Contacts of the helix formed by residues 917 - 937 (chain B) in PDB entry 3H2V
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 ASN 917 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059A VAL* 4.8 1.0 - - - +
912B TRP* 5.2 0.2 - - - +
913B SER 4.2 5.1 + - - +
914B SER 3.1 15.8 + - - +
915B LYS 4.6 0.2 - - - +
916B GLY* 1.3 75.0 - - - +
918B ASP* 1.3 63.1 + - - +
919B ILE* 3.0 25.3 + - - +
920B ILE* 3.0 35.0 + - + +
921B ALA* 3.3 7.1 + - - +
1056B LEU* 3.2 15.8 - - + +
1057B ARG 3.2 27.4 + - - +
1058B TRP* 3.4 26.7 - - - -
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Residues in contact with ASP 918 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1057A ARG* 3.4 41.4 + - - +
1059A VAL* 3.6 16.6 - - - +
914B SER 5.2 1.0 - - - +
916B GLY 4.1 0.4 - - - -
917B ASN* 1.3 71.3 - - - +
919B ILE* 1.3 59.8 + - - +
920B ILE 3.2 0.2 - - - -
921B ALA* 3.7 13.5 - - + +
922B ALA* 2.8 32.2 + - - +
925B ARG* 4.7 6.1 + - - +
963B ARG* 5.2 4.7 + - - -
964B LEU* 3.4 26.3 - - + +
1056B LEU* 3.4 7.5 - - + +
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Residues in contact with ILE 919 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
917B ASN* 3.0 12.7 + - - +
918B ASP* 1.3 79.8 - - - +
920B ILE* 1.3 55.1 + - - +
922B ALA* 3.6 5.4 - - - +
923B ALA* 3.0 27.4 + - - +
961B VAL* 4.0 24.5 - - + +
964B LEU* 3.7 16.4 - - + -
965B ALA* 3.9 31.0 - - + +
968B VAL* 4.9 0.2 - - + -
1037B THR* 4.6 1.8 - - + -
1038B VAL* 4.0 26.0 - - + -
1041B ALA* 4.3 12.8 - - + -
1056B LEU* 3.3 23.6 - - + -
1058B TRP* 4.5 12.1 - - + -
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Residues in contact with ILE 920 (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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909B ALA* 3.3 30.5 - - + +
912B TRP* 3.7 24.9 - - + +
913B SER 4.4 4.5 - - - +
914B SER* 4.4 3.4 - - - +
917B ASN* 3.0 31.6 + - + +
918B ASP 3.2 0.4 - - - -
919B ILE* 1.3 77.4 - - + +
921B ALA* 1.3 65.9 + - - +
923B ALA* 3.4 3.4 + - - +
924B LYS* 2.9 42.3 + - - +
1038B VAL* 4.2 11.4 - - + -
1058B TRP* 3.4 31.4 - - + -
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Residues in contact with ALA 921 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1057A ARG* 6.2 1.3 - - - -
914B SER* 4.5 18.5 + - - +
917B ASN 3.3 5.9 + - - +
918B ASP* 3.7 24.9 - - - +
920B ILE* 1.3 80.8 - - - +
922B ALA* 1.3 60.8 + - - +
924B LYS* 3.5 5.3 + - - +
925B ARG* 3.1 37.9 + - - +
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Residues in contact with ALA 922 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918B ASP 2.8 21.9 + - - +
919B ILE* 3.6 1.3 - - - +
921B ALA* 1.3 70.7 - - - +
923B ALA* 1.3 61.0 + - - +
925B ARG* 3.0 28.6 + - - +
926B MET* 2.8 31.9 + - - +
957B ALA* 3.9 9.5 - - - +
960B GLU* 5.1 6.3 - - + -
961B VAL* 3.5 27.8 - - + +
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Residues in contact with ALA 923 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905B LEU* 3.4 20.7 - - + +
909B ALA* 4.0 18.2 - - + -
919B ILE 3.0 18.6 + - - +
920B ILE* 3.8 3.8 - - - +
922B ALA* 1.3 75.7 - - - +
924B LYS* 1.3 64.1 + - - +
926B MET* 3.3 3.5 + - - -
927B ALA* 2.8 21.9 + - - +
961B VAL* 4.6 1.0 - - - +
1034B VAL* 4.4 20.2 - - + -
1038B VAL* 4.4 11.2 - - + -
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Residues in contact with LYS 924 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1051A ASP* 3.1 19.8 + - - +
906B HIS* 4.5 19.4 - - + +
909B ALA* 3.1 34.1 - - + -
910B ARG* 4.1 7.6 - - - +
912B TRP 3.0 21.6 + - - -
914B SER* 2.8 28.2 + - - +
920B ILE* 2.9 25.9 + - - +
921B ALA* 3.8 5.6 - - - +
923B ALA* 1.3 75.0 - - - +
925B ARG* 1.3 58.9 + - - +
927B ALA* 3.3 6.2 + - - +
928B LEU* 3.0 39.4 + - + +
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Residues in contact with ARG 925 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915A LYS* 4.3 19.0 - - - +
918B ASP* 4.7 6.7 + - - +
921B ALA* 3.1 22.3 + - - +
922B ALA* 3.0 42.5 + - - +
924B LYS* 1.3 73.2 - - - +
926B MET* 1.3 60.0 + - - +
928B LEU* 3.1 12.9 + - + +
929B LEU* 2.9 39.4 + - + +
956B LYS 5.6 0.4 - - - -
957B ALA* 4.2 20.6 - - + +
960B GLU* 5.5 7.1 - - - +
69F ASP* 4.3 25.2 - - + +
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Residues in contact with MET 926 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905B LEU* 4.0 5.6 - - + -
922B ALA 2.8 13.8 + - - +
923B ALA* 3.7 7.0 - - - +
925B ARG* 1.3 69.0 - - - +
927B ALA* 1.3 66.1 - - - +
929B LEU* 3.0 12.0 + - - +
930B MET* 3.0 26.4 + - - +
954B ILE* 4.1 9.2 - - + +
957B ALA* 3.2 28.0 - - + +
958B SER* 3.8 31.2 - - - +
961B VAL* 4.3 4.5 - - - -
1030B LEU* 3.8 14.4 - - + -
1031B MET* 3.7 22.4 - - + -
1034B VAL* 3.2 44.0 - - + -
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Residues in contact with ALA 927 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885B PHE* 4.5 2.0 - - + -
902B ALA* 3.3 31.0 - - - +
905B LEU* 3.7 9.5 - - + +
906B HIS* 3.8 28.3 - - + +
923B ALA 2.8 20.5 + - - +
924B LYS 3.6 4.7 - - - +
926B MET* 1.3 71.5 - - - +
928B LEU* 1.3 63.1 + - - +
930B MET* 3.3 9.6 - - - +
931B ALA* 3.2 18.5 + - - +
1031B MET* 4.6 0.2 - - - -
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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
----------------------------------------------------------
885B PHE* 3.7 29.4 - - + -
906B HIS* 4.7 8.5 - - + +
924B LYS* 3.0 25.4 + - + +
925B ARG* 3.1 13.0 + - + +
927B ALA* 1.3 76.3 - - - +
929B LEU* 1.3 58.6 + - - +
930B MET 3.2 0.4 - - - -
931B ALA* 3.4 7.2 + - + +
932B GLU* 3.2 19.2 + - - +
935B ARG* 4.5 2.3 + - - -
68F GLY* 3.7 30.3 - - - +
69F ASP* 5.3 1.6 - - - -
91F LYS* 4.3 31.5 - - + +
92F TYR* 4.7 7.9 - - + +
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Residues in contact with LEU 929 (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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925B ARG* 2.9 29.7 + - + +
926B MET* 3.0 10.1 + - - +
928B LEU* 1.3 74.0 - - - +
930B MET* 1.3 59.0 + - - +
931B ALA 3.3 0.2 - - - -
932B GLU* 3.4 13.0 + - - +
933B MET* 3.0 19.8 + - - +
950B CYS* 3.4 17.3 - - - -
953B ASP* 3.7 34.3 - - + +
954B ILE* 3.8 23.0 - - + +
957B ALA* 4.9 4.0 - - + -
68F GLY* 4.2 0.9 - - - -
69F ASP* 3.6 39.5 - - + +
121F ARG* 3.8 11.0 - - - +
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Residues in contact with MET 930 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898B MET* 3.4 36.1 - - + +
902B ALA* 3.6 17.6 - - + +
926B MET 3.0 7.7 + - - +
927B ALA 3.3 12.3 - - - +
929B LEU* 1.3 75.3 - - - +
931B ALA* 1.3 65.8 + - - +
933B MET* 3.2 8.2 + - - +
934B SER* 3.1 20.1 + - - -
954B ILE* 3.2 33.9 - - + -
995B LEU* 5.2 2.0 - - + -
1027B ALA* 4.0 14.8 - - + -
1030B LEU* 5.0 2.9 - - + -
1031B MET* 3.0 42.0 - - + -
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Residues in contact with ALA 931 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885B PHE* 4.0 16.8 - - + -
899B MET* 3.2 39.9 - - + +
902B ALA* 4.2 3.1 - - + -
927B ALA 3.2 9.3 + - - +
928B LEU* 3.5 11.0 - - + +
930B MET* 1.3 78.5 - - - +
932B GLU* 1.3 66.1 + - - +
934B SER* 3.0 16.5 + - - -
935B ARG* 3.3 12.2 + - - +
92F TYR* 4.7 5.6 - - + +
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Residues in contact with GLU 932 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928B LEU 3.2 13.0 + - - +
929B LEU* 3.5 11.2 - - - +
930B MET 3.2 0.2 - - - -
931B ALA* 1.3 77.3 - - - +
933B MET* 1.3 57.5 + - - +
935B ARG* 3.2 31.9 + - - +
936B LEU* 2.8 52.2 + - + +
946B ALA* 4.7 0.3 - - - +
950B CYS* 4.0 5.9 - - - -
65F GLY 4.8 1.4 - - - +
66F LEU 4.3 4.2 - - - +
67F PRO* 4.1 4.7 - - - +
68F GLY* 2.7 33.1 + - - -
121F ARG* 2.9 41.0 + - - +
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Residues in contact with MET 933 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898B MET* 3.9 20.2 - - + -
929B LEU 3.0 13.7 + - - +
930B MET* 3.5 12.6 - - - +
931B ALA 3.1 0.6 - - - -
932B GLU* 1.3 76.5 - - - +
934B SER* 1.3 54.9 + - - +
936B LEU* 3.6 6.2 - - - -
937B VAL* 2.7 42.2 + - + +
947B LEU* 3.1 48.9 - - + +
950B CYS* 3.5 19.3 - - - -
951B ALA* 3.6 14.6 - - + +
954B ILE* 4.0 15.3 - - - -
995B LEU* 4.7 17.9 - - - -
999B SER* 4.7 2.9 - - - -
1023B LEU* 5.1 9.0 - - + -
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Residues in contact with SER 934 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894B ILE* 3.4 6.6 - - - +
895B ASN* 3.4 29.3 + - - -
898B MET* 3.5 28.6 - - - +
899B MET* 2.8 28.6 - - - +
930B MET 3.1 6.5 + - - -
931B ALA* 3.0 16.8 + - - -
933B MET* 1.3 75.7 - - - +
935B ARG* 1.3 63.1 + - - +
937B VAL* 3.6 3.1 + - - +
938B ARG* 3.4 18.4 - - - +
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Residues in contact with ARG 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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892B GLU* 4.9 8.2 + - - -
893B VAL 4.3 6.1 - - - +
894B ILE* 3.5 24.7 - - + -
899B MET* 4.3 4.1 - - + +
928B LEU 4.5 3.8 + - - -
931B ALA* 3.3 9.5 + - - +
932B GLU* 3.2 45.8 + - - +
933B MET 3.1 0.2 - - - -
934B SER* 1.3 78.1 + - - +
936B LEU* 1.3 69.0 + - + +
938B ARG* 2.9 17.0 + - - +
939B GLY* 3.3 7.3 + - - -
65F GLY* 5.8 4.4 - - - -
66F LEU 4.5 9.3 + - - -
68F GLY* 4.8 3.2 - - - -
91F LYS 4.3 4.9 + - - -
92F TYR 3.6 23.4 + - - -
93F LYS* 3.7 28.8 + - - +
94F GLY* 4.0 4.9 + - - +
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Residues in contact with LEU 936 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932B GLU* 2.8 47.1 + - + +
933B MET* 3.2 4.5 + - - +
935B ARG* 1.3 73.8 - - + +
937B VAL* 1.3 53.3 + - - +
938B ARG 2.9 2.1 + - - -
939B GLY* 2.8 25.8 + - - +
943B THR* 3.8 29.0 + - + -
946B ALA* 3.6 22.7 - - + -
947B LEU* 3.6 42.8 - - + +
950B CYS* 3.7 13.5 - - + -
1006B LEU* 4.5 4.2 - - - +
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Residues in contact with VAL 937 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895B ASN* 3.6 38.6 - - + +
898B MET* 4.7 10.5 - - - -
933B MET* 2.7 25.3 + - + +
934B SER* 3.7 4.0 - - - +
935B ARG 3.0 0.6 + - - -
936B LEU* 1.3 70.4 - - - +
938B ARG* 1.3 65.5 + - - +
947B LEU* 4.9 8.0 - - + +
1002B LYS* 4.7 22.6 - - + -
1006B LEU* 5.4 5.5 - - - +
1020B THR* 5.2 12.2 + - + +
1023B LEU* 4.5 24.7 - - + -
1024B VAL* 6.3 0.4 - - + -
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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
------------------------------------------------------------
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