Contacts of the helix formed by residues 909 - 934 (chain B) in PDB entry 3QNF
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 GLN 909 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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875B VAL* 6.2 2.6 - - - +
910B GLN* 1.3 65.5 + - - +
911B THR* 3.2 13.8 + - - +
912B ILE* 3.4 39.2 - - + +
913B GLU* 4.2 1.7 + - - +
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Residues in contact with GLN 910 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876B MET* 5.4 11.7 - - - -
909B GLN* 1.3 76.0 - - - +
911B THR* 1.3 64.0 + - - +
912B ILE 3.3 0.4 - - - -
913B GLU* 3.4 21.2 + - - +
914B THR* 3.7 8.8 + - - -
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Residues in contact with THR 911 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875B VAL* 4.6 2.9 - - - +
876B MET* 3.0 32.9 + - + +
879B THR* 3.0 32.5 + - - +
880B ASN* 4.1 12.6 - - + +
891B VAL* 5.5 4.3 - - + -
909B GLN 4.3 9.7 + - - -
910B GLN* 1.3 76.2 - - - +
912B ILE* 1.3 67.9 + - - +
914B THR* 3.0 8.5 + - - -
915B ILE* 3.0 35.9 + - + +
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Residues in contact with ILE 912 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888B LEU* 6.1 5.8 - - + +
891B VAL* 5.0 18.4 - - + -
909B GLN* 3.4 30.7 - - + +
911B THR* 1.3 78.4 - - - +
913B GLU* 1.3 66.0 + - - +
915B ILE* 3.3 7.8 + - - +
916B GLU* 3.1 26.2 + - + +
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Residues in contact with GLU 913 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909B GLN 4.2 1.2 + - - +
910B GLN* 3.4 14.8 + - - +
911B THR 3.2 0.6 - - - -
912B ILE* 1.3 79.5 - - - +
914B THR* 1.3 60.3 + - - +
916B GLU* 3.8 5.8 + - - +
917B GLU* 3.2 23.7 + - - +
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Residues in contact with THR 914 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880B ASN* 3.9 19.3 - - + +
910B GLN 3.7 9.2 + - - -
911B THR* 3.0 11.4 + - - -
913B GLU* 1.3 76.5 - - - +
915B ILE* 1.3 55.1 + - - +
917B GLU* 3.1 8.9 + - + +
918B ASN* 2.7 49.7 + - - +
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Residues in contact with ILE 915 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879B THR* 3.9 24.2 - - - +
880B ASN* 4.7 0.9 - - - -
882B PHE* 4.0 21.1 - - + +
884B THR 4.7 0.4 - - - +
887B ARG 4.8 4.0 - - - +
888B LEU* 4.0 23.8 - - + +
891B VAL* 4.2 22.2 - - + -
911B THR* 3.0 33.4 + - + +
912B ILE* 3.8 7.0 - - - +
914B THR* 1.3 74.9 - - - +
916B GLU* 1.3 59.7 + - - +
918B ASN* 3.1 10.6 + - - +
919B ILE* 2.8 51.7 + - + +
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Residues in contact with GLU 916 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888B LEU* 5.6 4.4 - - + +
912B ILE* 3.1 20.3 + - + +
913B GLU* 3.9 6.3 - - - +
915B ILE* 1.3 76.6 - - - +
917B GLU* 1.3 60.3 + - - +
919B ILE* 3.8 9.9 - - - +
920B GLY* 3.5 16.1 + - - -
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Residues in contact with GLU 917 (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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913B GLU 3.2 14.2 + - - +
914B THR* 3.1 14.6 + - + +
916B GLU* 1.3 74.8 - - - +
918B ASN* 1.3 63.6 + - - +
920B GLY* 3.4 3.0 + - - -
921B TRP* 3.1 20.5 + - - +
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Residues in contact with ASN 918 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686B LEU* 3.8 27.3 - - + +
880B ASN 2.7 30.0 + - - +
882B PHE 3.1 24.9 + - - +
883B SER* 4.4 2.9 - - - -
914B THR* 2.7 28.9 + - - +
915B ILE* 3.1 10.5 + - - +
917B GLU* 1.3 69.7 - - - +
919B ILE* 1.3 69.2 + - - +
921B TRP* 2.8 19.5 + - - +
922B MET* 3.1 12.8 + - - +
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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
----------------------------------------------------------
883B SER* 2.9 35.6 + - - +
884B THR 3.0 27.4 - - - +
885B ARG* 3.6 13.2 - - + +
888B LEU* 5.2 2.7 - - + -
915B ILE* 2.8 46.1 + - + +
916B GLU* 3.8 10.3 - - - +
918B ASN* 1.3 72.9 - - - +
920B GLY* 1.3 70.3 + - - +
922B MET* 3.0 2.8 + - - +
923B ASP* 2.9 43.2 + - - +
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Residues in contact with GLY 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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916B GLU 3.5 7.8 + - - -
917B GLU* 3.4 6.8 + - - -
918B ASN 3.2 1.0 - - - -
919B ILE* 1.3 83.3 - - - +
921B TRP* 1.3 57.0 + - - +
923B ASP* 3.7 5.6 - - - +
924B LYS* 2.9 33.1 + - - +
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Residues in contact with TRP 921 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647B VAL* 4.5 7.6 - - - +
648B SER* 4.9 21.7 + - - -
654B ILE* 3.4 24.0 - - + +
683B MET* 3.7 34.7 - - + +
686B LEU* 4.2 23.8 - - + -
687B MET* 5.5 1.6 - - + -
917B GLU 3.1 12.4 + - - +
918B ASN* 2.8 16.6 + - - +
920B GLY* 1.3 76.5 - - - +
922B MET* 1.3 71.0 + - + -
924B LYS* 3.7 2.2 - - - -
925B ASN* 2.8 61.2 + - + +
926B PHE 5.5 0.2 - - - -
929B ILE* 3.6 29.4 - - + -
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Residues in contact with MET 922 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686B LEU* 5.3 8.3 - - + +
687B MET* 5.0 13.0 - - + -
690B ARG* 3.6 36.1 - - + +
692B MET* 3.2 44.0 - - + +
883B SER* 3.0 21.8 - - - +
918B ASN 3.1 6.7 + - - +
919B ILE 3.0 7.8 + - - +
921B TRP* 1.3 92.4 - - + +
923B ASP* 1.3 67.2 + - - +
924B LYS 3.1 1.8 - - - -
926B PHE* 2.8 47.9 + - + +
927B ASP* 4.7 1.0 + - - +
929B ILE* 6.3 0.2 - - - -
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Residues in contact with ASP 923 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690B ARG* 4.8 10.2 + - - -
883B SER 5.5 0.2 - - - +
885B ARG* 5.9 1.7 - - - +
919B ILE* 2.9 38.1 + - - +
920B GLY* 3.9 6.1 - - - +
922B MET* 1.3 79.5 - - - +
924B LYS* 1.3 58.9 + - - +
927B ASP* 4.8 8.5 - - - +
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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
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920B GLY 2.9 18.2 + - - +
921B TRP* 4.0 3.8 - - - +
923B ASP* 1.3 79.5 - - - +
925B ASN* 1.3 67.8 + - - +
926B PHE 4.0 0.2 - - - -
927B ASP* 5.5 0.8 - - - +
928B LYS* 3.6 24.0 + - - +
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Residues in contact with ASN 925 (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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647B VAL* 4.2 8.4 + - - +
653B SER* 5.5 0.2 - - - -
654B ILE* 3.4 32.2 + - + +
921B TRP* 2.8 65.9 + - + +
924B LYS* 1.3 85.0 - - - +
926B PHE* 1.3 66.4 + - - +
927B ASP 3.3 2.5 - - - -
928B LYS* 3.0 12.1 + - - +
929B ILE* 2.9 35.3 + - + +
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Residues in contact with PHE 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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687B MET* 5.6 2.2 - - + -
690B ARG* 5.8 3.1 - - - +
692B MET* 3.6 42.6 - - + -
695B VAL* 3.4 37.9 - - + -
921B TRP* 5.5 0.2 - - - -
922B MET* 2.8 40.5 + - + +
924B LYS 4.0 0.2 - - - -
925B ASN* 1.3 73.5 - - - +
927B ASP* 1.3 80.1 + - - +
929B ILE* 3.1 9.4 + - - +
930B ARG* 2.9 44.8 + - - +
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Residues in contact with ASP 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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922B MET 5.4 0.3 - - - +
923B ASP 4.8 9.0 - - - +
924B LYS 5.5 0.9 - - - +
925B ASN 3.3 0.8 - - - -
926B PHE* 1.3 95.4 - - - +
928B LYS* 1.3 59.8 + - + +
930B ARG* 2.8 30.9 + - - +
931B VAL* 3.1 35.0 + - + +
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Residues in contact with LYS 928 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653B SER* 3.5 27.1 - - - +
654B ILE* 3.7 17.9 - - + -
655B GLU* 2.7 28.7 - - + +
924B LYS* 3.6 26.1 + - - +
925B ASN* 3.0 8.9 + - - +
927B ASP* 1.3 77.0 - - + +
929B ILE* 1.3 60.8 + - - +
930B ARG 3.2 0.2 - - - -
931B VAL* 3.6 4.8 + - - +
932B TRP* 3.0 31.1 + - - +
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Residues in contact with ILE 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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654B ILE* 4.3 17.3 - - + -
658B LEU* 4.6 10.3 - - + -
683B MET* 4.6 7.6 - - - -
687B MET* 3.7 26.7 - - + -
695B VAL* 4.5 1.3 - - + -
699B PHE* 3.9 11.0 - - + -
921B TRP* 3.6 34.1 - - + -
925B ASN* 2.9 26.6 + - + +
926B PHE* 3.5 7.0 - - - +
928B LYS* 1.3 73.2 - - - +
930B ARG* 1.3 60.8 + - - +
932B TRP* 3.8 5.1 - - + +
933B LEU* 2.8 49.6 + - + +
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Residues in contact with ARG 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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695B VAL* 3.7 26.4 - - + +
698B GLN* 5.8 3.2 + - - +
926B PHE* 2.9 29.3 + - + +
927B ASP* 2.8 51.2 + - - +
928B LYS 3.2 0.2 - - - -
929B ILE* 1.3 79.4 - - - +
931B VAL* 1.3 79.6 + - - +
933B LEU* 3.2 4.8 + - - +
934B GLN* 3.0 21.2 + - - +
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Residues in contact with VAL 931 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
927B ASP* 3.1 17.5 + - + +
928B LYS* 4.1 4.7 - - - +
930B ARG* 1.3 99.6 - - - +
932B TRP* 1.3 63.4 + - - +
934B GLN* 3.2 25.2 + - + +
935B SER* 4.7 0.9 + - - -
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Residues in contact with TRP 932 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655B GLU* 4.0 26.7 - - + -
658B LEU* 3.3 46.0 - - + -
659B ASP* 2.7 29.8 + - - +
662B LEU* 3.8 20.4 - - + +
699B PHE* 5.7 1.1 - + - -
702B PHE* 3.7 44.9 - + - -
928B LYS 3.0 20.9 + - - +
929B ILE* 3.8 4.7 - - + +
931B VAL* 1.3 77.8 - - - +
933B LEU* 1.3 85.4 + - + +
934B GLN 3.3 0.5 + - - -
935B SER* 3.8 16.3 + - - -
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Residues in contact with LEU 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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695B VAL* 3.7 34.5 - - + +
698B GLN* 3.7 46.3 - - + +
699B PHE* 3.8 13.5 - - + +
702B PHE* 4.2 10.3 - - + -
929B ILE* 2.8 39.7 + - + +
930B ARG* 3.6 5.4 - - - +
932B TRP* 1.3 94.8 - - + +
934B GLN* 1.3 51.5 + - - +
935B SER* 2.5 26.3 + - - -
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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
----------------------------------------------------------
698B GLN* 5.0 5.1 + - - -
930B ARG 3.0 13.4 + - - +
931B VAL* 3.3 19.9 - - + +
932B TRP 3.2 1.4 - - - -
933B LEU* 1.3 69.5 - - - +
935B SER* 1.3 68.7 + - - +
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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