Contacts of the helix formed by residues 925 - 949 (chain B) in PDB entry 6IEH
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 THR 925 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923B LYS 4.1 0.8 + - - -
924B LEU* 1.3 76.4 - - - +
926B GLU* 1.3 66.1 + - - +
927B GLN* 4.2 7.0 + - - +
928B LEU* 3.0 21.7 + - - +
929B ALA 3.1 5.5 + - - -
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Residues in contact with GLU 926 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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924B LEU 3.5 3.0 + - - -
925B THR* 1.3 73.4 - - - +
927B GLN* 1.3 55.0 + - - +
929B ALA* 4.4 4.9 - - - +
930B GLY* 2.6 35.3 + - - +
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Residues in contact with GLN 927 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901B SER* 4.7 12.8 + - - +
904B GLN* 4.3 10.5 - - + +
925B THR* 3.0 8.1 + - - +
926B GLU* 1.3 76.8 - - - +
928B LEU* 1.3 58.3 + - - +
931B PRO* 3.2 22.2 - - - +
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Residues in contact with LEU 928 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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904B GLN* 5.5 5.8 - - - +
907B ALA* 5.6 4.5 - - + -
924B LEU* 4.3 12.6 - - + -
925B THR* 3.0 14.4 + - - +
927B GLN* 1.3 79.0 - - - +
929B ALA* 1.3 58.2 + - - +
931B PRO* 3.2 13.9 - - - +
932B LEU 3.8 1.4 + - - -
967B MET* 3.5 39.9 - - + +
968B ASP* 5.6 3.4 - - - -
971B TYR* 5.5 9.6 - - + -
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Residues in contact with ALA 929 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924B LEU* 3.8 25.8 - - + +
925B THR 3.1 10.4 + - - +
926B GLU* 3.6 2.9 - - - +
928B LEU* 1.3 74.3 - - - +
930B GLY* 1.3 67.5 + - - +
931B PRO 3.3 1.1 - - - -
932B LEU* 3.4 21.3 - - + +
933B ARG* 3.3 17.5 + - - +
967B MET* 5.2 1.3 - - - -
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Residues in contact with GLY 930 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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926B GLU* 2.6 23.1 + - - +
929B ALA* 1.3 74.6 - - - +
931B PRO* 1.3 63.5 - - - +
933B ARG* 3.2 8.4 - - - +
934B GLN* 3.2 27.9 + - - +
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Residues in contact with PRO 931 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896B LEU* 5.0 0.8 - - + +
900B LEU* 4.3 20.9 - - + -
904B GLN* 4.9 8.3 - - + -
908B LEU* 3.4 33.7 - - + +
927B GLN 3.2 23.1 - - - +
928B LEU 3.2 8.5 - - - +
930B GLY* 1.3 91.4 - - - +
932B LEU* 1.3 54.1 + - - +
933B ARG 3.2 0.7 - - - -
934B GLN* 3.4 14.5 - - + +
935B MET* 2.6 37.6 + - - +
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Residues in contact with LEU 932 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685B PRO* 6.5 0.7 - - + -
908B LEU* 4.5 5.1 - - + +
911B CYS* 5.3 4.7 - - - -
928B LEU 3.8 4.1 + - - +
929B ALA* 3.4 26.4 + - + +
931B PRO* 1.3 83.5 - - - +
933B ARG* 1.3 60.6 + - - +
935B MET* 3.6 14.5 + - + +
936B GLN* 3.4 20.8 + - + +
964B PRO* 4.5 20.4 - - + -
967B MET* 3.9 21.8 - - + -
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Residues in contact with ARG 933 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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929B ALA 3.3 7.2 + - - +
930B GLY* 3.2 12.9 + - - +
931B PRO 3.2 0.2 - - - -
932B LEU* 1.3 79.6 - - - +
934B GLN* 1.3 64.4 + - + +
936B GLN* 3.5 10.4 + - - +
937B GLU* 3.7 11.8 + - - +
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Residues in contact with GLN 934 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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894B ASN* 5.5 2.6 - - - +
896B LEU* 3.8 34.9 + - + +
900B LEU* 5.0 7.1 - - - +
930B GLY 3.2 10.7 + - - +
931B PRO* 3.0 20.5 + - + +
933B ARG* 1.3 81.7 - - + +
935B MET* 1.3 65.2 + - - +
937B GLU* 3.6 5.8 + - - +
938B CYS* 3.4 17.3 + - - +
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Residues in contact with MET 935 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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887B LEU* 4.3 7.9 - - + +
891B MET* 3.1 35.4 - - + -
896B LEU* 4.3 2.2 - - + +
908B LEU* 4.4 15.7 - - + -
911B CYS* 4.9 6.1 - - + -
912B PHE* 3.1 39.7 - - + -
931B PRO 2.6 17.2 + - - +
932B LEU* 3.8 18.8 - - + +
934B GLN* 1.3 73.0 - - - +
936B GLN* 1.3 66.5 + - - +
938B CYS* 3.0 6.6 + - - +
939B ALA* 2.7 29.2 + - - +
959B LEU 6.0 0.2 - - - +
962B PHE* 4.1 33.0 - - + -
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Residues in contact with GLN 936 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686B ASN 5.5 6.3 - - - +
932B LEU* 3.4 16.5 + - + +
933B ARG* 4.1 4.9 - - - +
934B GLN 3.3 1.0 - - - -
935B MET* 1.3 86.8 - - + +
937B GLU* 1.3 56.5 + - - +
939B ALA* 3.5 7.8 - - - +
940B LYS* 2.7 28.9 + - - +
959B LEU* 5.4 12.6 - - + +
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Residues in contact with GLU 937 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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933B ARG 3.7 8.8 + - - +
934B GLN* 3.6 9.3 + - - +
935B MET 3.2 0.2 - - - -
936B GLN* 1.3 74.6 - - - +
938B CYS* 1.3 58.5 + - - +
940B LYS* 2.9 9.5 + - - +
941B ARG* 2.9 28.5 + - - +
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Residues in contact with CYS 938 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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887B LEU* 4.1 11.6 - - + +
890B GLU* 4.7 10.1 - - - -
891B MET* 4.1 31.9 - - + -
894B ASN* 4.7 16.2 - - - +
896B LEU* 5.2 2.2 - - + -
934B GLN 3.4 9.9 + - - +
935B MET* 3.0 11.8 + - - +
937B GLU* 1.3 79.9 - - - +
939B ALA* 1.3 60.6 + - - +
941B ARG* 3.5 14.6 + - - +
942B ILE* 3.5 19.0 + - - +
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Residues in contact with ALA 939 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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887B LEU* 3.8 26.8 - - + +
935B MET* 2.7 21.2 + - - +
936B GLN* 3.5 9.9 - - - +
938B CYS* 1.3 72.8 - - - +
940B LYS* 1.3 62.7 + - - +
942B ILE* 3.4 1.3 + - - -
943B ALA* 3.2 17.0 + - - +
958B TYR* 3.4 26.7 - - + -
959B LEU* 5.1 8.5 - - - -
962B PHE* 4.4 9.0 - - + -
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Residues in contact with LYS 940 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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936B GLN 2.7 21.0 + - - +
937B GLU* 2.9 10.3 + - - +
939B ALA* 1.3 75.9 - - - +
941B ARG* 1.3 57.2 + - - +
942B ILE 3.4 0.2 - - - -
943B ALA* 3.5 7.8 - - - +
944B LYS* 3.1 24.4 + - - +
955B GLU* 6.0 1.7 - - + +
959B LEU* 5.8 3.3 - - - +
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Residues in contact with ARG 941 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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937B GLU 2.9 10.2 + - - +
938B CYS* 3.6 13.5 - - - +
939B ALA 3.2 0.2 - - - -
940B LYS* 1.3 74.5 - - - +
942B ILE* 1.3 68.4 + - + +
944B LYS* 3.2 9.0 + - - +
945B VAL* 3.2 24.6 + - - +
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Residues in contact with ILE 942 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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857B VAL* 5.8 0.4 - - + -
861B LEU* 3.9 30.3 - - + -
886B LEU* 4.5 20.0 - - + +
887B LEU* 4.8 16.2 - - + -
890B GLU* 4.7 13.5 - - + -
938B CYS* 3.5 15.2 + - - +
939B ALA 3.4 8.3 + - - +
941B ARG* 1.3 78.4 - - + +
943B ALA* 1.3 62.6 + - - +
945B VAL* 3.2 8.7 + - + +
946B SER* 2.9 33.9 + - - +
958B TYR* 4.1 24.2 - - + +
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Residues in contact with ALA 943 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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939B ALA 3.2 10.9 + - - +
940B LYS* 3.5 14.1 - - - +
942B ILE* 1.3 81.2 - - - +
944B LYS* 1.3 63.3 + - - +
946B SER* 3.4 6.8 + - - +
947B ALA* 3.2 23.0 + - - +
953B ILE* 4.7 7.8 - - + +
954B ASP 5.9 0.2 - - - -
955B GLU* 4.7 20.4 - - + +
958B TYR* 4.1 21.1 - - + -
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Residues in contact with LYS 944 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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940B LYS 3.1 13.9 + - - +
941B ARG* 3.2 14.3 + - - +
943B ALA* 1.3 76.6 - - - +
945B VAL* 1.3 66.1 + - + +
947B ALA* 3.5 4.7 + - - +
948B GLU* 3.2 31.9 + - - +
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Residues in contact with VAL 945 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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857B VAL* 4.3 17.6 - - + +
860B ARG* 5.5 12.6 - - + -
861B LEU* 3.6 32.3 - - + -
941B ARG 3.2 9.6 + - - +
942B ILE* 3.2 18.6 - - - +
944B LYS* 1.3 77.2 - - + +
946B SER* 1.3 64.5 + - - +
948B GLU* 3.3 20.3 + - + +
949B ALA* 3.1 22.7 + - - +
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Residues in contact with SER 946 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567B TYR* 4.6 4.2 + - - -
857B VAL* 4.2 16.6 - - - +
886B LEU* 5.9 0.5 - - - +
942B ILE* 2.9 25.0 + - - +
943B ALA* 3.9 6.7 - - - -
944B LYS 3.4 0.4 - - - -
945B VAL* 1.3 75.6 - - - +
947B ALA* 1.3 64.8 + - - +
949B ALA* 3.1 11.4 + - - +
950B LYS 3.4 0.2 + - - -
951B LEU* 3.4 33.7 + - - +
953B ILE* 4.0 18.4 - - - -
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Residues in contact with ALA 947 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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943B ALA 3.2 14.4 + - - +
944B LYS* 3.9 5.2 - - - +
945B VAL 3.2 0.2 - - - -
946B SER* 1.3 78.8 - - - +
948B GLU* 1.3 57.6 + - + +
950B LYS* 3.1 19.2 + - - -
951B LEU 4.2 4.5 + - - +
953B ILE* 4.0 18.8 - - + +
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Residues in contact with GLU 948 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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856B ARG* 5.3 3.6 + - - -
860B ARG* 5.9 1.8 + - - -
944B LYS* 3.2 21.7 - - - +
945B VAL* 3.4 25.0 - - + +
947B ALA* 1.3 76.2 - - + +
949B ALA* 1.3 57.5 + - - +
950B LYS* 3.2 5.7 + - - +
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Residues in contact with ALA 949 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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853B CYS* 3.4 24.4 - - - +
856B ARG* 4.2 26.9 - - + +
857B VAL* 3.5 33.2 - - + -
860B ARG* 6.3 0.9 - - + -
945B VAL 3.1 6.1 + - - +
946B SER 3.1 6.0 + - - +
948B GLU* 1.3 73.8 - - - +
950B LYS* 1.3 67.6 - - - +
951B LEU* 3.4 3.0 + - + -
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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) + - + + + + + -
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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