Contacts of the helix formed by residues 989 - 1015 (chain M) in PDB entry 6D6Q
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 PHE 989 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396M LYS* 3.7 40.2 - - + +
397M LYS* 4.8 15.0 - - + -
440M GLN* 5.3 5.2 - - - +
456M HIS* 4.1 16.8 - + - -
458M GLY* 3.8 27.6 - - - +
983M CYS* 5.8 0.2 - - - -
988M VAL* 1.3 90.6 - - + +
990M GLU* 1.3 65.3 + - - +
991M GLY 4.6 0.7 - - - +
992M SER* 4.5 9.6 - - - +
993M ILE* 3.4 18.9 + - - +
18O A 5.4 2.5 - - - -
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Residues in contact with GLU 990 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438M LEU* 4.2 10.3 - - - +
439M PRO* 5.1 4.0 - - - +
440M GLN* 3.0 41.7 + - - +
458M GLY 3.8 3.5 + - - +
459M LEU 5.0 0.2 - - - -
460M LEU* 3.4 23.1 - - + +
979M PHE* 3.2 33.5 - - + -
983M CYS* 3.3 32.6 - - + +
989M PHE* 1.3 73.7 - - - +
991M GLY* 1.3 62.0 + - - +
992M SER 3.1 2.2 - - - -
993M ILE* 2.8 27.6 + - + +
994M ILE* 2.9 15.2 + - - +
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Residues in contact with GLY 991 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457M GLY 4.8 4.0 - - - -
458M GLY* 3.8 13.3 + - - -
459M LEU 3.2 25.8 + - - -
461M PRO* 5.8 0.2 - - - -
990M GLU* 1.3 76.7 - - - +
992M SER* 1.3 55.7 + - - +
994M ILE* 3.2 9.8 + - - +
995M ARG* 2.9 37.2 + - - +
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Residues in contact with SER 992 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396M LYS* 4.4 7.8 + - - -
457M GLY 4.2 12.6 + - - -
914M PHE* 5.3 7.6 - - - -
916M GLU* 4.9 15.8 - - - +
966M LEU* 5.7 1.6 - - - -
988M VAL* 4.2 22.3 - - - +
989M PHE* 4.3 6.8 + - - +
990M GLU 3.1 1.2 - - - +
991M GLY* 1.3 75.8 - - - +
993M ILE* 1.3 57.6 + - - +
995M ARG* 3.4 10.1 + - - +
996M CYS* 2.9 29.5 + - - +
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Residues in contact with ILE 993 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
966M LEU* 4.6 17.9 - - + -
969M VAL* 4.7 20.0 - - + -
979M PHE* 5.0 10.5 - - + -
982M ILE* 5.1 6.5 - - + +
983M CYS* 4.9 13.9 - - - -
986M THR* 4.2 22.0 - - + -
988M VAL* 4.6 6.7 - - + +
989M PHE 3.4 21.3 - - - +
990M GLU* 2.8 20.9 + - + +
992M SER* 1.3 73.1 - - - +
994M ILE* 1.3 59.7 + - + -
996M CYS* 3.3 7.3 + - + +
997M MET* 2.9 42.3 + - + +
1035M VAL* 6.2 0.9 - - + -
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Residues in contact with ILE 994 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460M LEU* 4.3 16.8 - - + -
461M PRO* 4.7 12.1 - - + -
979M PHE* 4.0 21.5 - - + -
990M GLU 2.9 16.9 + - - +
991M GLY* 3.2 9.8 + - - +
993M ILE* 1.3 79.5 - - + +
995M ARG* 1.3 63.3 + - + +
997M MET* 3.2 1.9 + - - +
998M ARG* 2.9 56.1 + - - +
1034M ILE* 5.2 3.1 - - + +
1035M VAL* 3.8 42.8 - - + +
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Residues in contact with ARG 995 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192M LYS* 5.5 2.0 - - - +
457M GLY* 5.4 6.3 + - - -
464M LYS* 4.2 14.3 - - - +
991M GLY 2.9 21.0 + - - +
992M SER* 3.7 9.4 - - - +
994M ILE* 1.3 74.7 - - + +
996M CYS* 1.3 66.5 + - - +
998M ARG* 3.3 6.6 + - - +
999M ARG* 2.9 36.3 + - - +
20O C 2.2 80.6 + - - +
21O A 2.7 30.1 + - - -
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Residues in contact with CYS 996 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910M SER* 4.6 11.9 - - - -
913M VAL* 3.5 31.0 - - - +
914M PHE* 4.3 12.1 - - + -
966M LEU* 3.8 25.8 - - + -
970M VAL* 5.1 0.9 - - - -
992M SER 2.9 14.4 + - - +
993M ILE* 3.4 13.7 - - - +
995M ARG* 1.3 77.0 - - - +
997M MET* 1.3 67.0 + - + +
999M ARG* 3.7 5.2 - - - +
1000M LEU* 2.8 29.7 + - - +
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Residues in contact with MET 997 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
969M VAL* 6.2 1.1 - - - -
970M VAL* 3.8 36.3 - - + -
973M TRP* 3.4 35.2 - - + +
993M ILE* 2.9 34.6 + - + +
996M CYS* 1.3 78.9 - - - +
998M ARG* 1.3 58.1 + - - +
1000M LEU* 3.2 10.5 + - + +
1001M GLU* 2.9 28.1 + - - +
1030M ILE* 3.6 30.8 - - + +
1035M VAL* 3.6 26.5 - - + -
1036M PHE* 3.8 4.7 - - - -
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Residues in contact with ARG 998 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192M LYS* 4.5 17.5 - - - +
215M ASP* 3.8 33.7 + - - +
461M PRO* 3.6 29.8 - - - +
994M ILE* 2.9 32.0 + - - +
995M ARG* 3.9 6.1 - - - +
997M MET* 1.3 73.5 - - - +
999M ARG* 1.3 65.1 + - + +
1001M GLU* 3.1 5.5 + - - +
1002M GLU* 3.0 23.0 + - - +
1034M ILE 4.8 1.2 + - - -
1035M VAL* 3.0 26.8 + - + +
1036M PHE* 3.8 26.9 - - + +
1037M ALA* 4.7 14.1 + - - +
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Residues in contact with ARG 999 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882M SER* 3.6 26.7 + - - +
883M ALA* 5.5 1.0 - - - +
913M VAL* 3.3 40.7 + - + +
915M GLN* 4.2 20.0 + - - +
995M ARG* 2.9 28.6 + - + +
996M CYS* 3.7 4.7 - - - +
998M ARG* 1.3 76.0 - - + +
1000M LEU* 1.3 57.8 + - - +
1002M GLU* 3.3 15.7 + - - +
1003M LEU* 2.9 29.8 + - - +
20O C 5.3 5.6 + - - +
21O A 3.1 48.3 + - + +
22O C 4.0 14.4 - - + +
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Residues in contact with LEU1000 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906M THR* 3.3 33.4 - - - +
909M LEU* 4.6 9.6 - - + +
910M SER* 3.9 21.1 - - - +
913M VAL* 4.1 10.5 - - + +
970M VAL* 4.3 12.1 - - + -
996M CYS* 2.8 18.1 + - - +
997M MET* 3.3 15.9 - - + +
998M ARG 3.1 0.4 - - - -
999M ARG* 1.3 76.6 - - - +
1001M GLU* 1.3 56.0 + - - +
1003M LEU* 3.3 5.0 + - - +
1004M LEU* 2.9 47.9 + - + +
1030M ILE* 3.3 31.6 - - + -
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Residues in contact with GLU1001 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214M GLY 5.1 1.4 - - - +
997M MET 2.9 13.8 + - - +
998M ARG 3.1 7.2 + - - +
1000M LEU* 1.3 73.6 - - - +
1002M GLU* 1.3 69.3 + - - +
1004M LEU* 3.2 10.9 + - - +
1005M ARG* 3.0 59.1 + - - +
1027M ILE* 3.8 25.6 - - + +
1030M ILE* 5.0 5.6 - - + -
1031M LYS* 3.8 32.7 + - + -
1036M PHE* 3.7 17.9 - - + -
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Residues in contact with GLU1002 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214M GLY* 5.3 2.6 - - - -
882M SER* 4.4 4.1 + - - -
998M ARG 3.0 11.3 + - - +
999M ARG* 3.5 15.9 - - - +
1001M GLU* 1.3 78.1 + - - +
1003M LEU* 1.3 62.4 + - - +
1005M ARG* 3.1 25.3 + - - +
1006M GLN* 3.0 37.5 + - + +
22O C 2.8 59.9 + - - +
23O A 2.7 29.5 + - - +
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Residues in contact with LEU1003 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880M ILE* 4.3 4.3 - - + -
882M SER* 4.2 8.2 + - - +
883M ALA* 4.0 28.0 - - + -
888M LEU* 4.2 15.0 - - + -
909M LEU* 3.7 38.1 - - + +
912M PHE* 5.1 2.2 - - + -
913M VAL* 4.1 17.5 - - + -
999M ARG 2.9 17.6 + - - +
1000M LEU* 3.6 4.9 - - - +
1002M GLU* 1.3 76.8 - - - +
1004M LEU* 1.3 58.5 + - - +
1006M GLN* 3.3 23.5 + - + +
1007M MET* 2.9 42.8 + - + +
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Residues in contact with LEU1004 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906M THR* 4.3 12.8 - - + +
909M LEU* 3.5 26.9 - - + -
1000M LEU* 2.9 40.3 + - + +
1001M GLU* 3.5 4.9 - - - +
1002M GLU 3.2 0.2 - - - -
1003M LEU* 1.3 74.3 - - - +
1005M ARG* 1.3 66.4 + - - +
1007M MET* 3.3 3.2 + - - +
1008M CYS* 2.9 28.8 + - - -
1023M PHE* 4.2 26.1 - - + +
1026M GLY 4.3 2.2 - - - -
1027M ILE* 3.4 39.9 - - + +
1030M ILE* 3.8 12.8 - - + -
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Residues in contact with ARG1005 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214M GLY 3.0 27.3 + - - -
215M ASP 5.6 3.0 + - - -
1001M GLU* 3.0 43.8 + - - +
1002M GLU* 3.4 24.1 + - - +
1004M LEU* 1.3 76.6 - - - +
1006M GLN* 1.3 64.0 + - + +
1008M CYS* 3.3 6.8 + - - +
1009M GLN* 3.0 28.3 + - + +
1027M ILE* 4.0 11.0 - - + -
23O A 3.4 46.2 + - - -
24O C 4.0 14.3 + - - -
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Residues in contact with GLN1006 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879M GLU* 3.8 22.1 + - - +
880M ILE* 3.7 7.7 - - + +
881M SER* 3.3 33.5 + - - -
882M SER* 3.3 34.9 + - - -
1002M GLU* 3.0 32.6 + - + +
1003M LEU* 3.5 16.1 - - + +
1004M LEU 3.2 0.2 - - - -
1005M ARG* 1.3 78.3 - - + +
1007M MET* 1.3 57.9 + - - +
1009M GLN* 3.1 9.6 + - - +
1010M ALA* 2.9 26.6 + - - +
23O A 4.5 8.7 + - - +
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Residues in contact with MET1007 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880M ILE* 3.4 30.3 - - - -
888M LEU* 4.1 31.0 - - + -
892M MET* 3.3 28.8 - - + +
897M PHE* 4.6 12.3 - - + -
909M LEU* 4.6 11.4 - - + -
1003M LEU* 2.9 31.7 + - + +
1004M LEU* 3.8 2.5 - - - +
1006M GLN* 1.3 72.6 - - - +
1008M CYS* 1.3 66.9 + - - +
1010M ALA* 3.2 4.5 + - - +
1011M ALA* 2.9 24.4 + - - +
1023M PHE* 3.3 34.5 - - + -
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Residues in contact with CYS1008 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004M LEU 2.9 25.9 + - - -
1005M ARG* 3.4 9.2 - - - +
1007M MET* 1.3 77.4 - - - +
1009M GLN* 1.3 61.5 + - + +
1011M ALA 3.4 0.3 + - - -
1012M LYS* 2.9 28.9 + - - +
1020M GLU* 3.6 24.4 - - + +
1023M PHE* 3.2 28.2 - - - -
1024M ALA* 3.6 20.6 - - - -
1027M ILE* 4.4 6.1 - - - -
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Residues in contact with GLN1009 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879M GLU* 4.1 19.9 - - + +
1005M ARG* 3.0 20.2 + - + +
1006M GLN* 3.1 10.3 + - - +
1008M CYS* 1.3 79.5 - - - +
1010M ALA* 1.3 58.2 + - - +
1012M LYS* 3.2 37.6 + - - +
1013M ALA* 2.9 27.0 + - - +
25O C 3.4 43.1 + - - +
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Residues in contact with ALA1010 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876M VAL* 3.9 26.5 - - + +
879M GLU* 4.6 8.4 - - + +
880M ILE* 4.8 4.9 - - + -
892M MET* 3.7 21.1 - - + -
1006M GLN 2.9 12.1 + - - +
1007M MET* 3.2 10.0 + - - +
1009M GLN* 1.3 77.0 - - - +
1011M ALA* 1.3 59.1 + - - +
1013M ALA* 2.8 24.1 + - - +
1014M ILE* 3.0 16.6 + - - +
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Residues in contact with ALA1011 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892M MET* 4.6 3.6 - - + +
1007M MET 2.9 15.6 + - - +
1008M CYS 3.8 4.3 - - - +
1010M ALA* 1.3 74.7 - - - +
1012M LYS* 1.3 63.1 + - - +
1014M ILE* 3.4 10.9 - - - +
1015M GLY 3.2 16.1 + - - -
1016M ASN* 3.1 22.3 + - + +
1019M LEU* 4.1 23.3 - - + -
1020M GLU* 3.9 25.8 - - + +
1023M PHE* 5.4 0.2 - - + -
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Residues in contact with LYS1012 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148H VAL 6.0 1.3 - - - -
149H PHE 5.9 0.4 - - - -
150H SER* 4.5 25.1 - - - +
1008M CYS 2.9 11.8 + - - +
1009M GLN* 3.3 40.5 + - - +
1010M ALA 3.2 0.2 - - - -
1011M ALA* 1.3 76.5 - - - +
1013M ALA* 1.3 61.8 + - - +
1015M GLY* 4.0 6.6 + - - -
1016M ASN 4.4 1.6 - - - -
1020M GLU* 3.1 23.4 + - - +
25O C 5.0 6.7 + - - +
26O A 4.0 19.2 + - - -
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Residues in contact with ALA1013 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875M ARG 4.6 14.8 - - - +
876M VAL* 5.0 3.8 - - + -
879M GLU* 5.0 6.1 - - + -
1009M GLN 2.9 11.4 + - - +
1010M ALA* 2.8 15.3 + - - +
1012M LYS* 1.3 78.5 - - - +
1014M ILE* 1.3 68.2 + - + +
1015M GLY* 3.3 1.2 + - - -
----------------------------------------------------------
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Residues in contact with ILE1014 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H MET* 3.5 32.1 - - + -
41H ARG 5.4 2.0 - - - +
42H GLY* 5.1 10.4 - - - -
43H HIS* 5.3 3.3 + - - -
66H LEU* 5.2 7.1 - - + +
872M MET* 3.4 29.9 - - + +
876M VAL* 3.2 36.6 - - + -
892M MET* 5.1 7.2 - - - -
893M PHE* 3.8 18.2 - - + -
1010M ALA 3.0 10.1 + - - +
1011M ALA* 3.4 17.3 - - + +
1013M ALA* 1.3 75.5 - - - +
1015M GLY* 1.3 61.8 + - - +
1016M ASN* 3.8 10.8 - - + +
1019M LEU* 5.4 1.6 - - + -
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Residues in contact with GLY1015 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H ARG* 4.7 19.4 + - - +
42H GLY* 6.1 1.1 - - - -
1011M ALA 3.2 4.7 + - - -
1012M LYS 4.4 4.9 - - - -
1013M ALA 3.3 3.4 - - - -
1014M ILE* 1.3 79.8 - - - +
1016M ASN* 1.3 65.6 + - - +
1017M THR* 4.0 5.9 + - - -
----------------------------------------------------------
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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