Contacts of the helix formed by residues 830 - 858 (chain A) in PDB entry 3QCF
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 830 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828A ILE 3.6 1.0 + - - -
829A PRO* 1.3 71.3 - - - +
831A LYS* 1.3 59.5 + - - +
833A PHE* 3.1 8.5 + - - +
834A VAL* 2.8 30.2 + - + +
1080A ILE* 4.3 17.7 - - + -
1084A SER* 3.1 34.9 + - - +
1085A THR 4.3 0.7 - - - +
1086A VAL* 4.4 10.8 - - + -
1120A ILE* 3.2 41.5 - - + -
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Residues in contact with LYS 831 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829A PRO* 3.0 6.8 + - + +
830A VAL* 1.3 83.7 - - - +
832A GLN* 1.3 61.3 + - - +
834A VAL* 3.4 6.7 + - - +
835A LYS* 3.3 46.5 + - - +
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Residues in contact with GLN 832 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828A ILE* 4.6 13.2 - - + -
829A PRO* 3.0 23.9 + - + +
831A LYS* 1.3 80.2 - - - +
833A PHE* 1.3 57.9 + - - +
835A LYS* 3.3 37.1 + - - +
836A HIS* 2.9 29.6 + - + +
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Residues in contact with PHE 833 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828A ILE* 4.0 20.8 - - + +
829A PRO 2.9 12.0 + - - +
830A VAL 3.1 6.9 + - - +
832A GLN* 1.3 79.5 - - - +
834A VAL* 1.3 58.0 + - - +
836A HIS* 3.1 19.0 + + - +
837A ILE* 2.9 46.4 + - + +
1086A VAL* 3.6 50.0 - - + -
1088A VAL* 4.0 14.8 - - + -
1113A HIS* 3.7 33.7 - + - -
1116A LEU* 4.1 17.9 - - + -
1120A ILE* 4.0 13.2 - - + -
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Residues in contact with VAL 834 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830A VAL* 2.8 19.9 + - + +
831A LYS* 3.6 7.0 - - - +
833A PHE* 1.3 76.8 - - + +
835A LYS* 1.3 67.1 + - + +
836A HIS 3.3 0.7 + - - -
837A ILE* 3.3 18.4 + - - +
838A GLY* 3.4 8.1 + - - -
1117A LEU* 3.8 29.1 - - + +
1120A ILE* 4.0 29.4 - - + -
1121A LEU* 5.7 5.8 - - + -
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Residues in contact with LYS 835 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831A LYS* 3.3 44.1 + - - +
832A GLN* 3.3 39.4 + - - +
834A VAL* 1.3 80.2 - - + +
836A HIS* 1.3 61.6 + - - +
838A GLY* 3.2 4.6 + - - -
839A GLU* 3.2 18.7 + - - +
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Residues in contact with HIS 836 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828A ILE* 5.3 9.6 - - + -
832A GLN* 2.9 17.6 + - + +
833A PHE* 3.1 30.7 + + - +
835A LYS* 1.3 75.0 - - - +
837A ILE* 1.3 65.6 + - - +
839A GLU* 3.1 21.5 + - + +
840A LEU* 2.9 65.2 + - + +
851A ASP* 4.6 5.5 + - - -
1113A HIS* 5.2 0.6 + - - -
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Residues in contact with ILE 837 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833A PHE* 2.9 43.2 + - + +
834A VAL* 3.3 8.3 + - + +
836A HIS* 1.3 75.2 - - - +
838A GLY* 1.3 65.1 + - - +
839A GLU 3.1 0.2 + - - -
840A LEU* 3.1 8.1 + - - +
841A TYR* 3.0 49.3 + - + -
848A PHE* 4.5 0.9 - - + -
1113A HIS* 3.6 46.2 - - + +
1117A LEU* 3.9 34.8 - - + -
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Residues in contact with GLY 838 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834A VAL 3.4 5.6 + - - -
835A LYS* 3.2 9.2 + - - -
836A HIS 3.2 0.6 - - - -
837A ILE* 1.3 80.5 - - - +
839A GLU* 1.3 59.1 + - - +
841A TYR* 3.6 9.1 + - - +
842A SER* 3.3 19.2 + - - -
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Residues in contact with GLU 839 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835A LYS 3.2 9.8 + - - +
836A HIS* 3.1 24.3 + - - +
838A GLY* 1.3 73.8 - - - +
840A LEU* 1.3 66.3 - - + +
841A TYR 3.1 1.8 - - - -
842A SER* 3.0 30.8 + - - +
847A GLY* 4.8 2.9 + - - -
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Residues in contact with LEU 840 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836A HIS* 2.9 53.1 + - + +
837A ILE* 3.1 7.6 + - - +
839A GLU* 1.3 75.5 - - + +
841A TYR* 1.3 57.6 + - - +
845A GLN* 3.2 25.8 - - - -
847A GLY* 3.4 37.6 + - - +
848A PHE* 3.2 31.0 - - + +
850A GLU* 5.8 0.4 - - - +
851A ASP* 3.8 17.5 - - - +
1113A HIS* 3.8 25.6 - - + +
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Residues in contact with TYR 841 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837A ILE* 3.0 47.4 + - + +
838A GLY* 3.8 8.7 - - - +
839A GLU 3.1 0.2 - - - -
840A LEU* 1.3 74.6 - - - +
842A SER* 1.3 61.7 + - - +
843A ASN 3.8 0.2 + - - -
844A ASN* 4.0 1.9 + - - -
845A GLN* 2.9 45.7 + - + +
848A PHE* 3.4 25.4 - + - -
1110A ILE* 3.6 18.3 + - + +
1113A HIS* 5.4 0.9 - - + -
1114A ASP* 3.9 24.8 + - - +
1117A LEU* 5.7 2.9 - - + -
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Residues in contact with SER 842 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838A GLY 3.3 11.4 + - - -
839A GLU* 3.0 27.6 + - - +
841A TYR* 1.3 77.6 - - - +
843A ASN* 1.3 78.5 + - - +
846A HIS* 3.1 17.3 + - - +
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Residues in contact with ASN 843 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842A SER* 1.3 82.7 - - - +
844A ASN* 1.3 77.0 + - - +
846A HIS* 3.2 36.2 + - + +
899B LYS* 4.4 10.6 - - - +
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Residues in contact with ASN 844 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841A TYR 4.0 1.9 + - - -
842A SER 3.3 0.4 - - - -
843A ASN* 1.3 79.2 + - - +
845A GLN* 1.3 73.7 + - - +
846A HIS* 3.2 2.1 + - - -
849A SER* 5.6 0.3 + - - -
873B GLU* 5.1 7.7 - - - +
899B LYS* 3.0 46.8 - - - +
902B LYS* 4.8 20.3 - - + +
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Residues in contact with GLN 845 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840A LEU 3.2 14.4 - - - -
841A TYR* 2.9 44.9 + - + +
842A SER 3.2 0.2 + - - -
844A ASN* 1.3 78.2 + - - +
846A HIS* 1.3 64.6 + - - +
847A GLY 3.2 3.1 - - - -
848A PHE* 3.2 18.8 + - + +
849A SER* 3.4 13.2 + - - -
1106A GLU* 4.6 7.0 + - - +
1110A ILE* 3.6 26.9 - - - +
871B HIS* 4.6 15.8 + - - -
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Residues in contact with HIS 846 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842A SER 3.1 7.8 + - - +
843A ASN* 3.2 38.3 + - + +
844A ASN 3.1 2.6 - - - -
845A GLN* 1.3 77.4 - - - +
847A GLY* 1.3 61.7 + - - +
849A SER* 3.5 8.6 + - - -
850A GLU* 3.1 40.7 + - + +
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Residues in contact with GLY 847 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839A GLU 4.8 1.9 + - - -
840A LEU* 3.4 29.7 + - - +
842A SER 4.5 1.0 + - - -
845A GLN 3.2 0.8 - - - -
846A HIS* 1.3 79.2 - - - +
848A PHE* 1.3 59.2 + - - +
850A GLU* 3.5 13.8 - - - +
851A ASP* 2.8 34.8 + - - +
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Residues in contact with PHE 848 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837A ILE* 4.4 2.0 - - + -
840A LEU* 3.2 35.4 + - + +
841A TYR* 3.4 58.1 - + - -
845A GLN* 3.2 17.4 + - + +
847A GLY* 1.3 75.9 - - - +
849A SER* 1.3 59.0 + - - +
851A ASP* 3.4 4.5 + - - +
852A PHE* 2.9 31.9 + - - +
1106A GLU* 4.2 5.6 - - + +
1109A TYR* 4.1 18.4 - + + -
1110A ILE* 3.5 36.6 - - + -
1113A HIS* 3.6 35.2 - + + -
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Residues in contact with SER 849 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844A ASN 5.6 0.5 + - - -
845A GLN 3.4 8.8 + - - -
846A HIS* 3.7 11.2 - - - -
847A GLY 3.2 0.2 - - - -
848A PHE* 1.3 79.9 - - - +
850A GLU* 1.3 62.3 + - - +
852A PHE* 3.5 1.2 + - - +
853A GLU* 3.1 25.8 + - - +
1106A GLU* 2.9 32.5 + - - +
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Residues in contact with GLU 850 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840A LEU* 5.8 0.5 - - - +
846A HIS* 3.1 31.3 + - + +
847A GLY* 3.5 12.9 - - - +
849A SER* 1.3 78.7 - - - +
851A ASP* 1.3 69.9 + - - +
853A GLU* 3.8 5.5 - - - +
854A GLU* 3.2 23.6 + - - +
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Residues in contact with ASP 851 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836A HIS* 4.6 5.2 + - - -
840A LEU* 3.8 21.9 - - - +
847A GLY 2.8 23.2 + - - +
848A PHE 3.7 0.2 - - - +
850A GLU* 1.3 79.9 - - - +
852A PHE* 1.3 62.2 + - - +
854A GLU* 2.9 21.5 + - - +
855A VAL* 3.0 16.6 + - - +
1089A LEU* 3.8 23.8 - - + +
1109A TYR* 2.8 37.5 + - + +
1113A HIS* 5.2 0.3 + - - -
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Residues in contact with PHE 852 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848A PHE 2.9 21.4 + - - +
849A SER 4.1 2.7 - - - +
851A ASP* 1.3 74.7 - - - +
853A GLU* 1.3 58.5 + - - +
855A VAL* 3.2 14.7 + - + +
856A GLN* 2.9 61.5 + - + +
1092A LEU* 5.6 0.2 - - + -
1096A ARG* 4.1 6.7 - - - -
1103A VAL* 3.5 19.3 - - + -
1104A GLN 3.2 25.6 - - - -
1105A THR* 3.4 14.4 - - - -
1106A GLU* 3.5 34.5 - - + +
1109A TYR* 4.0 25.3 - + + -
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Residues in contact with GLU 853 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849A SER 3.1 18.0 + - - +
850A GLU* 3.8 6.1 - - - +
851A ASP 3.2 0.2 - - - -
852A PHE* 1.3 76.2 - - - +
854A GLU* 1.3 64.2 + - - +
856A GLN* 3.3 12.4 + - - +
857A ARG* 3.1 66.2 + - - +
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Residues in contact with GLU 854 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
850A GLU* 3.2 15.5 + - - +
851A ASP* 2.9 13.2 + - - +
853A GLU* 1.3 76.3 - - - +
855A VAL* 1.3 63.0 + - - +
857A ARG* 3.1 8.6 + - - +
858A CYS* 3.0 24.6 + - - +
1089A LEU* 4.0 21.1 - - + +
1093A LYS* 2.7 37.4 + - + +
----------------------------------------------------------
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Residues in contact with VAL 855 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851A ASP 3.0 12.5 + - - +
852A PHE* 3.4 15.0 - - + +
854A GLU* 1.3 76.5 - - - +
856A GLN* 1.3 60.9 + - - +
857A ARG 3.3 0.5 + - - -
858A CYS* 3.4 22.7 + - - -
859A THR 5.0 0.2 + - - -
1089A LEU* 3.5 29.4 - - + -
1092A LEU* 3.9 30.3 - - + +
1093A LYS* 4.1 7.2 - - + -
1096A ARG* 3.6 45.7 + - + +
1109A TYR* 4.8 2.2 - - + -
----------------------------------------------------------
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Residues in contact with GLN 856 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852A PHE* 2.9 51.7 + - + +
853A GLU* 3.3 18.3 + - - +
854A GLU 3.2 0.2 - - - -
855A VAL* 1.3 77.6 - - - +
857A ARG* 1.3 60.9 + - + +
858A CYS 3.5 0.2 - - - -
859A THR* 5.2 1.9 + - - -
860A ALA* 5.2 3.3 + - - +
1096A ARG* 3.1 35.1 + - - +
1101A TYR* 4.9 7.3 - - - -
1104A GLN 4.3 5.6 + - - +
----------------------------------------------------------
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Residues in contact with ARG 857 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853A GLU* 3.1 50.5 + - - +
854A GLU* 3.1 7.4 + - - +
856A GLN* 1.3 80.9 - - + +
858A CYS* 1.3 57.7 + - - +
859A THR 3.1 2.2 - - - -
860A ALA* 2.8 35.6 + - + +
----------------------------------------------------------
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Residues in contact with CYS 858 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854A GLU 3.0 13.8 + - - +
855A VAL* 3.4 16.0 + - - -
857A ARG* 1.3 75.8 - - - +
859A THR* 1.3 74.1 + - - +
862A MET* 3.4 20.3 - - - +
1093A LYS* 3.7 51.6 - - - +
1096A ARG* 4.0 8.5 - - - -
1097A THR* 5.9 0.2 - - - -
----------------------------------------------------------
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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