2 - - - -
959E ASP* 1.3 75.7 - - - +
961E GLN* 1.3 57.2 + - - +
963E ARG* 3.4 8.1 + - - +
964E GLU* 2.8 28.6 + - - +
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Residues in contact with GLN 961 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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957E ARG 2.8 19.3 + - - +
958E LYS* 3.2 9.6 + - - +
960E GLU* 1.3 73.3 - - - +
962E GLU* 1.3 60.8 + - - +
964E GLU* 3.4 8.3 - - - +
965E ILE* 2.9 29.6 + - - +
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Residues in contact with GLU 962 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958E LYS 2.9 13.5 + - - +
959E ASP* 3.4 13.0 - - - +
961E GLN* 1.3 76.5 - - - +
963E ARG* 1.3 56.5 + - - +
965E ILE* 3.3 6.8 + - - +
966E LEU* 2.9 27.8 + - - +
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Residues in contact with ARG 963 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
959E ASP 2.9 16.9 + - - +
960E GLU* 3.7 8.5 - - - +
962E GLU* 1.3 75.7 - - - +
964E GLU* 1.3 57.2 + - - +
966E LEU* 3.3 8.8 + - - +
967E MET* 2.8 29.1 + - - +
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Residues in contact with GLU 964 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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960E GLU 2.8 18.0 + - - +
961E GLN* 3.4 11.0 - - - +
962E GLU 3.2 0.4 - - - -
963E ARG* 1.3 75.0 - - - +
965E ILE* 1.3 59.8 + - - +
967E MET* 3.3 7.0 + - - +
968E ARG* 2.8 29.0 + - - +
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Residues in contact with ILE 965 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961E GLN 2.9 16.2 + - - +
962E GLU* 3.8 6.3 - - - +
964E GLU* 1.3 75.9 - - - +
966E LEU* 1.3 58.4 + - - +
968E ARG* 3.3 8.7 + - - +
969E ALA* 2.9 27.0 + - - +
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Residues in contact with LEU 966 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962E GLU 2.9 17.7 + - - +
963E ARG* 3.5 10.5 - - - +
964E GLU 3.2 0.2 - - - -
965E ILE* 1.3 77.7 - - - +
967E MET* 1.3 55.4 + - - +
969E ALA* 3.4 10.0 - - - +
970E ALA* 2.8 23.7 + - - +
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Residues in contact with MET 967 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963E ARG 2.8 17.5 + - - +
964E GLU* 3.7 7.0 - - - +
965E ILE 3.3 0.4 - - - -
966E LEU* 1.3 73.9 - - - +
968E ARG* 1.3 56.8 + - - +
969E ALA 3.2 0.2 - - - -
970E ALA* 3.0 10.8 + - + +
971E LYS* 2.4 34.9 + - - +
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Residues in contact with ARG 968 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964E GLU 2.8 17.6 + - - +
965E ILE* 3.5 9.4 - - - +
967E MET* 1.3 73.9 - - - +
969E ALA* 1.3 63.0 + - - +
971E LYS* 3.3 24.9 + - - +
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Residues in contact with ALA 969 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
965E ILE 2.9 14.6 + - - +
966E LEU* 3.4 12.8 - - - +
968E ARG* 1.3 76.8 - - - +
970E ALA* 1.3 56.2 + - - +
971E LYS 3.1 12.0 - - - +
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Residues in contact with ALA 970 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
966E LEU 2.8 15.6 + - - +
967E MET* 3.0 13.2 + - + +
969E ALA* 1.3 74.1 - - - +
971E LYS* 1.3 62.6 + - - +
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Residues in contact with LYS 971 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967E MET 2.4 23.8 + - - +
968E ARG* 3.3 19.5 - - - +
969E ALA 3.1 14.5 - - - +
970E ALA* 1.3 76.0 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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