Contacts of the helix formed by residues 1004 - 1026 (chain M) in PDB entry 3HOU
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 ASN1004 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002M GLY* 3.2 4.8 + - - -
1003M LYS* 1.3 80.8 - - - +
1005M GLU* 1.3 64.2 + - - +
1006M ILE* 3.1 10.6 + - - +
1007M ILE* 3.0 34.7 + - - +
1008M GLN* 2.8 33.2 + - - +
163Q GLU* 5.2 1.8 - - - +
167Q ARG* 3.0 51.5 + - - +
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Residues in contact with GLU1005 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004M ASN* 1.3 73.9 - - - +
1006M ILE* 1.3 69.1 + - + +
1008M GLN* 4.2 9.2 - - - +
1009M ASN* 2.5 46.4 + - - +
1012M ARG* 3.6 22.7 + - - -
163Q GLU* 5.8 1.2 + - - +
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Residues in contact with ILE1006 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004M ASN* 3.1 4.1 + - - +
1005M GLU* 1.3 80.2 - - + +
1007M ILE* 1.3 61.3 + - - +
1009M ASN* 3.5 6.6 + - - +
1010M ALA* 3.1 19.8 + - - +
160Q GLU 4.9 1.8 - - - +
163Q GLU* 3.0 49.6 - - + +
164Q LEU* 3.7 13.5 - - + +
167Q ARG* 3.6 19.3 - - + -
168Q TYR* 3.9 25.1 - - + +
211Q TYR* 4.1 18.2 - - - +
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Residues in contact with ILE1007 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1000M LEU* 4.0 23.7 - - + +
1001M ARG 4.4 0.7 - - - +
1002M GLY* 3.9 32.3 - - - +
1004M ASN* 3.0 29.7 + - - +
1006M ILE* 1.3 74.8 - - - +
1008M GLN* 1.3 61.4 + - - +
1010M ALA* 3.0 8.3 + - - +
1011M GLN* 2.8 26.5 + - - +
167Q ARG* 3.8 23.8 - - + +
168Q TYR* 4.2 24.2 - - + +
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Residues in contact with GLN1008 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1000M LEU 5.5 0.6 + - - -
1001M ARG* 3.2 14.3 + - - +
1002M GLY 2.6 25.5 + - - +
1003M LYS* 4.5 2.8 - - - +
1004M ASN 2.8 34.1 + - - +
1005M GLU* 3.8 17.0 - - - +
1007M ILE* 1.3 74.8 - - - +
1009M ASN* 1.3 63.1 + - - +
1011M GLN* 3.2 18.0 - - - +
1012M ARG* 3.1 29.1 + - - +
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Residues in contact with ASN1009 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005M GLU* 2.5 53.2 + - - +
1006M ILE* 3.6 6.3 - - - +
1008M GLN* 1.3 70.3 - - - +
1010M ALA* 1.3 67.4 + - - +
1012M ARG* 2.7 49.0 + - - +
1013M ASP* 2.9 21.5 + - - +
197Q LYS* 5.5 9.0 - - - +
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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
----------------------------------------------------------
867M ILE* 4.7 5.7 - - + +
1000M LEU* 3.5 19.4 - - + +
1006M ILE 3.1 11.6 + - - +
1007M ILE* 3.0 10.9 + - - +
1009M ASN* 1.3 77.4 - - - +
1011M GLN* 1.3 62.7 + - - +
1013M ASP* 3.1 14.9 + - - +
1014M ALA* 2.9 23.6 + - - +
168Q TYR* 3.9 17.7 - - - +
209Q ALA* 6.2 0.9 - - + -
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Residues in contact with GLN1011 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994M GLN 5.9 0.6 + - - -
997M LEU 3.7 5.4 + - - -
998M LEU* 3.4 11.3 - - + +
999M VAL* 2.9 28.7 + - - -
1000M LEU* 3.4 27.7 + - + +
1007M ILE* 2.8 10.8 + - + +
1008M GLN* 3.2 24.7 - - - +
1010M ALA* 1.3 75.8 - - - +
1012M ARG* 1.3 67.9 + - + +
1014M ALA* 2.9 15.8 + - - +
1015M VAL* 2.7 43.4 + - - +
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Residues in contact with ARG1012 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005M GLU* 3.6 21.4 + - - -
1008M GLN* 3.1 19.0 + - - +
1009M ASN* 2.7 39.8 + - - +
1011M GLN* 1.3 86.1 - - + +
1013M ASP* 1.3 60.0 + - - +
1015M VAL* 3.5 3.4 + - - +
1016M THR* 2.8 24.3 + - - -
207Q ARG* 5.4 5.4 - - - +
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Residues in contact with ASP1013 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009M ASN* 2.9 26.3 + - - +
1010M ALA* 3.3 15.9 - - - +
1012M ARG* 1.3 77.0 - - - +
1014M ALA* 1.3 65.3 + - - +
1015M VAL 2.8 1.1 + - - -
1016M THR* 2.7 23.3 + - - -
197Q LYS* 5.6 2.3 + - - -
205Q SER 3.2 11.1 - - - +
207Q ARG* 3.1 48.2 + - - +
208Q TYR* 4.8 4.7 - - + -
209Q ALA* 4.3 20.3 + - - +
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Residues in contact with ALA1014 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867M ILE* 4.9 7.2 - - + -
870M GLU 4.6 4.0 - - - -
871M ASP* 4.2 18.1 - - - +
873M MET* 5.1 4.7 - - - +
999M VAL* 4.2 24.7 - - + -
1000M LEU* 5.2 2.0 - - + -
1010M ALA 2.9 12.4 + - - +
1011M GLN* 3.2 14.4 - - - +
1013M ASP* 1.3 76.4 - - - +
1015M VAL* 1.3 61.5 + - + +
1016M THR 3.5 0.2 - - - -
1018M PHE* 5.5 1.7 + - - +
205Q SER* 3.6 24.3 - - - -
207Q ARG 5.1 0.2 - - - -
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Residues in contact with VAL1015 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873M MET* 6.4 0.2 - - - -
994M GLN 5.6 1.3 - - - +
997M LEU* 3.4 29.6 - - + +
999M VAL* 4.3 3.1 - - + -
1011M GLN* 2.7 36.8 + - - +
1012M ARG* 3.9 4.5 - - - +
1013M ASP 3.0 1.0 - - - -
1014M ALA* 1.3 82.8 - - + +
1016M THR* 1.3 65.1 - - - +
1017M LEU 3.4 2.5 - - - -
1018M PHE* 3.1 17.2 + - + -
1019M CYS* 3.0 40.8 + - - -
1053M PHE* 4.3 10.3 - - + -
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Residues in contact with THR1016 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942M PHE* 3.9 31.6 - - + -
1012M ARG 2.8 15.2 + - - -
1013M ASP* 2.7 26.7 + - - -
1014M ALA 3.5 0.2 - - - -
1015M VAL* 1.3 76.3 - - - +
1017M LEU* 1.3 63.3 + - - +
1019M CYS* 3.5 5.5 + - - +
1020M CYS* 3.4 22.6 + - - -
1023M ARG* 5.2 1.9 + - - +
205Q SER 3.6 6.1 - - - -
206Q GLY* 4.7 0.2 - - - -
207Q ARG* 4.1 19.8 + - - +
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Residues in contact with LEU1017 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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883M LEU* 3.5 28.9 - - + -
942M PHE* 5.3 0.2 - - - -
943M LEU* 3.8 19.1 - - + -
946M VAL* 6.2 0.7 - - + -
947M PHE* 4.0 17.0 - - + -
954M TRP* 5.4 1.3 - - + -
956M LEU* 3.6 20.0 - - + -
1015M VAL 3.4 0.4 - - - -
1016M THR* 1.3 76.4 - - - +
1018M PHE* 1.3 68.1 + - - +
1020M CYS* 3.2 12.9 + - - +
1021M LEU* 3.3 8.5 + - - +
202Q SER 4.3 0.2 - - - +
203Q GLU 3.7 17.0 - - - +
204Q THR 3.5 21.3 - - - +
205Q SER* 3.4 8.1 + - - +
206Q GLY* 3.2 26.2 - - - +
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Residues in contact with PHE1018 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873M MET* 6.1 1.1 - - + -
956M LEU* 4.3 11.8 - - + +
957M PRO* 3.3 42.4 - - + -
958M VAL* 4.1 17.9 - - + -
960M ILE* 4.3 14.6 - - + -
997M LEU* 3.5 35.0 - - + -
1014M ALA 5.5 1.3 + - - +
1015M VAL* 3.1 17.0 + - + +
1017M LEU* 1.3 78.0 - - - +
1019M CYS* 1.3 60.7 + - - +
1021M LEU* 2.8 41.7 + - + +
1022M LEU* 2.8 18.6 + - + -
1049M ILE* 4.4 9.0 - - + -
1053M PHE* 3.8 23.6 - + + -
204Q THR 5.6 0.2 + - - -
205Q SER* 5.6 0.4 - - - +
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Residues in contact with CYS1019 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994M GLN* 4.3 28.9 - - - -
997M LEU* 4.4 8.3 - - - -
1015M VAL* 3.0 41.4 + - - +
1016M THR* 3.9 4.5 - - - +
1018M PHE* 1.3 72.2 - - - +
1020M CYS* 1.3 67.5 + - - +
1022M LEU* 2.9 9.3 + - - +
1023M ARG* 2.8 50.3 + - - +
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Residues in contact with CYS1020 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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883M LEU* 4.9 0.9 - - + -
885M THR* 4.8 1.8 + - - -
939M ASP* 3.9 37.2 - - + +
942M PHE* 4.4 13.5 - - - -
943M LEU* 3.9 36.6 - - + -
1016M THR* 3.4 17.2 + - - -
1017M LEU* 3.2 11.1 + - + +
1019M CYS* 1.3 75.6 - - - +
1021M LEU* 1.3 65.0 + - - +
1023M ARG* 3.9 4.3 - - - +
1024M SER* 2.8 26.0 + - - -
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Residues in contact with LEU1021 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881M GLN* 3.6 34.3 - - + +
882M SER 3.7 2.9 - - - +
883M LEU* 3.3 32.4 - - + +
956M LEU* 4.1 11.4 - - + -
960M ILE* 4.3 11.2 - - + -
1017M LEU 3.3 3.1 + - - +
1018M PHE* 2.8 36.9 + - + +
1020M CYS* 1.3 78.1 - - - +
1022M LEU* 1.3 63.5 + - - +
1024M SER* 2.8 20.3 + - - -
1025M ARG* 3.0 47.1 + - + +
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Residues in contact with LEU1022 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
960M ILE* 3.8 23.3 - - + +
990M VAL* 4.2 7.6 - - + -
993M LEU* 3.4 30.5 - - + -
994M GLN* 3.7 28.0 - - + -
997M LEU* 4.0 14.4 - - + -
1018M PHE* 2.8 12.7 + - + +
1019M CYS* 2.9 15.5 + - + +
1021M LEU* 1.3 74.6 - - - +
1023M ARG* 1.3 58.5 + - + +
1025M ARG* 2.9 6.1 + - - +
1026M LEU* 2.8 59.8 + - + +
1049M ILE* 3.9 7.9 - - + -
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Residues in contact with ARG1023 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935M GLN* 3.1 30.2 - - - +
936M LEU* 3.9 22.6 - - + +
939M ASP* 2.6 49.7 + - - +
990M VAL* 4.9 11.2 - - + -
994M GLN* 3.1 33.8 + - - +
1016M THR* 5.2 2.0 + - - +
1019M CYS* 2.8 38.8 + - - +
1020M CYS* 4.0 8.0 - - - +
1022M LEU* 1.3 69.9 - - - +
1024M SER* 1.3 65.8 + - - +
1025M ARG 3.1 0.7 + - - -
1026M LEU 3.5 9.7 + - - +
1027M ALA* 3.5 17.7 + - - +
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Residues in contact with SER1024 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883M LEU* 4.1 3.8 - - - -
884M ASP* 3.5 18.2 + - - +
885M THR* 3.2 39.3 + - - -
897M TYR* 3.1 10.1 - - - -
936M LEU* 5.7 0.9 - - - -
1020M CYS 2.8 14.7 + - - -
1021M LEU* 2.8 18.8 + - - -
1023M ARG* 1.3 77.4 - - - +
1025M ARG* 1.3 59.8 + - - +
1030M ARG* 2.8 26.3 + - - -
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Residues in contact with ARG1025 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881M GLN* 4.2 8.8 + - - +
882M SER* 2.7 40.2 + - - +
884M ASP* 3.1 28.0 + - - -
960M ILE* 4.3 23.8 - - + +
961M ARG* 3.8 42.4 - - - +
964M ILE* 5.6 0.2 - - + -
1021M LEU* 3.4 30.2 - - + +
1022M LEU 2.9 6.0 + - - +
1024M SER* 1.3 81.3 + - - +
1026M LEU* 1.3 60.3 + - + +
1027M ALA 3.4 6.1 + - - -
1030M ARG* 3.8 9.3 - - - +
1035M TYR* 2.8 44.7 + - + +
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Residues in contact with LEU1026 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932M GLU* 4.9 1.4 - - - +
960M ILE* 5.1 1.3 - - + -
964M ILE* 4.3 20.6 - - + -
986M ILE* 3.9 2.9 - - - +
990M VAL* 3.6 33.0 - - + +
1022M LEU* 2.8 45.5 + - + +
1023M ARG* 3.5 4.9 + - - -
1025M ARG* 1.3 88.6 - - + +
1027M ALA* 1.3 59.9 + - - +
1028M THR 3.6 1.7 + - - -
1031M VAL* 3.4 18.1 - - + +
1035M TYR* 4.4 3.4 - - + -
1037M LEU* 5.8 1.6 - - + -
1042M PHE* 4.9 8.5 - - + -
1045M VAL* 4.9 9.2 - - + -
1046M LEU* 4.0 20.6 - - + -
1049M ILE* 4.0 13.7 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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